From beedd5780ded1a34260fe5d40315f9d4ca54d7ec Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 22 Oct 2024 08:45:28 -0700 Subject: [PATCH] template vocabulary update --- web/templates/hpai/schema.json | 3643 +++++++++++++-------- web/templates/hpai/schema.yaml | 2051 ++++++++---- web/templates/hpai/schema_enums.tsv | 249 +- web/templates/hpai/schema_slots.tsv | 33 +- web/templates/mpox/schema.json | 27 +- web/templates/mpox/schema.yaml | 21 +- web/templates/mpox/schema_enums.tsv | 2 +- web/templates/mpox/schema_slots.tsv | 9 +- web/templates/wastewater/schema.json | 315 +- web/templates/wastewater/schema.yaml | 128 +- web/templates/wastewater/schema_enums.tsv | 130 +- web/templates/wastewater/schema_slots.tsv | 526 +-- 12 files changed, 4634 insertions(+), 2500 deletions(-) diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index 08b813be..58fd8481 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -2638,9 +2638,9 @@ } } }, - "PurposeOfSampling": { - "name": "PurposeOfSampling", - "title": "purpose of sampling", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Cluster/Outbreak investigation [GENEPIO:0100001]": { @@ -2688,9 +2688,9 @@ } } }, - "PresamplingActivity": { - "name": "PresamplingActivity", - "title": "presampling activity", + "PresamplingActivityMenu": { + "name": "PresamplingActivityMenu", + "title": "presampling activity menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Addition of substances to food/water [GENEPIO:0100536]": { @@ -2756,9 +2756,9 @@ } } }, - "SampleStorageDurationUnit": { - "name": "SampleStorageDurationUnit", - "title": "sample storage duration unit", + "SampleStorageDurationUnitMenu": { + "name": "SampleStorageDurationUnitMenu", + "title": "sample storage duration unit menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Second [UO:0000010]": { @@ -2798,9 +2798,9 @@ } } }, - "SpecimenProcessing": { - "name": "SpecimenProcessing", - "title": "specimen processing", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Concentration [OBI:0600041]": { @@ -2825,9 +2825,9 @@ } } }, - "ExperimentalSpecimenRoleType": { - "name": "ExperimentalSpecimenRoleType", - "title": "experimental specimen role type", + "ExperimentalSpecimenRoleTypeMenu": { + "name": "ExperimentalSpecimenRoleTypeMenu", + "title": "experimental specimen role type menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Positive experimental control [GENEPIO:0101018]": { @@ -3771,9 +3771,9 @@ } } }, - "HostGender": { - "name": "HostGender", - "title": "host_gender", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host_gender menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Female [NCIT:C46110]": { @@ -5585,25 +5585,32 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "<10 people": { - "text": "<10 people" + "text": "<10 people", + "description": "An estimation of population size for a group smaller than 10 people." }, "10 - 100 people": { - "text": "10 - 100 people" + "text": "10 - 100 people", + "description": "An estimation of population size for a group smaller than 100 people and larger than 10 people." }, "100 - 1,000 people": { - "text": "100 - 1,000 people" + "text": "100 - 1,000 people", + "description": "An estimation of population size for a group smaller than 1,000 people and larger than 100 people." }, "1,000 - 10,000 people": { - "text": "1,000 - 10,000 people" + "text": "1,000 - 10,000 people", + "description": "An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people." }, "10,000 - 100,000 people": { - "text": "10,000 - 100,000 people" + "text": "10,000 - 100,000 people", + "description": "An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people." }, "100,000 - 1,000,000 people": { - "text": "100,000 - 1,000,000 people" + "text": "100,000 - 1,000,000 people", + "description": "An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people." }, "1,000,000+ people": { - "text": "1,000,000+ people" + "text": "1,000,000+ people", + "description": "An estimation of population size for a group larger than 1,000,000 people." } } }, @@ -5784,6 +5791,861 @@ } } }, + "WaterDepthUnitsMenu": { + "name": "WaterDepthUnitsMenu", + "title": "water_depth_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", + "meaning": "UO:0000015" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", + "meaning": "UO:0000008" + }, + "kilometer (km) [UO:0010066]": { + "text": "kilometer (km) [UO:0010066]", + "description": "A length unit which is equal to one thousand meters.", + "meaning": "UO:0010066" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", + "meaning": "UO:0010011" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", + "meaning": "UO:0010013" + } + } + }, + "SedimentDepthUnitsMenu": { + "name": "SedimentDepthUnitsMenu", + "title": "sediment_depth_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", + "meaning": "UO:0000015" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", + "meaning": "UO:0000008" + }, + "kilometer (km) [UO:0010066]": { + "text": "kilometer (km) [UO:0010066]", + "description": "A length unit which is equal to one thousand meters.", + "meaning": "UO:0010066" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", + "meaning": "UO:0010011" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", + "meaning": "UO:0010013" + } + } + }, + "AirTemperatureUnitsMenu": { + "name": "AirTemperatureUnitsMenu", + "title": "air_temperature_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "WaterTemperatureUnitsMenu": { + "name": "WaterTemperatureUnitsMenu", + "title": "water_temperature_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "SequencingPlatformMenu": { + "name": "SequencingPlatformMenu", + "title": "sequencing_platform menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Illumina [GENEPIO:0001923]": { + "text": "Illumina [GENEPIO:0001923]", + "description": "A sequencing platform provided by the Illumina company.", + "meaning": "GENEPIO:0001923" + }, + "Pacific Biosciences [GENEPIO:0001927]": { + "text": "Pacific Biosciences [GENEPIO:0001927]", + "description": "A sequencing platform provided by the Pacific Biosciences company.", + "meaning": "GENEPIO:0001927" + }, + "Ion Torrent [GENEPIO:0002683]": { + "text": "Ion Torrent [GENEPIO:0002683]", + "description": "A sequencing platform provided by the Ion Torrent company.", + "meaning": "GENEPIO:0002683" + }, + "Oxford Nanopore Technologies [GENEPIO:0100986]": { + "text": "Oxford Nanopore Technologies [GENEPIO:0100986]", + "description": "An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK.", + "meaning": "GENEPIO:0100986" + }, + "BGI Genomics [GENEPIO:0004324]": { + "text": "BGI Genomics [GENEPIO:0004324]", + "description": "A sequencing platform provided by the BGI Genomics company.", + "meaning": "GENEPIO:0004324" + }, + "MGI [GENEPIO:0004325]": { + "text": "MGI [GENEPIO:0004325]", + "description": "A sequencing platform provided by the MGI company.", + "meaning": "GENEPIO:0004325" + }, + "Roche LS454 [GENEPIO:0001926]": { + "text": "Roche LS454 [GENEPIO:0001926]", + "description": "A sequencing platform provided by the 454 Life Sciences company.", + "meaning": "GENEPIO:0001926" + }, + "SOLiD sequencing [GENEPIO:0002684]": { + "text": "SOLiD sequencing [GENEPIO:0002684]", + "description": "A sequencing platform provided by Life Technologies Corporation.", + "meaning": "GENEPIO:0002684" + }, + "Complete Genomics [GENEPIO:0001924]": { + "text": "Complete Genomics [GENEPIO:0001924]", + "description": "An in-house sequencing platform provided by Complete Genomics.", + "meaning": "GENEPIO:0001924" + }, + "Helicos [GENEPIO:0002682]": { + "text": "Helicos [GENEPIO:0002682]", + "description": "A sequencing platform brand provided by Helicos corporation (now defunct).", + "meaning": "GENEPIO:0002682" + }, + "Applied Biosystems [GENEPIO:0100985]": { + "text": "Applied Biosystems [GENEPIO:0100985]", + "description": "A sequencing platform provided by ThermoFisher.", + "meaning": "GENEPIO:0100985" + } + } + }, + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing_instrument menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Illumina [GENEPIO:0100105]": { + "text": "Illumina [GENEPIO:0100105]", + "description": "A DNA sequencer manufactured by the Illumina corporation.", + "meaning": "GENEPIO:0100105" + }, + "Illumina Genome Analyzer [GENEPIO:0100106]": { + "text": "Illumina Genome Analyzer [GENEPIO:0100106]", + "description": "A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.", + "meaning": "GENEPIO:0100106", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina Genome Analyzer II [OBI:0000703]": { + "text": "Illumina Genome Analyzer II [OBI:0000703]", + "description": "A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0000703", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina Genome Analyzer IIx [OBI:0002000]": { + "text": "Illumina Genome Analyzer IIx [OBI:0002000]", + "description": "An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", + "meaning": "OBI:0002000", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina HiScanSQ [GENEPIO:0100109]": { + "text": "Illumina HiScanSQ [GENEPIO:0100109]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an \"SQ Module\" to support microfluidics.", + "meaning": "GENEPIO:0100109", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina HiSeq [GENEPIO:0100110]": { + "text": "Illumina HiSeq [GENEPIO:0100110]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.", + "meaning": "GENEPIO:0100110", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina HiSeq X [GENEPIO:0100111]": { + "text": "Illumina HiSeq X [GENEPIO:0100111]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000.", + "meaning": "GENEPIO:0100111", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq X Five [GENEPIO:0100112]": { + "text": "Illumina HiSeq X Five [GENEPIO:0100112]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", + "meaning": "GENEPIO:0100112", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq X Ten [GENEPIO:0100113]": { + "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", + "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", + "meaning": "GENEPIO:0100113", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 1000 [OBI:0002022]": { + "text": "Illumina HiSeq 1000 [OBI:0002022]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002022", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 1500 [GENEPIO:0100115]": { + "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day.", + "meaning": "GENEPIO:0100115", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 2000 [OBI:0002001]": { + "text": "Illumina HiSeq 2000 [OBI:0002001]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", + "meaning": "OBI:0002001", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 2500 [OBI:0002002]": { + "text": "Illumina HiSeq 2500 [OBI:0002002]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", + "meaning": "OBI:0002002", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 3000 [OBI:0002048]": { + "text": "Illumina HiSeq 3000 [OBI:0002048]", + "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", + "meaning": "OBI:0002048", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 4000 [OBI:0002049]": { + "text": "Illumina HiSeq 4000 [OBI:0002049]", + "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", + "meaning": "OBI:0002049", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina iSeq [GENEPIO:0100120]": { + "text": "Illumina iSeq [GENEPIO:0100120]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", + "meaning": "GENEPIO:0100120", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina iSeq 100 [GENEPIO:0100121]": { + "text": "Illumina iSeq 100 [GENEPIO:0100121]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", + "meaning": "GENEPIO:0100121", + "is_a": "Illumina iSeq [GENEPIO:0100120]" + }, + "Illumina NovaSeq [GENEPIO:0100122]": { + "text": "Illumina NovaSeq [GENEPIO:0100122]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode.", + "meaning": "GENEPIO:0100122", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina NovaSeq 6000 [GENEPIO:0100123]": { + "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", + "meaning": "GENEPIO:0100123", + "is_a": "Illumina NovaSeq [GENEPIO:0100122]" + }, + "Illumina MiniSeq [GENEPIO:0100124]": { + "text": "Illumina MiniSeq [GENEPIO:0100124]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", + "meaning": "GENEPIO:0100124", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina MiSeq [OBI:0002003]": { + "text": "Illumina MiSeq [OBI:0002003]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", + "meaning": "OBI:0002003", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina NextSeq [GENEPIO:0100126]": { + "text": "Illumina NextSeq [GENEPIO:0100126]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", + "meaning": "GENEPIO:0100126", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina NextSeq 500 [OBI:0002021]": { + "text": "Illumina NextSeq 500 [OBI:0002021]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002021", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "Illumina NextSeq 550 [GENEPIO:0100128]": { + "text": "Illumina NextSeq 550 [GENEPIO:0100128]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", + "meaning": "GENEPIO:0100128", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "Illumina NextSeq 1000 [GENEPIO:0004432]": { + "text": "Illumina NextSeq 1000 [GENEPIO:0004432]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", + "meaning": "GENEPIO:0004432", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "Illumina NextSeq 2000 [GENEPIO:0100129]": { + "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", + "meaning": "GENEPIO:0100129", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "PacBio [GENEPIO:0100130]": { + "text": "PacBio [GENEPIO:0100130]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation.", + "meaning": "GENEPIO:0100130" + }, + "PacBio RS [GENEPIO:0100131]": { + "text": "PacBio RS [GENEPIO:0100131]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", + "meaning": "GENEPIO:0100131", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "PacBio RS II [OBI:0002012]": { + "text": "PacBio RS II [OBI:0002012]", + "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", + "meaning": "OBI:0002012", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "PacBio Sequel [GENEPIO:0100133]": { + "text": "PacBio Sequel [GENEPIO:0100133]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", + "meaning": "GENEPIO:0100133", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "PacBio Sequel II [GENEPIO:0100134]": { + "text": "PacBio Sequel II [GENEPIO:0100134]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", + "meaning": "GENEPIO:0100134", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "Ion Torrent [GENEPIO:0100135]": { + "text": "Ion Torrent [GENEPIO:0100135]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation.", + "meaning": "GENEPIO:0100135" + }, + "Ion Torrent PGM [GENEPIO:0100136]": { + "text": "Ion Torrent PGM [GENEPIO:0100136]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", + "meaning": "GENEPIO:0100136", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Ion Torrent Proton [GENEPIO:0100137]": { + "text": "Ion Torrent Proton [GENEPIO:0100137]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", + "meaning": "GENEPIO:0100137", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Ion Torrent S5 XL [GENEPIO:0100138]": { + "text": "Ion Torrent S5 XL [GENEPIO:0100138]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", + "meaning": "GENEPIO:0100138", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Ion Torrent S5 [GENEPIO:0100139]": { + "text": "Ion Torrent S5 [GENEPIO:0100139]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", + "meaning": "GENEPIO:0100139", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Oxford Nanopore [GENEPIO:0100140]": { + "text": "Oxford Nanopore [GENEPIO:0100140]", + "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation.", + "meaning": "GENEPIO:0100140" + }, + "Oxford Nanopore Flongle [GENEPIO:0004433]": { + "text": "Oxford Nanopore Flongle [GENEPIO:0004433]", + "description": "An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.", + "meaning": "GENEPIO:0004433", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore GridION [GENEPIO:0100141]": { + "text": "Oxford Nanopore GridION [GENEPIO:0100141]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", + "meaning": "GENEPIO:0100141", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore MinION [GENEPIO:0100142]": { + "text": "Oxford Nanopore MinION [GENEPIO:0100142]", + "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", + "meaning": "GENEPIO:0100142", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore PromethION [GENEPIO:0100143]": { + "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", + "meaning": "GENEPIO:0100143", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "BGI Genomics sequencing instrument [GENEPIO:0100144]": { + "text": "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation.", + "meaning": "GENEPIO:0100144" + }, + "BGISEQ-500 [GENEPIO:0100145]": { + "text": "BGISEQ-500 [GENEPIO:0100145]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", + "meaning": "GENEPIO:0100145", + "is_a": "BGI Genomics sequencing instrument [GENEPIO:0100144]" + }, + "MGI sequencing instrument [GENEPIO:0100146]": { + "text": "MGI sequencing instrument [GENEPIO:0100146]", + "description": "A DNA sequencer manufactured by the MGI corporation.", + "meaning": "GENEPIO:0100146" + }, + "MGISEQ-2000RS [GENEPIO:0100971]": { + "text": "MGISEQ-2000RS [GENEPIO:0100971]", + "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing.", + "meaning": "GENEPIO:0100971", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G99 [GENEPIO:0100972]": { + "text": "MGI DNBSEQ-G99 [GENEPIO:0100972]", + "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds.", + "meaning": "GENEPIO:0100972", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G400 [GENEPIO:0100148]": { + "text": "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run.", + "meaning": "GENEPIO:0100148", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]": { + "text": "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400.", + "meaning": "GENEPIO:0100149", + "is_a": "MGI DNBSEQ-G400 [GENEPIO:0100148]" + }, + "MGI DNBSEQ-T7 [GENEPIO:0100147]": { + "text": "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day.", + "meaning": "GENEPIO:0100147", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-E25 [GENEPIO:0100973]": { + "text": "MGI DNBSEQ-E25 [GENEPIO:0100973]", + "description": "An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab.", + "meaning": "GENEPIO:0100973", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G50 [GENEPIO:0100150]": { + "text": "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", + "meaning": "GENEPIO:0100150", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "454 Genome Sequencer [GENEPIO:0001937]": { + "text": "454 Genome Sequencer [GENEPIO:0001937]", + "description": "A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing.", + "meaning": "GENEPIO:0001937" + }, + "454 Genome Sequencer 20 [OBI:0000689]": { + "text": "454 Genome Sequencer 20 [OBI:0000689]", + "description": "A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem.", + "meaning": "OBI:0000689", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer FLX [OBI:0000702]": { + "text": "454 Genome Sequencer FLX [OBI:0000702]", + "description": "A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.", + "meaning": "OBI:0000702", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer FLX+ [GENEPIO:0100982]": { + "text": "454 Genome Sequencer FLX+ [GENEPIO:0100982]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+.", + "meaning": "GENEPIO:0100982", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]": { + "text": "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads.", + "meaning": "GENEPIO:0001936", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer Junior [GENEPIO:0001938]": { + "text": "454 Genome Sequencer Junior [GENEPIO:0001938]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and is more compact.", + "meaning": "GENEPIO:0001938", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "SOLiD System [OBI:0000696]": { + "text": "SOLiD System [OBI:0000696]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation.", + "meaning": "OBI:0000696" + }, + "SOLiD 5500 [GENEPIO:0001929]": { + "text": "SOLiD 5500 [GENEPIO:0001929]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series.", + "meaning": "GENEPIO:0001929", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]": { + "text": "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model.", + "meaning": "GENEPIO:0001930", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]": { + "text": "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer.", + "meaning": "GENEPIO:0100984", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 3 Plus System [OBI:0002007]": { + "text": "SOLiD 3 Plus System [OBI:0002007]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.", + "meaning": "OBI:0002007", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 4 System [OBI:0002024]": { + "text": "SOLiD 4 System [OBI:0002024]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput.", + "meaning": "OBI:0002024", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 4hq System [GENEPIO:0001928]": { + "text": "SOLiD 4hq System [GENEPIO:0001928]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput.", + "meaning": "GENEPIO:0001928", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD PI System [GENEPIO:0001931]": { + "text": "SOLiD PI System [GENEPIO:0001931]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput.", + "meaning": "GENEPIO:0001931", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD System 2.0 [GENEPIO:0001932]": { + "text": "SOLiD System 2.0 [GENEPIO:0001932]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", + "meaning": "GENEPIO:0001932", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD System 3.0 [GENEPIO:0001933]": { + "text": "SOLiD System 3.0 [GENEPIO:0001933]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", + "meaning": "GENEPIO:0001933", + "is_a": "SOLiD System [OBI:0000696]" + }, + "HeliScope Single Molecule Sequencer [OBI:0000717]": { + "text": "HeliScope Single Molecule Sequencer [OBI:0000717]", + "description": "A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry.", + "meaning": "OBI:0000717" + }, + "Applied Biosystems sequencing instrument model [GENEPIO:0100974]": { + "text": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "description": "A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis.", + "meaning": "GENEPIO:0100974" + }, + "AB 310 Genetic Analyzer [GENEPIO:0100975]": { + "text": "AB 310 Genetic Analyzer [GENEPIO:0100975]", + "description": "An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated.", + "meaning": "GENEPIO:0100975", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3130 Genetic Analyzer [GENEPIO:0100976]": { + "text": "AB 3130 Genetic Analyzer [GENEPIO:0100976]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries.", + "meaning": "GENEPIO:0100976", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3130xL Genetic Analyzer [GENEPIO:0100977]": { + "text": "AB 3130xL Genetic Analyzer [GENEPIO:0100977]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries.", + "meaning": "GENEPIO:0100977", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3500 Genetic Analyzer [GENEPIO:0100978]": { + "text": "AB 3500 Genetic Analyzer [GENEPIO:0100978]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates.", + "meaning": "GENEPIO:0100978", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3500xL Genetic Analyzer [GENEPIO:0100979]": { + "text": "AB 3500xL Genetic Analyzer [GENEPIO:0100979]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates.", + "meaning": "GENEPIO:0100979", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3730 Genetic Analyzer [GENEPIO:0100980]": { + "text": "AB 3730 Genetic Analyzer [GENEPIO:0100980]", + "description": "An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing.", + "meaning": "GENEPIO:0100980", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3730xL Genetic Analyzer [GENEPIO:0100981]": { + "text": "AB 3730xL Genetic Analyzer [GENEPIO:0100981]", + "description": "An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing.", + "meaning": "GENEPIO:0100981", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + } + } + }, + "GenomicTargetEnrichmentMethodMenu": { + "name": "GenomicTargetEnrichmentMethodMenu", + "title": "genomic_target_enrichment_method menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Hybrid selection method (bait-capture) [GENEPIO:0001950]": { + "text": "Hybrid selection method (bait-capture) [GENEPIO:0001950]", + "description": "Selection by hybridization in array or solution.", + "meaning": "GENEPIO:0001950" + }, + "rRNA depletion method [GENEPIO:0101020]": { + "text": "rRNA depletion method [GENEPIO:0101020]", + "description": "Removal of background RNA for the purposes of enriching the genomic target.", + "meaning": "GENEPIO:0101020" + } + } + }, + "QualityControlDeterminationMenu": { + "name": "QualityControlDeterminationMenu", + "title": "quality_control_determination menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "No quality control issues identified [GENEPIO:0100562]": { + "text": "No quality control issues identified [GENEPIO:0100562]", + "description": "A statement confirming that quality control processes were carried out and no quality issues were detected.", + "meaning": "GENEPIO:0100562" + }, + "Sequence passed quality control [GENEPIO:0100563]": { + "text": "Sequence passed quality control [GENEPIO:0100563]", + "description": "A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", + "meaning": "GENEPIO:0100563" + }, + "Sequence failed quality control [GENEPIO:0100564]": { + "text": "Sequence failed quality control [GENEPIO:0100564]", + "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", + "meaning": "GENEPIO:0100564" + }, + "Minor quality control issues identified [GENEPIO:0100565]": { + "text": "Minor quality control issues identified [GENEPIO:0100565]", + "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", + "meaning": "GENEPIO:0100565" + }, + "Sequence flagged for potential quality control issues [GENEPIO:0100566]": { + "text": "Sequence flagged for potential quality control issues [GENEPIO:0100566]", + "description": "A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", + "meaning": "GENEPIO:0100566" + }, + "Quality control not performed [GENEPIO:0100567]": { + "text": "Quality control not performed [GENEPIO:0100567]", + "description": "A statement confirming that quality control processes have not been carried out.", + "meaning": "GENEPIO:0100567" + } + } + }, + "QualityControlIssuesMenu": { + "name": "QualityControlIssuesMenu", + "title": "quality_control_issues menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Low quality sequence [GENEPIO:0100568]": { + "text": "Low quality sequence [GENEPIO:0100568]", + "description": "Sequence data that does not meet quality control thresholds.", + "meaning": "GENEPIO:0100568" + }, + "Sequence contaminated [GENEPIO:0100569]": { + "text": "Sequence contaminated [GENEPIO:0100569]", + "description": "Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", + "meaning": "GENEPIO:0100569" + }, + "Low average genome coverage [GENEPIO:0100570]": { + "text": "Low average genome coverage [GENEPIO:0100570]", + "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", + "meaning": "GENEPIO:0100570" + }, + "Low percent genome captured [GENEPIO:0100571]": { + "text": "Low percent genome captured [GENEPIO:0100571]", + "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", + "meaning": "GENEPIO:0100571" + }, + "Read lengths shorter than expected [GENEPIO:0100572]": { + "text": "Read lengths shorter than expected [GENEPIO:0100572]", + "description": "Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", + "meaning": "GENEPIO:0100572" + }, + "Sequence amplification artifacts [GENEPIO:0100573]": { + "text": "Sequence amplification artifacts [GENEPIO:0100573]", + "description": "Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", + "meaning": "GENEPIO:0100573" + }, + "Low signal to noise ratio [GENEPIO:0100574]": { + "text": "Low signal to noise ratio [GENEPIO:0100574]", + "description": "Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", + "meaning": "GENEPIO:0100574" + }, + "Low coverage of characteristic mutations [GENEPIO:0100575]": { + "text": "Low coverage of characteristic mutations [GENEPIO:0100575]", + "description": "Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", + "meaning": "GENEPIO:0100575" + } + } + }, + "DiagnosticTargetPresenceMenu": { + "name": "DiagnosticTargetPresenceMenu", + "title": "diagnostic target presence menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "diagnostic target present [GENEPIO:0100987]": { + "text": "diagnostic target present [GENEPIO:0100987]", + "description": "A quality inhering in a bearer by virtue of the bearer's existence.", + "meaning": "GENEPIO:0100987" + }, + "diagnostic target absent [GENEPIO:0100988]": { + "text": "diagnostic target absent [GENEPIO:0100988]", + "description": "Aquality denoting the lack of an entity.", + "meaning": "GENEPIO:0100988" + } + } + }, + "DiagnosticMeasurementUnitMenu": { + "name": "DiagnosticMeasurementUnitMenu", + "title": "diagnostic measurement unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "gene copies per liter (GC/L)": { + "text": "gene copies per liter (GC/L)", + "description": "A unit that measures the number of copies of a given gene within a liter of a biological material." + }, + "cycle threshold (Ct) [GENEPIO:0100657]": { + "text": "cycle threshold (Ct) [GENEPIO:0100657]", + "description": "A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test.", + "meaning": "GENEPIO:0100657" + }, + "colony forming units per milliliter (CFU/mL) [UO:0000213]": { + "text": "colony forming units per milliliter (CFU/mL) [UO:0000213]", + "description": "A unit of microbial density that describes the number of colony forming units within a milliliter of material.", + "meaning": "UO:0000213" + }, + "colony forming units per 100 milliliter (CFU/100 mL)": { + "text": "colony forming units per 100 milliliter (CFU/100 mL)", + "description": "A unit of microbial density that describes the number of colony forming units within 100 milliliters of material." + }, + "colony forming units per grams total solids (CFU/gTS)": { + "text": "colony forming units per grams total solids (CFU/gTS)", + "description": "A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material." + }, + "most probable number per milliliter (MPN/mL)": { + "text": "most probable number per milliliter (MPN/mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within one milliliter of material." + }, + "most probable number per 100 milliliter (MPN/100 mL)": { + "text": "most probable number per 100 milliliter (MPN/100 mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material." + } + } + }, + "DiagnosticMeasurementMethodMenu": { + "name": "DiagnosticMeasurementMethodMenu", + "title": "diagnostic measurement method menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]": { + "text": "Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]", + "description": "An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.", + "meaning": "OBI:0000893" + }, + "Digital real time polymerase chain reaction (dPCR)": { + "text": "Digital real time polymerase chain reaction (dPCR)", + "description": "A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction" + }, + "Bacteria culture test": { + "text": "Bacteria culture test", + "description": "An assay to identify the presence of bacteria" + } + } + }, + "ExperimentalInterventionMenu": { + "name": "ExperimentalInterventionMenu", + "title": "experimental_intervention menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Addition of substances to food/water [GENEPIO:0100536]": { + "text": "Addition of substances to food/water [GENEPIO:0100536]", + "description": "The addition of substances to food or water administered to an individual or group of individuals.", + "meaning": "GENEPIO:0100536" + }, + "Antimicrobial pre-treatment [GENEPIO:0100537]": { + "text": "Antimicrobial pre-treatment [GENEPIO:0100537]", + "description": "The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity.", + "meaning": "GENEPIO:0100537" + }, + "Certified animal husbandry practices [GENEPIO:0100538]": { + "text": "Certified animal husbandry practices [GENEPIO:0100538]", + "description": "The implementation of animal husbandy practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100538" + }, + "Certified organic farming practices [GENEPIO:0100539]": { + "text": "Certified organic farming practices [GENEPIO:0100539]", + "description": "The implementation of organic farming practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100539" + }, + "Change in storage conditions [GENEPIO:0100540]": { + "text": "Change in storage conditions [GENEPIO:0100540]", + "description": "A change in the storage conditions of a material or a substance.", + "meaning": "GENEPIO:0100540" + }, + "Cleaning/disinfection [GENEPIO:0100541]": { + "text": "Cleaning/disinfection [GENEPIO:0100541]", + "description": "A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment.", + "meaning": "GENEPIO:0100541" + }, + "Extended downtime between activities [GENEPIO:0100542]": { + "text": "Extended downtime between activities [GENEPIO:0100542]", + "description": "A prolonged period of inactivity between processes or events.", + "meaning": "GENEPIO:0100542" + }, + "Fertilizer pre-treatment [GENEPIO:0100543]": { + "text": "Fertilizer pre-treatment [GENEPIO:0100543]", + "description": "The addition of fertilizer to a material or environment prior to some other event or activity.", + "meaning": "GENEPIO:0100543" + }, + "Logistic slaughter [GENEPIO:0100545]": { + "text": "Logistic slaughter [GENEPIO:0100545]", + "description": "The logistical planning of events and processes upstream of the immediate slaughter of an animal (which may include controlling transport climate; traffic conditions, number of pick-up farms, as well as time and distance during transport; queuing at the abattoir etc) that optimize operations and reduce stress on the animal.", + "meaning": "GENEPIO:0100545" + }, + "Microbial pre-treatment [GENEPIO:0100546]": { + "text": "Microbial pre-treatment [GENEPIO:0100546]", + "description": "The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity.", + "meaning": "GENEPIO:0100546" + }, + "Probiotic pre-treatment [GENEPIO:0100547]": { + "text": "Probiotic pre-treatment [GENEPIO:0100547]", + "description": "The addition of a probiotic substance to an individual or material prior to some other event or activity.", + "meaning": "GENEPIO:0100547" + }, + "Vaccination [NCIT:C15346]": { + "text": "Vaccination [NCIT:C15346]", + "description": "Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment.", + "meaning": "NCIT:C15346" + } + } + }, "AirPressureMeasurementUnitMenu": { "name": "AirPressureMeasurementUnitMenu", "title": "air_pressure_measurement_unit menu", @@ -5827,28 +6689,36 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "cubic meter per second (m^3/s)": { - "text": "cubic meter per second (m^3/s)" + "text": "cubic meter per second (m^3/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second." }, "cubic meter per minute (m^3/min)": { - "text": "cubic meter per minute (m^3/min)" + "text": "cubic meter per minute (m^3/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute." }, "cubic meter per hour (m^3/h)": { - "text": "cubic meter per hour (m^3/h)" + "text": "cubic meter per hour (m^3/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour." }, "liter per second (L/s)": { - "text": "liter per second (L/s)" + "text": "liter per second (L/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second." }, "liter per minute (L/min)": { - "text": "liter per minute (L/min)" + "text": "liter per minute (L/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute." }, "liter per hour (L/h)": { - "text": "liter per hour (L/h)" + "text": "liter per hour (L/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour." }, "liter per day (L/day)": { - "text": "liter per day (L/day)" + "text": "liter per day (L/day)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day." }, "million gallons per day (MGD)": { - "text": "million gallons per day (MGD)" + "text": "million gallons per day (MGD)", + "description": "A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day." } } }, @@ -5858,28 +6728,36 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "cubic meter per second (m^3/s)": { - "text": "cubic meter per second (m^3/s)" + "text": "cubic meter per second (m^3/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second." }, "cubic meter per minute (m^3/min)": { - "text": "cubic meter per minute (m^3/min)" + "text": "cubic meter per minute (m^3/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute." }, "cubic meter per hour (m^3/h)": { - "text": "cubic meter per hour (m^3/h)" + "text": "cubic meter per hour (m^3/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour." }, "liter per second (L/s)": { - "text": "liter per second (L/s)" + "text": "liter per second (L/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second." }, "liter per minute (L/min)": { - "text": "liter per minute (L/min)" + "text": "liter per minute (L/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute." }, "liter per hour (L/h)": { - "text": "liter per hour (L/h)" + "text": "liter per hour (L/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour." }, "liter per day (L/day)": { - "text": "liter per day (L/day)" + "text": "liter per day (L/day)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day." }, "million gallons per day (MGD)": { - "text": "million gallons per day (MGD)" + "text": "million gallons per day (MGD)", + "description": "A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day." } } }, @@ -5889,7 +6767,8 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "nephelometric turbidity unit (NTU)": { - "text": "nephelometric turbidity unit (NTU)" + "text": "nephelometric turbidity unit (NTU)", + "description": "A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample." }, "formazin nephelometric unit (FNU) [UO:0000318]": { "text": "formazin nephelometric unit (FNU) [UO:0000318]", @@ -6013,7 +6892,8 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "milliequivalent per liter (meq/L)": { - "text": "milliequivalent per liter (meq/L)" + "text": "milliequivalent per liter (meq/L)", + "description": "A unit of ion concentration that represents chemical activity per volume." }, "milligram per liter (mg/L) [UO:0000273]": { "text": "milligram per liter (mg/L) [UO:0000273]", @@ -6033,13 +6913,16 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "milliSiemen per centimeter (mS/cm)": { - "text": "milliSiemen per centimeter (mS/cm)" + "text": "milliSiemen per centimeter (mS/cm)", + "description": "A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m)." }, "microSiemen per centimeter (μS/cm)": { - "text": "microSiemen per centimeter (μS/cm)" + "text": "microSiemen per centimeter (μS/cm)", + "description": "A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m)." }, "Siemen per meter (S/m)": { - "text": "Siemen per meter (S/m)" + "text": "Siemen per meter (S/m)", + "description": "An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m)." } } }, @@ -6049,10 +6932,12 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "practical salinity unit (PSU)": { - "text": "practical salinity unit (PSU)" + "text": "practical salinity unit (PSU)", + "description": "A unitless measure of salinity that is equivalent to per thousand." }, "weight for weight (% w/w)": { - "text": "weight for weight (% w/w)" + "text": "weight for weight (% w/w)", + "description": "A unitless comparison based on weight rather than volume, which is equivalent to per hundred." }, "parts per thousand [UO:0000168]": { "text": "parts per thousand [UO:0000168]", @@ -6082,7 +6967,8 @@ "meaning": "UO:0000175" }, "gram per total solids (g/gTS)": { - "text": "gram per total solids (g/gTS)" + "text": "gram per total solids (g/gTS)", + "description": "A unitless comparison of the weight of a substance as a proportion to the weight of total solids." } } }, @@ -6092,7 +6978,8 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "gram per total solids (g/gTS)": { - "text": "gram per total solids (g/gTS)" + "text": "gram per total solids (g/gTS)", + "description": "A unitless comparison of the weight of a substance as a proportion to the weight of total solids." }, "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]": { "text": "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]", @@ -6154,10 +7041,12 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "log10 gene copies per 100 milliliter (log10 GC/100 mL)": { - "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)" + "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)", + "description": "A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material." }, "gene copies per liter (GC/L)": { - "text": "gene copies per liter (GC/L)" + "text": "gene copies per liter (GC/L)", + "description": "A unit that measures the number of copies of a given gene within a liter of a biological material." }, "PCR quantification cycle [UO:0010077]": { "text": "PCR quantification cycle [UO:0010077]", @@ -6165,7 +7054,8 @@ "meaning": "UO:0010077" }, "log10 gene copies per nanogram total DNA": { - "text": "log10 gene copies per nanogram total DNA" + "text": "log10 gene copies per nanogram total DNA", + "description": "A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material." } } }, @@ -6204,16 +7094,20 @@ "meaning": "UO:0000213" }, "colony forming units per 100 milliliter (CFU/100 mL)": { - "text": "colony forming units per 100 milliliter (CFU/100 mL)" + "text": "colony forming units per 100 milliliter (CFU/100 mL)", + "description": "A unit of microbial density that describes the number of colony forming units within 100 milliliters of material." }, "colony forming units per grams total solids (CFU/gTS)": { - "text": "colony forming units per grams total solids (CFU/gTS)" + "text": "colony forming units per grams total solids (CFU/gTS)", + "description": "A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material." }, "most probable number per milliliter (MPN/mL)": { - "text": "most probable number per milliliter (MPN/mL)" + "text": "most probable number per milliliter (MPN/mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within one milliliter of material." }, "most probable number per 100 milliliter (MPN/100 mL)": { - "text": "most probable number per 100 milliliter (MPN/100 mL)" + "text": "most probable number per 100 milliliter (MPN/100 mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material." } } }, @@ -8309,7 +9203,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -10548,7 +11442,7 @@ ], "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -10613,6 +11507,202 @@ } ] }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100440", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101025", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "WaterDepthUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100697", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101026", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "SedimentDepthUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100441", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101027", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "AirTemperatureUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100698", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101028", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "WaterTemperatureUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, "precipitation_measurement_value": { "name": "precipitation_measurement_value", "description": "The amount of water which has fallen during a precipitation process.", @@ -10642,231 +11732,6 @@ } ] }, - "water_depth": { - "name": "water_depth", - "description": "The depth of some water.", - "title": "water_depth", - "comments": [ - "Provide the numerical depth only of water only (without units)." - ], - "examples": [ - { - "value": "5" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100440", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "water_depth_units": { - "name": "water_depth_units", - "description": "The units of measurement for water depth.", - "title": "water_depth_units", - "comments": [ - "Provide the units of measurement for which the depth was recorded." - ], - "examples": [ - { - "value": "meter (m) [UO:0000008]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101025", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "WaterDepthUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "sediment_depth": { - "name": "sediment_depth", - "description": "The depth of some sediment.", - "title": "sediment_depth", - "comments": [ - "Provide the numerical depth only of the sediment (without units)." - ], - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100697", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "sediment_depth_units": { - "name": "sediment_depth_units", - "description": "The units of measurement for sediment depth.", - "title": "sediment_depth_units", - "comments": [ - "Provide the units of measurement for which the depth was recorded." - ], - "examples": [ - { - "value": "meter (m) [UO:0000008]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101026", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "SedimentDepthUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "air_temperature": { - "name": "air_temperature", - "description": "The temperature of some air.", - "title": "air_temperature", - "comments": [ - "Provide the numerical value for the temperature of the air (without units)." - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100441", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "air_temperature_units": { - "name": "air_temperature_units", - "description": "The units of measurement for air temperature.", - "title": "air_temperature_units", - "comments": [ - "Provide the units of measurement for which the temperature was recorded." - ], - "examples": [ - { - "value": "degree Celsius (C) [UO:0000027]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101027", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "AirTemperatureUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "water_temperature": { - "name": "water_temperature", - "description": "The temperature of some water.", - "title": "water_temperature", - "comments": [ - "Provide the numerical value for the temperature of the water (without units)." - ], - "examples": [ - { - "value": "4" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100698", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "water_temperature_units": { - "name": "water_temperature_units", - "description": "The units of measurement for water temperature.", - "title": "water_temperature_units", - "comments": [ - "Provide the units of measurement for which the temperature was recorded." - ], - "examples": [ - { - "value": "degree Celsius (C) [UO:0000027]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101028", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "WaterTemperatureUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", - "comments": [ - "Provide the weather conditions at the time of sample collection." - ], - "examples": [ - { - "value": "Rain [ENVO:01001564]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100442", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "multivalued": true, - "any_of": [ - { - "range": "WeatherTypeMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", @@ -12032,7 +12897,7 @@ ], "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -14362,7 +15227,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -14777,27 +15642,27 @@ "host_common_name": { "name": "host_common_name", "rank": 67, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_scientific_name": { "name": "host_scientific_name", "rank": 68, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_ecotype": { "name": "host_ecotype", "rank": 69, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_breed": { "name": "host_breed", "rank": 70, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_food_production_name": { "name": "host_food_production_name", "rank": 71, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_age": { "name": "host_age", @@ -14812,12 +15677,12 @@ "host_age_bin": { "name": "host_age_bin", "rank": 74, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_disease": { "name": "host_disease", "rank": 75, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_health_state": { "name": "host_health_state", @@ -14979,789 +15844,784 @@ "rank": 107, "slot_group": "Environmental conditions and measurements" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "rank": 108, - "slot_group": "Environmental conditions and measurements" - }, "water_depth": { "name": "water_depth", - "rank": 109, + "rank": 108, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 110, + "rank": 109, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 111, + "rank": 110, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 112, + "rank": 111, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 113, + "rank": 112, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 114, + "rank": 113, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 115, + "rank": 114, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 116, + "rank": 115, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 117, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 116, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", - "rank": 118, + "rank": 117, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", - "rank": 119, + "rank": 118, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_value": { "name": "ambient_temperature_measurement_value", - "rank": 120, + "rank": 119, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_unit": { "name": "ambient_temperature_measurement_unit", - "rank": 121, + "rank": 120, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_value": { "name": "ph_measurement_value", - "rank": 122, + "rank": 121, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_method": { "name": "ph_measurement_method", - "rank": 123, + "rank": 122, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_value": { "name": "total_daily_flow_rate_measurement_value", - "rank": 124, + "rank": 123, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_unit": { "name": "total_daily_flow_rate_measurement_unit", - "rank": 125, + "rank": 124, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_method": { "name": "total_daily_flow_rate_measurement_method", - "rank": 126, + "rank": 125, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_value": { "name": "instantaneous_flow_rate_measurement_value", - "rank": 127, + "rank": 126, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_unit": { "name": "instantaneous_flow_rate_measurement_unit", - "rank": 128, + "rank": 127, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_method": { "name": "instantaneous_flow_rate_measurement_method", - "rank": 129, + "rank": 128, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_value": { "name": "turbidity_measurement_value", - "rank": 130, + "rank": 129, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_unit": { "name": "turbidity_measurement_unit", - "rank": 131, + "rank": 130, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_method": { "name": "turbidity_measurement_method", - "rank": 132, + "rank": 131, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_value": { "name": "dissolved_oxygen_measurement_value", - "rank": 133, + "rank": 132, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_unit": { "name": "dissolved_oxygen_measurement_unit", - "rank": 134, + "rank": 133, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_method": { "name": "dissolved_oxygen_measurement_method", - "rank": 135, + "rank": 134, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_value": { "name": "oxygen_reduction_potential_orp_measurement_value", - "rank": 136, + "rank": 135, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_unit": { "name": "oxygen_reduction_potential_orp_measurement_unit", - "rank": 137, + "rank": 136, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_method": { "name": "oxygen_reduction_potential_orp_measurement_method", - "rank": 138, + "rank": 137, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_value": { "name": "chemical_oxygen_demand_cod_measurement_value", - "rank": 139, + "rank": 138, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_unit": { "name": "chemical_oxygen_demand_cod_measurement_unit", - "rank": 140, + "rank": 139, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_method": { "name": "chemical_oxygen_demand_cod_measurement_method", - "rank": 141, + "rank": 140, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", - "rank": 142, + "rank": 141, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", - "rank": 143, + "rank": 142, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", - "rank": 144, + "rank": 143, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_value": { "name": "total_suspended_solids_tss_measurement_value", - "rank": 145, + "rank": 144, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_unit": { "name": "total_suspended_solids_tss_measurement_unit", - "rank": 146, + "rank": 145, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_method": { "name": "total_suspended_solids_tss_measurement_method", - "rank": 147, + "rank": 146, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_value": { "name": "total_dissolved_solids_tds_measurement_value", - "rank": 148, + "rank": 147, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_unit": { "name": "total_dissolved_solids_tds_measurement_unit", - "rank": 149, + "rank": 148, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_method": { "name": "total_dissolved_solids_tds_measurement_method", - "rank": 150, + "rank": 149, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_value": { "name": "total_solids_ts_measurement_value", - "rank": 151, + "rank": 150, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_unit": { "name": "total_solids_ts_measurement_unit", - "rank": 152, + "rank": 151, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_method": { "name": "total_solids_ts_measurement_method", - "rank": 153, + "rank": 152, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_value": { "name": "alkalinity_measurement_value", - "rank": 154, + "rank": 153, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_unit": { "name": "alkalinity_measurement_unit", - "rank": 155, + "rank": 154, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_method": { "name": "alkalinity_measurement_method", - "rank": 156, + "rank": 155, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_value": { "name": "conductivity_measurement_value", - "rank": 157, + "rank": 156, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_unit": { "name": "conductivity_measurement_unit", - "rank": 158, + "rank": 157, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_method": { "name": "conductivity_measurement_method", - "rank": 159, + "rank": 158, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_value": { "name": "salinity_measurement_value", - "rank": 160, + "rank": 159, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_unit": { "name": "salinity_measurement_unit", - "rank": 161, + "rank": 160, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_method": { "name": "salinity_measurement_method", - "rank": 162, + "rank": 161, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_value": { "name": "total_nitrogen_tn_measurement_value", - "rank": 163, + "rank": 162, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_unit": { "name": "total_nitrogen_tn_measurement_unit", - "rank": 164, + "rank": 163, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_method": { "name": "total_nitrogen_tn_measurement_method", - "rank": 165, + "rank": 164, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_value": { "name": "total_phosphorus_tp_measurement_value", - "rank": 166, + "rank": 165, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_unit": { "name": "total_phosphorus_tp_measurement_unit", - "rank": 167, + "rank": 166, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_method": { "name": "total_phosphorus_tp_measurement_method", - "rank": 168, + "rank": 167, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_indicator_": { "name": "fecal_contamination_indicator_", - "rank": 169, + "rank": 168, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_value": { "name": "fecal_contamination_value", - "rank": 170, + "rank": 169, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_unit": { "name": "fecal_contamination_unit", - "rank": 171, + "rank": 170, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_method": { "name": "fecal_contamination_method", - "rank": 172, + "rank": 171, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_value": { "name": "fecal_coliform_count_value", - "rank": 173, + "rank": 172, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_unit": { "name": "fecal_coliform_count_unit", - "rank": 174, + "rank": 173, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_method": { "name": "fecal_coliform_count_method", - "rank": 175, + "rank": 174, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_indicator": { "name": "urinary_contamination_indicator", - "rank": 176, + "rank": 175, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_value": { "name": "urinary_contamination_value", - "rank": 177, + "rank": 176, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_unit": { "name": "urinary_contamination_unit", - "rank": 178, + "rank": 177, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_method": { "name": "urinary_contamination_method", - "rank": 179, + "rank": 178, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_value_at_collection": { "name": "sample_temperature_value_at_collection", - "rank": 180, + "rank": 179, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_unit_at_collection": { "name": "sample_temperature_unit_at_collection", - "rank": 181, + "rank": 180, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_value_when_received": { "name": "sample_temperature_value_when_received", - "rank": 182, + "rank": 181, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_unit_when_received": { "name": "sample_temperature_unit_when_received", - "rank": 183, + "rank": 182, "slot_group": "Environmental conditions and measurements" }, "library_id": { "name": "library_id", - "rank": 184, + "rank": 183, "slot_group": "Sequence information" }, "sequencing_assay_type": { "name": "sequencing_assay_type", - "rank": 185, + "rank": 184, "slot_group": "Sequence information" }, "sequencing_date": { "name": "sequencing_date", - "rank": 186, + "rank": 185, "slot_group": "Sequence information" }, "purpose_of_sequencing__": { "name": "purpose_of_sequencing__", - "rank": 187, + "rank": 186, "slot_group": "Sequence information" }, "purpose_of_sequencing_details": { "name": "purpose_of_sequencing_details", - "rank": 188, + "rank": 187, "slot_group": "Sequence information" }, "sequenced_by": { "name": "sequenced_by", - "rank": 189, + "rank": 188, "slot_group": "Sequence information" }, "sequenced_by_laboratory_name": { "name": "sequenced_by_laboratory_name", - "rank": 190, + "rank": 189, "slot_group": "Sequence information" }, "sequenced_by_contact_name": { "name": "sequenced_by_contact_name", - "rank": 191, + "rank": 190, "slot_group": "Sequence information" }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", - "rank": 192, + "rank": 191, "slot_group": "Sequence information" }, "sequence_submitted_by": { "name": "sequence_submitted_by", - "rank": 193, + "rank": 192, "slot_group": "Sequence information" }, "sequence_submitter_contact_email": { "name": "sequence_submitter_contact_email", - "rank": 194, + "rank": 193, "slot_group": "Sequence information" }, "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", - "rank": 195, - "slot_group": "Sample collection and processing" + "rank": 194, + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", - "rank": 196, - "slot_group": "Sample collection and processing" + "rank": 195, + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", - "rank": 197, - "slot_group": "Sample collection and processing" + "rank": 196, + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", - "rank": 198, + "rank": 197, "slot_group": "Sequence information" }, "sequencing_platform": { "name": "sequencing_platform", - "rank": 199, + "rank": 198, "slot_group": "Sequence information" }, "sequencing_instrument": { "name": "sequencing_instrument", - "rank": 200, + "rank": 199, "slot_group": "Sequence information" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 201, + "rank": 200, "slot_group": "Sequence information" }, "dna_fragment_length": { "name": "dna_fragment_length", - "rank": 202, + "rank": 201, "slot_group": "Sequence information" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 203, + "rank": 202, "slot_group": "Sequence information" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 204, + "rank": 203, "slot_group": "Sequence information" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 205, + "rank": 204, "slot_group": "Sequence information" }, "amplicon_size": { "name": "amplicon_size", - "rank": 206, + "rank": 205, "slot_group": "Sequence information" }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 207, + "rank": 206, "slot_group": "Sequence information" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 208, + "rank": 207, "slot_group": "Sequence information" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 209, + "rank": 208, "slot_group": "Sequence information" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - "rank": 210, + "rank": 209, "slot_group": "Sequence information" }, "fast5_filename": { "name": "fast5_filename", - "rank": 211, + "rank": 210, "slot_group": "Sequence information" }, "genome_sequence_file_name": { "name": "genome_sequence_file_name", - "rank": 212, + "rank": 211, "slot_group": "Sequence information" }, "assembly_filename": { "name": "assembly_filename", - "rank": 213, + "rank": 212, "slot_group": "Sequence information" }, "quality_control_method_name": { "name": "quality_control_method_name", - "rank": 214, + "rank": 213, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_method_version": { "name": "quality_control_method_version", - "rank": 215, + "rank": 214, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_determination": { "name": "quality_control_determination", - "rank": 216, + "rank": 215, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_issues": { "name": "quality_control_issues", - "rank": 217, + "rank": 216, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_details": { "name": "quality_control_details", - "rank": 218, + "rank": 217, "slot_group": "Bioinformatics and QC metrics" }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", - "rank": 219, + "rank": 218, "slot_group": "Bioinformatics and QC metrics" }, "dehosting_method": { "name": "dehosting_method", - "rank": 220, + "rank": 219, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_name": { "name": "sequence_assembly_software_name", - "rank": 221, + "rank": 220, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_version": { "name": "sequence_assembly_software_version", - "rank": 222, + "rank": 221, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "name": "consensus_sequence_software_name", - "rank": 223, + "rank": 222, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "name": "consensus_sequence_software_version", - "rank": 224, + "rank": 223, "slot_group": "Bioinformatics and QC metrics" }, "breadth_of_coverage_value": { "name": "breadth_of_coverage_value", - "rank": 225, + "rank": 224, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_value": { "name": "depth_of_coverage_value", - "rank": 226, + "rank": 225, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_threshold": { "name": "depth_of_coverage_threshold", - "rank": 227, + "rank": 226, "slot_group": "Bioinformatics and QC metrics" }, "genome_completeness": { "name": "genome_completeness", - "rank": 228, + "rank": 227, "slot_group": "Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "name": "number_of_base_pairs_sequenced", - "rank": 229, + "rank": 228, "slot_group": "Bioinformatics and QC metrics" }, "number_of_total_reads": { "name": "number_of_total_reads", - "rank": 230, + "rank": 229, "slot_group": "Bioinformatics and QC metrics" }, "number_of_unique_reads": { "name": "number_of_unique_reads", - "rank": 231, + "rank": 230, "slot_group": "Bioinformatics and QC metrics" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", - "rank": 232, + "rank": 231, "slot_group": "Bioinformatics and QC metrics" }, "number_of_contigs": { "name": "number_of_contigs", - "rank": 233, + "rank": 232, "slot_group": "Bioinformatics and QC metrics" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", - "rank": 234, + "rank": 233, "slot_group": "Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", - "rank": 235, + "rank": 234, "slot_group": "Bioinformatics and QC metrics" }, "n50": { "name": "n50", - "rank": 236, + "rank": 235, "slot_group": "Bioinformatics and QC metrics" }, "percent_read_contamination_": { "name": "percent_read_contamination_", - "rank": 237, + "rank": 236, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_length": { "name": "sequence_assembly_length", - "rank": 238, + "rank": 237, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 239, + "rank": 238, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 240, + "rank": 239, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 241, + "rank": 240, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 242, + "rank": 241, "slot_group": "Bioinformatics and QC metrics" }, "read_mapping_software_name": { "name": "read_mapping_software_name", - "rank": 243, + "rank": 242, "slot_group": "Taxonomic identification information" }, "read_mapping_software_version": { "name": "read_mapping_software_version", - "rank": 244, + "rank": 243, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_name": { "name": "taxonomic_reference_database_name", - "rank": 245, + "rank": 244, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_version": { "name": "taxonomic_reference_database_version", - "rank": 246, + "rank": 245, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_report_filename": { "name": "taxonomic_analysis_report_filename", - "rank": 247, + "rank": 246, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_date": { "name": "taxonomic_analysis_date", - "rank": 248, + "rank": 247, "slot_group": "Taxonomic identification information" }, "read_mapping_criteria": { "name": "read_mapping_criteria", - "rank": 249, + "rank": 248, "slot_group": "Taxonomic identification information" }, "genetic_target_name": { "name": "genetic_target_name", - "rank": 250, + "rank": 249, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region": { "name": "genetic_target_region", - "rank": 251, + "rank": 250, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region_reference_genome": { "name": "genetic_target_region_reference_genome", - "rank": 252, + "rank": 251, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_target_presence": { "name": "diagnostic_target_presence", - "rank": 253, + "rank": 252, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_value": { "name": "diagnostic_measurement_value", - "rank": 254, + "rank": 253, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_unit": { "name": "diagnostic_measurement_unit", - "rank": 255, + "rank": 254, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_method": { "name": "diagnostic_measurement_method", - "rank": 256, + "rank": 255, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_value": { "name": "diagnostic_testing_threshold_value", - "rank": 257, + "rank": 256, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_units": { "name": "diagnostic_testing_threshold_units", - "rank": 258, + "rank": 257, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_details": { "name": "diagnostic_testing_details", - "rank": 259, + "rank": 258, "slot_group": "Pathogen diagnostic testing" }, "prevalence_metrics": { "name": "prevalence_metrics", - "rank": 260, + "rank": 259, "slot_group": "Risk assessment information" }, "prevalence_metrics_details": { "name": "prevalence_metrics_details", - "rank": 261, + "rank": 260, "slot_group": "Risk assessment information" }, "stage_of_production": { "name": "stage_of_production", - "rank": 262, + "rank": 261, "slot_group": "Risk assessment information" }, "experimental_intervention": { "name": "experimental_intervention", - "rank": 263, + "rank": 262, "slot_group": "Risk assessment information" }, "experiment_intervention_details": { "name": "experiment_intervention_details", - "rank": 264, + "rank": 263, "slot_group": "Risk assessment information" } }, @@ -16436,7 +17296,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -17878,7 +18738,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -17918,7 +18778,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -17953,7 +18813,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_breed": { @@ -17981,7 +18841,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_food_production_name": { @@ -18008,7 +18868,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostFoodProductionNameMenu" @@ -18106,7 +18966,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostAgeBinMenu" @@ -18140,7 +19000,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostDiseaseMenu" @@ -19007,7 +19867,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -19080,39 +19940,6 @@ } ] }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", - "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." - ], - "examples": [ - { - "value": "12" - } - ], - "from_schema": "https://example.com/hpai", - "rank": 108, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", - "owner": "HPAI", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "slot_group": "Environmental conditions and measurements", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "water_depth": { "name": "water_depth", "description": "The depth of some water.", @@ -19126,7 +19953,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 109, + "rank": 108, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "HPAI", @@ -19151,7 +19978,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 110, + "rank": 109, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "HPAI", @@ -19183,7 +20010,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 111, + "rank": 110, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "HPAI", @@ -19208,7 +20035,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 112, + "rank": 111, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "HPAI", @@ -19240,7 +20067,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 113, + "rank": 112, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "HPAI", @@ -19265,7 +20092,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 114, + "rank": 113, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "HPAI", @@ -19297,7 +20124,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 115, + "rank": 114, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "HPAI", @@ -19322,7 +20149,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 116, + "rank": 115, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "HPAI", @@ -19341,22 +20168,22 @@ } ] }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "12" } ], "from_schema": "https://example.com/hpai", - "rank": 117, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 116, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "HPAI", "domain_of": [ "HPAI", @@ -19364,10 +20191,10 @@ "HPAIEnviro" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "recommended": true, "any_of": [ { - "range": "WeatherTypeMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -19387,7 +20214,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 118, + "rank": 117, "slot_uri": "GENEPIO:0100912", "alias": "precipitation_measurement_unit", "owner": "HPAI", @@ -19420,7 +20247,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 119, + "rank": 118, "slot_uri": "GENEPIO:0100913", "alias": "precipitation_measurement_method", "owner": "HPAI", @@ -19445,7 +20272,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 120, + "rank": 119, "slot_uri": "GENEPIO:0100935", "alias": "ambient_temperature_measurement_value", "owner": "HPAI", @@ -19470,7 +20297,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 121, + "rank": 120, "slot_uri": "GENEPIO:0100936", "alias": "ambient_temperature_measurement_unit", "owner": "HPAI", @@ -19502,7 +20329,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 122, + "rank": 121, "slot_uri": "GENEPIO:0001736", "alias": "ph_measurement_value", "owner": "HPAI", @@ -19527,7 +20354,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 123, + "rank": 122, "slot_uri": "GENEPIO:0100781", "alias": "ph_measurement_method", "owner": "HPAI", @@ -19552,7 +20379,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 124, + "rank": 123, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", "owner": "HPAI", @@ -19577,7 +20404,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 125, + "rank": 124, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", "owner": "HPAI", @@ -19609,7 +20436,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 126, + "rank": 125, "slot_uri": "GENEPIO:0100907", "alias": "total_daily_flow_rate_measurement_method", "owner": "HPAI", @@ -19634,7 +20461,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 127, + "rank": 126, "slot_uri": "GENEPIO:0100908", "alias": "instantaneous_flow_rate_measurement_value", "owner": "HPAI", @@ -19659,7 +20486,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 128, + "rank": 127, "slot_uri": "GENEPIO:0100909", "alias": "instantaneous_flow_rate_measurement_unit", "owner": "HPAI", @@ -19691,7 +20518,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 129, + "rank": 128, "slot_uri": "GENEPIO:0100910", "alias": "instantaneous_flow_rate_measurement_method", "owner": "HPAI", @@ -19716,7 +20543,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 130, + "rank": 129, "slot_uri": "GENEPIO:0100783", "alias": "turbidity_measurement_value", "owner": "HPAI", @@ -19742,7 +20569,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 131, + "rank": 130, "slot_uri": "GENEPIO:0100914", "alias": "turbidity_measurement_unit", "owner": "HPAI", @@ -19775,7 +20602,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 132, + "rank": 131, "slot_uri": "GENEPIO:0101013", "alias": "turbidity_measurement_method", "owner": "HPAI", @@ -19800,7 +20627,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 133, + "rank": 132, "slot_uri": "GENEPIO:0100915", "alias": "dissolved_oxygen_measurement_value", "owner": "HPAI", @@ -19825,7 +20652,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 134, + "rank": 133, "slot_uri": "GENEPIO:0100784", "alias": "dissolved_oxygen_measurement_unit", "owner": "HPAI", @@ -19857,7 +20684,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 135, + "rank": 134, "slot_uri": "GENEPIO:0100785", "alias": "dissolved_oxygen_measurement_method", "owner": "HPAI", @@ -19882,7 +20709,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 136, + "rank": 135, "slot_uri": "GENEPIO:0100917", "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "HPAI", @@ -19907,7 +20734,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 137, + "rank": 136, "slot_uri": "GENEPIO:0100786", "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "HPAI", @@ -19939,7 +20766,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 138, + "rank": 137, "slot_uri": "GENEPIO:0100787", "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "HPAI", @@ -19964,7 +20791,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 139, + "rank": 138, "slot_uri": "GENEPIO:0100788", "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "HPAI", @@ -19989,7 +20816,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 140, + "rank": 139, "slot_uri": "GENEPIO:0100789", "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "HPAI", @@ -20021,7 +20848,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 141, + "rank": 140, "slot_uri": "GENEPIO:0100790", "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "HPAI", @@ -20046,7 +20873,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 142, + "rank": 141, "slot_uri": "GENEPIO:0100791", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "HPAI", @@ -20071,7 +20898,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 143, + "rank": 142, "slot_uri": "GENEPIO:0100792", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "HPAI", @@ -20103,7 +20930,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 144, + "rank": 143, "slot_uri": "GENEPIO:0100793", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "HPAI", @@ -20128,7 +20955,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 145, + "rank": 144, "slot_uri": "GENEPIO:0100794", "alias": "total_suspended_solids_tss_measurement_value", "owner": "HPAI", @@ -20153,7 +20980,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 146, + "rank": 145, "slot_uri": "GENEPIO:0100795", "alias": "total_suspended_solids_tss_measurement_unit", "owner": "HPAI", @@ -20185,7 +21012,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 147, + "rank": 146, "slot_uri": "GENEPIO:0100796", "alias": "total_suspended_solids_tss_measurement_method", "owner": "HPAI", @@ -20210,7 +21037,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 148, + "rank": 147, "slot_uri": "GENEPIO:0100797", "alias": "total_dissolved_solids_tds_measurement_value", "owner": "HPAI", @@ -20235,7 +21062,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 149, + "rank": 148, "slot_uri": "GENEPIO:0100798", "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "HPAI", @@ -20267,7 +21094,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 150, + "rank": 149, "slot_uri": "GENEPIO:0100799", "alias": "total_dissolved_solids_tds_measurement_method", "owner": "HPAI", @@ -20292,7 +21119,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 151, + "rank": 150, "slot_uri": "GENEPIO:0100800", "alias": "total_solids_ts_measurement_value", "owner": "HPAI", @@ -20317,7 +21144,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 152, + "rank": 151, "slot_uri": "GENEPIO:0100801", "alias": "total_solids_ts_measurement_unit", "owner": "HPAI", @@ -20349,7 +21176,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 153, + "rank": 152, "slot_uri": "GENEPIO:0100802", "alias": "total_solids_ts_measurement_method", "owner": "HPAI", @@ -20374,7 +21201,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 154, + "rank": 153, "slot_uri": "GENEPIO:0100878", "alias": "alkalinity_measurement_value", "owner": "HPAI", @@ -20399,7 +21226,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 155, + "rank": 154, "slot_uri": "GENEPIO:0100879", "alias": "alkalinity_measurement_unit", "owner": "HPAI", @@ -20431,7 +21258,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 156, + "rank": 155, "slot_uri": "GENEPIO:0100880", "alias": "alkalinity_measurement_method", "owner": "HPAI", @@ -20456,7 +21283,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 157, + "rank": 156, "slot_uri": "GENEPIO:0100916", "alias": "conductivity_measurement_value", "owner": "HPAI", @@ -20481,7 +21308,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 158, + "rank": 157, "slot_uri": "GENEPIO:0100803", "alias": "conductivity_measurement_unit", "owner": "HPAI", @@ -20513,7 +21340,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 159, + "rank": 158, "slot_uri": "GENEPIO:0100804", "alias": "conductivity_measurement_method", "owner": "HPAI", @@ -20538,7 +21365,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 160, + "rank": 159, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", "owner": "HPAI", @@ -20563,7 +21390,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 161, + "rank": 160, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", "owner": "HPAI", @@ -20595,7 +21422,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 162, + "rank": 161, "slot_uri": "GENEPIO:0100807", "alias": "salinity_measurement_method", "owner": "HPAI", @@ -20620,7 +21447,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 163, + "rank": 162, "slot_uri": "GENEPIO:0100808", "alias": "total_nitrogen_tn_measurement_value", "owner": "HPAI", @@ -20645,7 +21472,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 164, + "rank": 163, "slot_uri": "GENEPIO:0100809", "alias": "total_nitrogen_tn_measurement_unit", "owner": "HPAI", @@ -20677,7 +21504,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 165, + "rank": 164, "slot_uri": "GENEPIO:0100810", "alias": "total_nitrogen_tn_measurement_method", "owner": "HPAI", @@ -20702,7 +21529,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 166, + "rank": 165, "slot_uri": "GENEPIO:0100811", "alias": "total_phosphorus_tp_measurement_value", "owner": "HPAI", @@ -20727,7 +21554,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 167, + "rank": 166, "slot_uri": "GENEPIO:0100812", "alias": "total_phosphorus_tp_measurement_unit", "owner": "HPAI", @@ -20739,7 +21566,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -20759,7 +21586,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 168, + "rank": 167, "slot_uri": "GENEPIO:0100813", "alias": "total_phosphorus_tp_measurement_method", "owner": "HPAI", @@ -20784,7 +21611,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 169, + "rank": 168, "slot_uri": "GENEPIO:0100814", "alias": "fecal_contamination_indicator_", "owner": "HPAI", @@ -20817,7 +21644,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 170, + "rank": 169, "slot_uri": "GENEPIO:0100815", "alias": "fecal_contamination_value", "owner": "HPAI", @@ -20843,7 +21670,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 171, + "rank": 170, "slot_uri": "GENEPIO:0100816", "alias": "fecal_contamination_unit", "owner": "HPAI", @@ -20876,7 +21703,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 172, + "rank": 171, "slot_uri": "GENEPIO:0100817", "alias": "fecal_contamination_method", "owner": "HPAI", @@ -20901,7 +21728,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 173, + "rank": 172, "slot_uri": "GENEPIO:0100818", "alias": "fecal_coliform_count_value", "owner": "HPAI", @@ -20926,7 +21753,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 174, + "rank": 173, "slot_uri": "GENEPIO:0100819", "alias": "fecal_coliform_count_unit", "owner": "HPAI", @@ -20958,7 +21785,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 175, + "rank": 174, "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "HPAI", @@ -20983,7 +21810,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 176, + "rank": 175, "slot_uri": "GENEPIO:0100837", "alias": "urinary_contamination_indicator", "owner": "HPAI", @@ -21015,7 +21842,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 177, + "rank": 176, "slot_uri": "GENEPIO:0100838", "alias": "urinary_contamination_value", "owner": "HPAI", @@ -21040,7 +21867,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 178, + "rank": 177, "slot_uri": "GENEPIO:0100839", "alias": "urinary_contamination_unit", "owner": "HPAI", @@ -21072,7 +21899,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 179, + "rank": 178, "slot_uri": "GENEPIO:0100840", "alias": "urinary_contamination_method", "owner": "HPAI", @@ -21097,7 +21924,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 180, + "rank": 179, "slot_uri": "GENEPIO:0100821", "alias": "sample_temperature_value_at_collection", "owner": "HPAI", @@ -21122,7 +21949,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 181, + "rank": 180, "slot_uri": "GENEPIO:0100822", "alias": "sample_temperature_unit_at_collection", "owner": "HPAI", @@ -21154,7 +21981,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 182, + "rank": 181, "slot_uri": "GENEPIO:0100823", "alias": "sample_temperature_value_when_received", "owner": "HPAI", @@ -21179,7 +22006,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 183, + "rank": 182, "slot_uri": "GENEPIO:0100824", "alias": "sample_temperature_unit_when_received", "owner": "HPAI", @@ -21211,7 +22038,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 184, + "rank": 183, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "HPAI", @@ -21238,7 +22065,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 185, + "rank": 184, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "HPAI", @@ -21268,7 +22095,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 186, + "rank": 185, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "HPAI", @@ -21295,7 +22122,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 187, + "rank": 186, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing__", "owner": "HPAI", @@ -21331,7 +22158,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 188, + "rank": 187, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "HPAI", @@ -21362,7 +22189,7 @@ "GISAID:sequenced_by", "BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 189, + "rank": 188, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "HPAI", @@ -21397,7 +22224,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 190, + "rank": 189, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "HPAI", @@ -21424,7 +22251,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 191, + "rank": 190, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "HPAI", @@ -21459,7 +22286,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 192, + "rank": 191, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "HPAI", @@ -21494,7 +22321,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 193, + "rank": 192, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "HPAI", @@ -21529,7 +22356,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 194, + "rank": 193, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "HPAI", @@ -21565,7 +22392,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 195, + "rank": 194, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "HPAI", @@ -21576,7 +22403,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -21592,7 +22419,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 196, + "rank": 195, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "HPAI", @@ -21603,7 +22430,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -21614,7 +22441,7 @@ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/hpai", - "rank": 197, + "rank": 196, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", "owner": "HPAI", @@ -21625,7 +22452,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -21642,7 +22469,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 198, + "rank": 197, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "HPAI", @@ -21669,7 +22496,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 199, + "rank": 198, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "HPAI", @@ -21703,7 +22530,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 200, + "rank": 199, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "HPAI", @@ -21737,7 +22564,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 201, + "rank": 200, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "HPAI", @@ -21764,7 +22591,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 202, + "rank": 201, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "HPAI", @@ -21791,7 +22618,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 203, + "rank": 202, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "HPAI", @@ -21818,7 +22645,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 204, + "rank": 203, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "HPAI", @@ -21845,7 +22672,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 205, + "rank": 204, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "HPAI", @@ -21872,7 +22699,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 206, + "rank": 205, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "HPAI", @@ -21899,7 +22726,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 207, + "rank": 206, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "HPAI", @@ -21926,7 +22753,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 208, + "rank": 207, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "HPAI", @@ -21953,7 +22780,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 209, + "rank": 208, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "HPAI", @@ -21980,7 +22807,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 210, + "rank": 209, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "HPAI", @@ -22007,7 +22834,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 211, + "rank": 210, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "HPAI", @@ -22034,7 +22861,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 212, + "rank": 211, "slot_uri": "GENEPIO:0101715", "alias": "genome_sequence_file_name", "owner": "HPAI", @@ -22061,7 +22888,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 213, + "rank": 212, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "HPAI", @@ -22088,7 +22915,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 214, + "rank": 213, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "HPAI", @@ -22115,7 +22942,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 215, + "rank": 214, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "HPAI", @@ -22142,7 +22969,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 216, + "rank": 215, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "HPAI", @@ -22177,7 +23004,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 217, + "rank": 216, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "HPAI", @@ -22212,7 +23039,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 218, + "rank": 217, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "HPAI", @@ -22239,7 +23066,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 219, + "rank": 218, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "HPAI", @@ -22274,7 +23101,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 220, + "rank": 219, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "HPAI", @@ -22309,7 +23136,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 221, + "rank": 220, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "HPAI", @@ -22343,7 +23170,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 222, + "rank": 221, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "HPAI", @@ -22377,7 +23204,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 223, + "rank": 222, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "HPAI", @@ -22411,7 +23238,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 224, + "rank": 223, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "HPAI", @@ -22445,7 +23272,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 225, + "rank": 224, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "HPAI", @@ -22472,7 +23299,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 226, + "rank": 225, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "HPAI", @@ -22499,7 +23326,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 227, + "rank": 226, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "HPAI", @@ -22526,7 +23353,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 228, + "rank": 227, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "HPAI", @@ -22553,7 +23380,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 229, + "rank": 228, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "HPAI", @@ -22580,7 +23407,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 230, + "rank": 229, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "HPAI", @@ -22607,7 +23434,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 231, + "rank": 230, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "HPAI", @@ -22634,7 +23461,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 232, + "rank": 231, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "HPAI", @@ -22661,7 +23488,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 233, + "rank": 232, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "HPAI", @@ -22688,7 +23515,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 234, + "rank": 233, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "HPAI", @@ -22715,7 +23542,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 235, + "rank": 234, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "HPAI", @@ -22742,7 +23569,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 236, + "rank": 235, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "HPAI", @@ -22769,7 +23596,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 237, + "rank": 236, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "HPAI", @@ -22796,7 +23623,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 238, + "rank": 237, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "HPAI", @@ -22823,7 +23650,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 239, + "rank": 238, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "HPAI", @@ -22850,7 +23677,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 240, + "rank": 239, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "HPAI", @@ -22877,7 +23704,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 241, + "rank": 240, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "HPAI", @@ -22904,7 +23731,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 242, + "rank": 241, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "HPAI", @@ -22931,7 +23758,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 243, + "rank": 242, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "HPAI", @@ -22958,7 +23785,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 244, + "rank": 243, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "HPAI", @@ -22985,7 +23812,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 245, + "rank": 244, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "HPAI", @@ -23012,7 +23839,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 246, + "rank": 245, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "HPAI", @@ -23039,7 +23866,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 247, + "rank": 246, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "HPAI", @@ -23066,7 +23893,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 248, + "rank": 247, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "HPAI", @@ -23093,7 +23920,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 249, + "rank": 248, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "HPAI", @@ -23120,7 +23947,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 250, + "rank": 249, "slot_uri": "GENEPIO:0101116", "alias": "genetic_target_name", "owner": "HPAI", @@ -23146,7 +23973,7 @@ "description": "The specific region or segment of a genetic sequence used for testing or analysis.", "title": "genetic target region", "from_schema": "https://example.com/hpai", - "rank": 251, + "rank": 250, "slot_uri": "GENEPIO:0101117", "alias": "genetic_target_region", "owner": "HPAI", @@ -23165,7 +23992,7 @@ "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", "title": "genetic target region reference genome", "from_schema": "https://example.com/hpai", - "rank": 252, + "rank": 251, "slot_uri": "GENEPIO:0101118", "alias": "genetic_target_region_reference_genome", "owner": "HPAI", @@ -23192,7 +24019,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 253, + "rank": 252, "slot_uri": "GENEPIO:0100962", "alias": "diagnostic_target_presence", "owner": "HPAI", @@ -23226,7 +24053,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 254, + "rank": 253, "slot_uri": "GENEPIO:0100963", "alias": "diagnostic_measurement_value", "owner": "HPAI", @@ -23253,7 +24080,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 255, + "rank": 254, "slot_uri": "GENEPIO:0100964", "alias": "diagnostic_measurement_unit", "owner": "HPAI", @@ -23287,7 +24114,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 256, + "rank": 255, "slot_uri": "GENEPIO:0100965", "alias": "diagnostic_measurement_method", "owner": "HPAI", @@ -23313,7 +24140,7 @@ "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold value", "from_schema": "https://example.com/hpai", - "rank": 257, + "rank": 256, "slot_uri": "GENEPIO:0101104", "alias": "diagnostic_testing_threshold_value", "owner": "HPAI", @@ -23332,7 +24159,7 @@ "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold units", "from_schema": "https://example.com/hpai", - "rank": 258, + "rank": 257, "slot_uri": "GENEPIO:0101105", "alias": "diagnostic_testing_threshold_units", "owner": "HPAI", @@ -23351,7 +24178,7 @@ "description": "Describe any details of the diagnsotic testing.", "title": "diagnostic testing details", "from_schema": "https://example.com/hpai", - "rank": 259, + "rank": 258, "slot_uri": "GENEPIO:0101106", "alias": "diagnostic_testing_details", "owner": "HPAI", @@ -23378,7 +24205,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 260, + "rank": 259, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "HPAI", @@ -23406,7 +24233,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 261, + "rank": 260, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "HPAI", @@ -23434,7 +24261,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 262, + "rank": 261, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "HPAI", @@ -23449,7 +24276,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -23469,7 +24296,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 263, + "rank": 262, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "HPAI", @@ -23505,7 +24332,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 264, + "rank": 263, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "HPAI", @@ -23872,17 +24699,17 @@ "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", "rank": 68, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", "rank": 69, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", "rank": 70, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", @@ -24891,7 +25718,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -26334,7 +27161,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -26361,7 +27188,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -26383,7 +27210,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -28207,7 +29034,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -28612,789 +29439,784 @@ "rank": 64, "slot_group": "Environmental conditions and measurements" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "rank": 65, - "slot_group": "Environmental conditions and measurements" - }, "water_depth": { "name": "water_depth", - "rank": 66, + "rank": 65, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 67, + "rank": 66, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 68, + "rank": 67, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 69, + "rank": 68, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 70, + "rank": 69, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 71, + "rank": 70, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 72, + "rank": 71, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 73, + "rank": 72, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 74, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 73, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", - "rank": 75, + "rank": 74, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", - "rank": 76, + "rank": 75, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_value": { "name": "ambient_temperature_measurement_value", - "rank": 77, + "rank": 76, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_unit": { "name": "ambient_temperature_measurement_unit", - "rank": 78, + "rank": 77, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_value": { "name": "ph_measurement_value", - "rank": 79, + "rank": 78, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_method": { "name": "ph_measurement_method", - "rank": 80, + "rank": 79, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_value": { "name": "total_daily_flow_rate_measurement_value", - "rank": 81, + "rank": 80, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_unit": { "name": "total_daily_flow_rate_measurement_unit", - "rank": 82, + "rank": 81, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_method": { "name": "total_daily_flow_rate_measurement_method", - "rank": 83, + "rank": 82, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_value": { "name": "instantaneous_flow_rate_measurement_value", - "rank": 84, + "rank": 83, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_unit": { "name": "instantaneous_flow_rate_measurement_unit", - "rank": 85, + "rank": 84, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_method": { "name": "instantaneous_flow_rate_measurement_method", - "rank": 86, + "rank": 85, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_value": { "name": "turbidity_measurement_value", - "rank": 87, + "rank": 86, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_unit": { "name": "turbidity_measurement_unit", - "rank": 88, + "rank": 87, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_method": { "name": "turbidity_measurement_method", - "rank": 89, + "rank": 88, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_value": { "name": "dissolved_oxygen_measurement_value", - "rank": 90, + "rank": 89, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_unit": { "name": "dissolved_oxygen_measurement_unit", - "rank": 91, + "rank": 90, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_method": { "name": "dissolved_oxygen_measurement_method", - "rank": 92, + "rank": 91, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_value": { "name": "oxygen_reduction_potential_orp_measurement_value", - "rank": 93, + "rank": 92, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_unit": { "name": "oxygen_reduction_potential_orp_measurement_unit", - "rank": 94, + "rank": 93, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_method": { "name": "oxygen_reduction_potential_orp_measurement_method", - "rank": 95, + "rank": 94, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_value": { "name": "chemical_oxygen_demand_cod_measurement_value", - "rank": 96, + "rank": 95, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_unit": { "name": "chemical_oxygen_demand_cod_measurement_unit", - "rank": 97, + "rank": 96, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_method": { "name": "chemical_oxygen_demand_cod_measurement_method", - "rank": 98, + "rank": 97, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", - "rank": 99, + "rank": 98, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", - "rank": 100, + "rank": 99, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", - "rank": 101, + "rank": 100, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_value": { "name": "total_suspended_solids_tss_measurement_value", - "rank": 102, + "rank": 101, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_unit": { "name": "total_suspended_solids_tss_measurement_unit", - "rank": 103, + "rank": 102, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_method": { "name": "total_suspended_solids_tss_measurement_method", - "rank": 104, + "rank": 103, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_value": { "name": "total_dissolved_solids_tds_measurement_value", - "rank": 105, + "rank": 104, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_unit": { "name": "total_dissolved_solids_tds_measurement_unit", - "rank": 106, + "rank": 105, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_method": { "name": "total_dissolved_solids_tds_measurement_method", - "rank": 107, + "rank": 106, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_value": { "name": "total_solids_ts_measurement_value", - "rank": 108, + "rank": 107, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_unit": { "name": "total_solids_ts_measurement_unit", - "rank": 109, + "rank": 108, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_method": { "name": "total_solids_ts_measurement_method", - "rank": 110, + "rank": 109, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_value": { "name": "alkalinity_measurement_value", - "rank": 111, + "rank": 110, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_unit": { "name": "alkalinity_measurement_unit", - "rank": 112, + "rank": 111, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_method": { "name": "alkalinity_measurement_method", - "rank": 113, + "rank": 112, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_value": { "name": "conductivity_measurement_value", - "rank": 114, + "rank": 113, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_unit": { "name": "conductivity_measurement_unit", - "rank": 115, + "rank": 114, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_method": { "name": "conductivity_measurement_method", - "rank": 116, + "rank": 115, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_value": { "name": "salinity_measurement_value", - "rank": 117, + "rank": 116, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_unit": { "name": "salinity_measurement_unit", - "rank": 118, + "rank": 117, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_method": { "name": "salinity_measurement_method", - "rank": 119, + "rank": 118, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_value": { "name": "total_nitrogen_tn_measurement_value", - "rank": 120, + "rank": 119, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_unit": { "name": "total_nitrogen_tn_measurement_unit", - "rank": 121, + "rank": 120, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_method": { "name": "total_nitrogen_tn_measurement_method", - "rank": 122, + "rank": 121, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_value": { "name": "total_phosphorus_tp_measurement_value", - "rank": 123, + "rank": 122, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_unit": { "name": "total_phosphorus_tp_measurement_unit", - "rank": 124, + "rank": 123, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_method": { "name": "total_phosphorus_tp_measurement_method", - "rank": 125, + "rank": 124, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_indicator_": { "name": "fecal_contamination_indicator_", - "rank": 126, + "rank": 125, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_value": { "name": "fecal_contamination_value", - "rank": 127, + "rank": 126, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_unit": { "name": "fecal_contamination_unit", - "rank": 128, + "rank": 127, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_method": { "name": "fecal_contamination_method", - "rank": 129, + "rank": 128, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_value": { "name": "fecal_coliform_count_value", - "rank": 130, + "rank": 129, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_unit": { "name": "fecal_coliform_count_unit", - "rank": 131, + "rank": 130, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_method": { "name": "fecal_coliform_count_method", - "rank": 132, + "rank": 131, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_indicator": { "name": "urinary_contamination_indicator", - "rank": 133, + "rank": 132, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_value": { "name": "urinary_contamination_value", - "rank": 134, + "rank": 133, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_unit": { "name": "urinary_contamination_unit", - "rank": 135, + "rank": 134, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_method": { "name": "urinary_contamination_method", - "rank": 136, + "rank": 135, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_value_at_collection": { "name": "sample_temperature_value_at_collection", - "rank": 137, + "rank": 136, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_unit_at_collection": { "name": "sample_temperature_unit_at_collection", - "rank": 138, + "rank": 137, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_value_when_received": { "name": "sample_temperature_value_when_received", - "rank": 139, + "rank": 138, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_unit_when_received": { "name": "sample_temperature_unit_when_received", - "rank": 140, + "rank": 139, "slot_group": "Environmental conditions and measurements" }, "library_id": { "name": "library_id", - "rank": 141, + "rank": 140, "slot_group": "Sequence information" }, "sequencing_assay_type": { "name": "sequencing_assay_type", - "rank": 142, + "rank": 141, "slot_group": "Sequence information" }, "sequencing_date": { "name": "sequencing_date", - "rank": 143, + "rank": 142, "slot_group": "Sequence information" }, "purpose_of_sequencing__": { "name": "purpose_of_sequencing__", - "rank": 144, + "rank": 143, "slot_group": "Sequence information" }, "purpose_of_sequencing_details": { "name": "purpose_of_sequencing_details", - "rank": 145, + "rank": 144, "slot_group": "Sequence information" }, "sequenced_by": { "name": "sequenced_by", - "rank": 146, + "rank": 145, "slot_group": "Sequence information" }, "sequenced_by_laboratory_name": { "name": "sequenced_by_laboratory_name", - "rank": 147, + "rank": 146, "slot_group": "Sequence information" }, "sequenced_by_contact_name": { "name": "sequenced_by_contact_name", - "rank": 148, + "rank": 147, "slot_group": "Sequence information" }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", - "rank": 149, + "rank": 148, "slot_group": "Sequence information" }, "sequence_submitted_by": { "name": "sequence_submitted_by", - "rank": 150, + "rank": 149, "slot_group": "Sequence information" }, "sequence_submitter_contact_email": { "name": "sequence_submitter_contact_email", - "rank": 151, + "rank": 150, "slot_group": "Sequence information" }, "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", - "rank": 152, - "slot_group": "Sample collection and processing" + "rank": 151, + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", - "rank": 153, - "slot_group": "Sample collection and processing" + "rank": 152, + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", - "rank": 154, - "slot_group": "Sample collection and processing" + "rank": 153, + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", - "rank": 155, + "rank": 154, "slot_group": "Sequence information" }, "sequencing_platform": { "name": "sequencing_platform", - "rank": 156, + "rank": 155, "slot_group": "Sequence information" }, "sequencing_instrument": { "name": "sequencing_instrument", - "rank": 157, + "rank": 156, "slot_group": "Sequence information" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 158, + "rank": 157, "slot_group": "Sequence information" }, "dna_fragment_length": { "name": "dna_fragment_length", - "rank": 159, + "rank": 158, "slot_group": "Sequence information" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 160, + "rank": 159, "slot_group": "Sequence information" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 161, + "rank": 160, "slot_group": "Sequence information" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 162, + "rank": 161, "slot_group": "Sequence information" }, "amplicon_size": { "name": "amplicon_size", - "rank": 163, + "rank": 162, "slot_group": "Sequence information" }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 164, + "rank": 163, "slot_group": "Sequence information" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 165, + "rank": 164, "slot_group": "Sequence information" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 166, + "rank": 165, "slot_group": "Sequence information" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - "rank": 167, + "rank": 166, "slot_group": "Sequence information" }, "fast5_filename": { "name": "fast5_filename", - "rank": 168, + "rank": 167, "slot_group": "Sequence information" }, "genome_sequence_file_name": { "name": "genome_sequence_file_name", - "rank": 169, + "rank": 168, "slot_group": "Sequence information" }, "assembly_filename": { "name": "assembly_filename", - "rank": 170, + "rank": 169, "slot_group": "Sequence information" }, "quality_control_method_name": { "name": "quality_control_method_name", - "rank": 171, + "rank": 170, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_method_version": { "name": "quality_control_method_version", - "rank": 172, + "rank": 171, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_determination": { "name": "quality_control_determination", - "rank": 173, + "rank": 172, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_issues": { "name": "quality_control_issues", - "rank": 174, + "rank": 173, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_details": { "name": "quality_control_details", - "rank": 175, + "rank": 174, "slot_group": "Bioinformatics and QC metrics" }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", - "rank": 176, + "rank": 175, "slot_group": "Bioinformatics and QC metrics" }, "dehosting_method": { "name": "dehosting_method", - "rank": 177, + "rank": 176, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_name": { "name": "sequence_assembly_software_name", - "rank": 178, + "rank": 177, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_version": { "name": "sequence_assembly_software_version", - "rank": 179, + "rank": 178, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "name": "consensus_sequence_software_name", - "rank": 180, + "rank": 179, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "name": "consensus_sequence_software_version", - "rank": 181, + "rank": 180, "slot_group": "Bioinformatics and QC metrics" }, "breadth_of_coverage_value": { "name": "breadth_of_coverage_value", - "rank": 182, + "rank": 181, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_value": { "name": "depth_of_coverage_value", - "rank": 183, + "rank": 182, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_threshold": { "name": "depth_of_coverage_threshold", - "rank": 184, + "rank": 183, "slot_group": "Bioinformatics and QC metrics" }, "genome_completeness": { "name": "genome_completeness", - "rank": 185, + "rank": 184, "slot_group": "Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "name": "number_of_base_pairs_sequenced", - "rank": 186, + "rank": 185, "slot_group": "Bioinformatics and QC metrics" }, "number_of_total_reads": { "name": "number_of_total_reads", - "rank": 187, + "rank": 186, "slot_group": "Bioinformatics and QC metrics" }, "number_of_unique_reads": { "name": "number_of_unique_reads", - "rank": 188, + "rank": 187, "slot_group": "Bioinformatics and QC metrics" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", - "rank": 189, + "rank": 188, "slot_group": "Bioinformatics and QC metrics" }, "number_of_contigs": { "name": "number_of_contigs", - "rank": 190, + "rank": 189, "slot_group": "Bioinformatics and QC metrics" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", - "rank": 191, + "rank": 190, "slot_group": "Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", - "rank": 192, + "rank": 191, "slot_group": "Bioinformatics and QC metrics" }, "n50": { "name": "n50", - "rank": 193, + "rank": 192, "slot_group": "Bioinformatics and QC metrics" }, "percent_read_contamination_": { "name": "percent_read_contamination_", - "rank": 194, + "rank": 193, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_length": { "name": "sequence_assembly_length", - "rank": 195, + "rank": 194, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 196, + "rank": 195, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 197, + "rank": 196, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 198, + "rank": 197, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 199, + "rank": 198, "slot_group": "Bioinformatics and QC metrics" }, "read_mapping_software_name": { "name": "read_mapping_software_name", - "rank": 200, + "rank": 199, "slot_group": "Taxonomic identification information" }, "read_mapping_software_version": { "name": "read_mapping_software_version", - "rank": 201, + "rank": 200, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_name": { "name": "taxonomic_reference_database_name", - "rank": 202, + "rank": 201, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_version": { "name": "taxonomic_reference_database_version", - "rank": 203, + "rank": 202, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_report_filename": { "name": "taxonomic_analysis_report_filename", - "rank": 204, + "rank": 203, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_date": { "name": "taxonomic_analysis_date", - "rank": 205, + "rank": 204, "slot_group": "Taxonomic identification information" }, "read_mapping_criteria": { "name": "read_mapping_criteria", - "rank": 206, + "rank": 205, "slot_group": "Taxonomic identification information" }, "genetic_target_name": { "name": "genetic_target_name", - "rank": 207, + "rank": 206, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region": { "name": "genetic_target_region", - "rank": 208, + "rank": 207, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region_reference_genome": { "name": "genetic_target_region_reference_genome", - "rank": 209, + "rank": 208, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_target_presence": { "name": "diagnostic_target_presence", - "rank": 210, + "rank": 209, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_value": { "name": "diagnostic_measurement_value", - "rank": 211, + "rank": 210, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_unit": { "name": "diagnostic_measurement_unit", - "rank": 212, + "rank": 211, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_method": { "name": "diagnostic_measurement_method", - "rank": 213, + "rank": 212, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_value": { "name": "diagnostic_testing_threshold_value", - "rank": 214, + "rank": 213, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_units": { "name": "diagnostic_testing_threshold_units", - "rank": 215, + "rank": 214, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_details": { "name": "diagnostic_testing_details", - "rank": 216, + "rank": 215, "slot_group": "Pathogen diagnostic testing" }, "prevalence_metrics": { "name": "prevalence_metrics", - "rank": 217, + "rank": 216, "slot_group": "Risk assessment information" }, "prevalence_metrics_details": { "name": "prevalence_metrics_details", - "rank": 218, + "rank": 217, "slot_group": "Risk assessment information" }, "stage_of_production": { "name": "stage_of_production", - "rank": 219, + "rank": 218, "slot_group": "Risk assessment information" }, "experimental_intervention": { "name": "experimental_intervention", - "rank": 220, + "rank": 219, "slot_group": "Risk assessment information" }, "experiment_intervention_details": { "name": "experiment_intervention_details", - "rank": 221, + "rank": 220, "slot_group": "Risk assessment information" } }, @@ -30069,7 +30891,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -31294,7 +32116,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -31367,39 +32189,6 @@ } ] }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", - "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." - ], - "examples": [ - { - "value": "12" - } - ], - "from_schema": "https://example.com/hpai", - "rank": 65, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", - "owner": "HPAIWW", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "slot_group": "Environmental conditions and measurements", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "water_depth": { "name": "water_depth", "description": "The depth of some water.", @@ -31413,7 +32202,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 66, + "rank": 65, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "HPAIWW", @@ -31438,7 +32227,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 67, + "rank": 66, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "HPAIWW", @@ -31470,7 +32259,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 68, + "rank": 67, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "HPAIWW", @@ -31495,7 +32284,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 69, + "rank": 68, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "HPAIWW", @@ -31527,7 +32316,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 70, + "rank": 69, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "HPAIWW", @@ -31552,7 +32341,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 71, + "rank": 70, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "HPAIWW", @@ -31584,7 +32373,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 72, + "rank": 71, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "HPAIWW", @@ -31609,7 +32398,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 73, + "rank": 72, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "HPAIWW", @@ -31628,22 +32417,22 @@ } ] }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "12" } ], "from_schema": "https://example.com/hpai", - "rank": 74, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 73, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "HPAIWW", "domain_of": [ "HPAI", @@ -31651,10 +32440,10 @@ "HPAIEnviro" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "recommended": true, "any_of": [ { - "range": "WeatherTypeMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -31674,7 +32463,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 75, + "rank": 74, "slot_uri": "GENEPIO:0100912", "alias": "precipitation_measurement_unit", "owner": "HPAIWW", @@ -31707,7 +32496,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 76, + "rank": 75, "slot_uri": "GENEPIO:0100913", "alias": "precipitation_measurement_method", "owner": "HPAIWW", @@ -31732,7 +32521,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 77, + "rank": 76, "slot_uri": "GENEPIO:0100935", "alias": "ambient_temperature_measurement_value", "owner": "HPAIWW", @@ -31757,7 +32546,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 78, + "rank": 77, "slot_uri": "GENEPIO:0100936", "alias": "ambient_temperature_measurement_unit", "owner": "HPAIWW", @@ -31789,7 +32578,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 79, + "rank": 78, "slot_uri": "GENEPIO:0001736", "alias": "ph_measurement_value", "owner": "HPAIWW", @@ -31814,7 +32603,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 80, + "rank": 79, "slot_uri": "GENEPIO:0100781", "alias": "ph_measurement_method", "owner": "HPAIWW", @@ -31839,7 +32628,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 81, + "rank": 80, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", "owner": "HPAIWW", @@ -31864,7 +32653,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 82, + "rank": 81, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", "owner": "HPAIWW", @@ -31896,7 +32685,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 83, + "rank": 82, "slot_uri": "GENEPIO:0100907", "alias": "total_daily_flow_rate_measurement_method", "owner": "HPAIWW", @@ -31921,7 +32710,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 84, + "rank": 83, "slot_uri": "GENEPIO:0100908", "alias": "instantaneous_flow_rate_measurement_value", "owner": "HPAIWW", @@ -31946,7 +32735,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 85, + "rank": 84, "slot_uri": "GENEPIO:0100909", "alias": "instantaneous_flow_rate_measurement_unit", "owner": "HPAIWW", @@ -31978,7 +32767,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 86, + "rank": 85, "slot_uri": "GENEPIO:0100910", "alias": "instantaneous_flow_rate_measurement_method", "owner": "HPAIWW", @@ -32003,7 +32792,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 87, + "rank": 86, "slot_uri": "GENEPIO:0100783", "alias": "turbidity_measurement_value", "owner": "HPAIWW", @@ -32029,7 +32818,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 88, + "rank": 87, "slot_uri": "GENEPIO:0100914", "alias": "turbidity_measurement_unit", "owner": "HPAIWW", @@ -32062,7 +32851,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 89, + "rank": 88, "slot_uri": "GENEPIO:0101013", "alias": "turbidity_measurement_method", "owner": "HPAIWW", @@ -32087,7 +32876,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 90, + "rank": 89, "slot_uri": "GENEPIO:0100915", "alias": "dissolved_oxygen_measurement_value", "owner": "HPAIWW", @@ -32112,7 +32901,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 91, + "rank": 90, "slot_uri": "GENEPIO:0100784", "alias": "dissolved_oxygen_measurement_unit", "owner": "HPAIWW", @@ -32144,7 +32933,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 92, + "rank": 91, "slot_uri": "GENEPIO:0100785", "alias": "dissolved_oxygen_measurement_method", "owner": "HPAIWW", @@ -32169,7 +32958,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 93, + "rank": 92, "slot_uri": "GENEPIO:0100917", "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "HPAIWW", @@ -32194,7 +32983,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 94, + "rank": 93, "slot_uri": "GENEPIO:0100786", "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "HPAIWW", @@ -32226,7 +33015,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 95, + "rank": 94, "slot_uri": "GENEPIO:0100787", "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "HPAIWW", @@ -32251,7 +33040,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 96, + "rank": 95, "slot_uri": "GENEPIO:0100788", "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "HPAIWW", @@ -32276,7 +33065,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 97, + "rank": 96, "slot_uri": "GENEPIO:0100789", "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "HPAIWW", @@ -32308,7 +33097,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 98, + "rank": 97, "slot_uri": "GENEPIO:0100790", "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "HPAIWW", @@ -32333,7 +33122,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 99, + "rank": 98, "slot_uri": "GENEPIO:0100791", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "HPAIWW", @@ -32358,7 +33147,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 100, + "rank": 99, "slot_uri": "GENEPIO:0100792", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "HPAIWW", @@ -32390,7 +33179,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 101, + "rank": 100, "slot_uri": "GENEPIO:0100793", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "HPAIWW", @@ -32415,7 +33204,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 102, + "rank": 101, "slot_uri": "GENEPIO:0100794", "alias": "total_suspended_solids_tss_measurement_value", "owner": "HPAIWW", @@ -32440,7 +33229,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 103, + "rank": 102, "slot_uri": "GENEPIO:0100795", "alias": "total_suspended_solids_tss_measurement_unit", "owner": "HPAIWW", @@ -32472,7 +33261,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 104, + "rank": 103, "slot_uri": "GENEPIO:0100796", "alias": "total_suspended_solids_tss_measurement_method", "owner": "HPAIWW", @@ -32497,7 +33286,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 105, + "rank": 104, "slot_uri": "GENEPIO:0100797", "alias": "total_dissolved_solids_tds_measurement_value", "owner": "HPAIWW", @@ -32522,7 +33311,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 106, + "rank": 105, "slot_uri": "GENEPIO:0100798", "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "HPAIWW", @@ -32554,7 +33343,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 107, + "rank": 106, "slot_uri": "GENEPIO:0100799", "alias": "total_dissolved_solids_tds_measurement_method", "owner": "HPAIWW", @@ -32579,7 +33368,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 108, + "rank": 107, "slot_uri": "GENEPIO:0100800", "alias": "total_solids_ts_measurement_value", "owner": "HPAIWW", @@ -32604,7 +33393,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 109, + "rank": 108, "slot_uri": "GENEPIO:0100801", "alias": "total_solids_ts_measurement_unit", "owner": "HPAIWW", @@ -32636,7 +33425,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 110, + "rank": 109, "slot_uri": "GENEPIO:0100802", "alias": "total_solids_ts_measurement_method", "owner": "HPAIWW", @@ -32661,7 +33450,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 111, + "rank": 110, "slot_uri": "GENEPIO:0100878", "alias": "alkalinity_measurement_value", "owner": "HPAIWW", @@ -32686,7 +33475,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 112, + "rank": 111, "slot_uri": "GENEPIO:0100879", "alias": "alkalinity_measurement_unit", "owner": "HPAIWW", @@ -32718,7 +33507,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 113, + "rank": 112, "slot_uri": "GENEPIO:0100880", "alias": "alkalinity_measurement_method", "owner": "HPAIWW", @@ -32743,7 +33532,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 114, + "rank": 113, "slot_uri": "GENEPIO:0100916", "alias": "conductivity_measurement_value", "owner": "HPAIWW", @@ -32768,7 +33557,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 115, + "rank": 114, "slot_uri": "GENEPIO:0100803", "alias": "conductivity_measurement_unit", "owner": "HPAIWW", @@ -32800,7 +33589,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 116, + "rank": 115, "slot_uri": "GENEPIO:0100804", "alias": "conductivity_measurement_method", "owner": "HPAIWW", @@ -32825,7 +33614,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 117, + "rank": 116, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", "owner": "HPAIWW", @@ -32850,7 +33639,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 118, + "rank": 117, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", "owner": "HPAIWW", @@ -32882,7 +33671,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 119, + "rank": 118, "slot_uri": "GENEPIO:0100807", "alias": "salinity_measurement_method", "owner": "HPAIWW", @@ -32907,7 +33696,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 120, + "rank": 119, "slot_uri": "GENEPIO:0100808", "alias": "total_nitrogen_tn_measurement_value", "owner": "HPAIWW", @@ -32932,7 +33721,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 121, + "rank": 120, "slot_uri": "GENEPIO:0100809", "alias": "total_nitrogen_tn_measurement_unit", "owner": "HPAIWW", @@ -32964,7 +33753,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 122, + "rank": 121, "slot_uri": "GENEPIO:0100810", "alias": "total_nitrogen_tn_measurement_method", "owner": "HPAIWW", @@ -32989,7 +33778,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 123, + "rank": 122, "slot_uri": "GENEPIO:0100811", "alias": "total_phosphorus_tp_measurement_value", "owner": "HPAIWW", @@ -33014,7 +33803,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 124, + "rank": 123, "slot_uri": "GENEPIO:0100812", "alias": "total_phosphorus_tp_measurement_unit", "owner": "HPAIWW", @@ -33026,7 +33815,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -33046,7 +33835,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 125, + "rank": 124, "slot_uri": "GENEPIO:0100813", "alias": "total_phosphorus_tp_measurement_method", "owner": "HPAIWW", @@ -33071,7 +33860,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 126, + "rank": 125, "slot_uri": "GENEPIO:0100814", "alias": "fecal_contamination_indicator_", "owner": "HPAIWW", @@ -33104,7 +33893,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 127, + "rank": 126, "slot_uri": "GENEPIO:0100815", "alias": "fecal_contamination_value", "owner": "HPAIWW", @@ -33130,7 +33919,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 128, + "rank": 127, "slot_uri": "GENEPIO:0100816", "alias": "fecal_contamination_unit", "owner": "HPAIWW", @@ -33163,7 +33952,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 129, + "rank": 128, "slot_uri": "GENEPIO:0100817", "alias": "fecal_contamination_method", "owner": "HPAIWW", @@ -33188,7 +33977,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 130, + "rank": 129, "slot_uri": "GENEPIO:0100818", "alias": "fecal_coliform_count_value", "owner": "HPAIWW", @@ -33213,7 +34002,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 131, + "rank": 130, "slot_uri": "GENEPIO:0100819", "alias": "fecal_coliform_count_unit", "owner": "HPAIWW", @@ -33245,7 +34034,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 132, + "rank": 131, "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "HPAIWW", @@ -33270,7 +34059,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 133, + "rank": 132, "slot_uri": "GENEPIO:0100837", "alias": "urinary_contamination_indicator", "owner": "HPAIWW", @@ -33302,7 +34091,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 134, + "rank": 133, "slot_uri": "GENEPIO:0100838", "alias": "urinary_contamination_value", "owner": "HPAIWW", @@ -33327,7 +34116,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 135, + "rank": 134, "slot_uri": "GENEPIO:0100839", "alias": "urinary_contamination_unit", "owner": "HPAIWW", @@ -33359,7 +34148,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 136, + "rank": 135, "slot_uri": "GENEPIO:0100840", "alias": "urinary_contamination_method", "owner": "HPAIWW", @@ -33384,7 +34173,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 137, + "rank": 136, "slot_uri": "GENEPIO:0100821", "alias": "sample_temperature_value_at_collection", "owner": "HPAIWW", @@ -33409,7 +34198,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 138, + "rank": 137, "slot_uri": "GENEPIO:0100822", "alias": "sample_temperature_unit_at_collection", "owner": "HPAIWW", @@ -33441,7 +34230,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 139, + "rank": 138, "slot_uri": "GENEPIO:0100823", "alias": "sample_temperature_value_when_received", "owner": "HPAIWW", @@ -33466,7 +34255,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 140, + "rank": 139, "slot_uri": "GENEPIO:0100824", "alias": "sample_temperature_unit_when_received", "owner": "HPAIWW", @@ -33498,7 +34287,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 141, + "rank": 140, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "HPAIWW", @@ -33525,7 +34314,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 142, + "rank": 141, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "HPAIWW", @@ -33555,7 +34344,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 143, + "rank": 142, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "HPAIWW", @@ -33582,7 +34371,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 144, + "rank": 143, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing__", "owner": "HPAIWW", @@ -33618,7 +34407,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 145, + "rank": 144, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "HPAIWW", @@ -33649,7 +34438,7 @@ "GISAID:sequenced_by", "BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 146, + "rank": 145, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "HPAIWW", @@ -33684,7 +34473,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 147, + "rank": 146, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "HPAIWW", @@ -33711,7 +34500,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 148, + "rank": 147, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "HPAIWW", @@ -33746,7 +34535,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 149, + "rank": 148, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "HPAIWW", @@ -33781,7 +34570,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 150, + "rank": 149, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "HPAIWW", @@ -33816,7 +34605,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 151, + "rank": 150, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "HPAIWW", @@ -33852,7 +34641,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 152, + "rank": 151, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "HPAIWW", @@ -33863,7 +34652,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -33879,7 +34668,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 153, + "rank": 152, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "HPAIWW", @@ -33890,7 +34679,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -33901,7 +34690,7 @@ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/hpai", - "rank": 154, + "rank": 153, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", "owner": "HPAIWW", @@ -33912,7 +34701,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -33929,7 +34718,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 155, + "rank": 154, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "HPAIWW", @@ -33956,7 +34745,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 156, + "rank": 155, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "HPAIWW", @@ -33990,7 +34779,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 157, + "rank": 156, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "HPAIWW", @@ -34024,7 +34813,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 158, + "rank": 157, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "HPAIWW", @@ -34051,7 +34840,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 159, + "rank": 158, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "HPAIWW", @@ -34078,7 +34867,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 160, + "rank": 159, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "HPAIWW", @@ -34105,7 +34894,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 161, + "rank": 160, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "HPAIWW", @@ -34132,7 +34921,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 162, + "rank": 161, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "HPAIWW", @@ -34159,7 +34948,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 163, + "rank": 162, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "HPAIWW", @@ -34186,7 +34975,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 164, + "rank": 163, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "HPAIWW", @@ -34213,7 +35002,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 165, + "rank": 164, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "HPAIWW", @@ -34240,7 +35029,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 166, + "rank": 165, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "HPAIWW", @@ -34267,7 +35056,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 167, + "rank": 166, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "HPAIWW", @@ -34294,7 +35083,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 168, + "rank": 167, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "HPAIWW", @@ -34321,7 +35110,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 169, + "rank": 168, "slot_uri": "GENEPIO:0101715", "alias": "genome_sequence_file_name", "owner": "HPAIWW", @@ -34348,7 +35137,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 170, + "rank": 169, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "HPAIWW", @@ -34375,7 +35164,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 171, + "rank": 170, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "HPAIWW", @@ -34402,7 +35191,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 172, + "rank": 171, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "HPAIWW", @@ -34429,7 +35218,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 173, + "rank": 172, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "HPAIWW", @@ -34464,7 +35253,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 174, + "rank": 173, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "HPAIWW", @@ -34499,7 +35288,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 175, + "rank": 174, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "HPAIWW", @@ -34526,7 +35315,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 176, + "rank": 175, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "HPAIWW", @@ -34561,7 +35350,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 177, + "rank": 176, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "HPAIWW", @@ -34596,7 +35385,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 178, + "rank": 177, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "HPAIWW", @@ -34630,7 +35419,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 179, + "rank": 178, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "HPAIWW", @@ -34664,7 +35453,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 180, + "rank": 179, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "HPAIWW", @@ -34698,7 +35487,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 181, + "rank": 180, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "HPAIWW", @@ -34732,7 +35521,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 182, + "rank": 181, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "HPAIWW", @@ -34759,7 +35548,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 183, + "rank": 182, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "HPAIWW", @@ -34786,7 +35575,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 184, + "rank": 183, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "HPAIWW", @@ -34813,7 +35602,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 185, + "rank": 184, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "HPAIWW", @@ -34840,7 +35629,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 186, + "rank": 185, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "HPAIWW", @@ -34867,7 +35656,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 187, + "rank": 186, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "HPAIWW", @@ -34894,7 +35683,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 188, + "rank": 187, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "HPAIWW", @@ -34921,7 +35710,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 189, + "rank": 188, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "HPAIWW", @@ -34948,7 +35737,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 190, + "rank": 189, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "HPAIWW", @@ -34975,7 +35764,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 191, + "rank": 190, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "HPAIWW", @@ -35002,7 +35791,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 192, + "rank": 191, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "HPAIWW", @@ -35029,7 +35818,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 193, + "rank": 192, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "HPAIWW", @@ -35056,7 +35845,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 194, + "rank": 193, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "HPAIWW", @@ -35083,7 +35872,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 195, + "rank": 194, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "HPAIWW", @@ -35110,7 +35899,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 196, + "rank": 195, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "HPAIWW", @@ -35137,7 +35926,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 197, + "rank": 196, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "HPAIWW", @@ -35164,7 +35953,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 198, + "rank": 197, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "HPAIWW", @@ -35191,7 +35980,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 199, + "rank": 198, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "HPAIWW", @@ -35218,7 +36007,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 200, + "rank": 199, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "HPAIWW", @@ -35245,7 +36034,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 201, + "rank": 200, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "HPAIWW", @@ -35272,7 +36061,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 202, + "rank": 201, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "HPAIWW", @@ -35299,7 +36088,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 203, + "rank": 202, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "HPAIWW", @@ -35326,7 +36115,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 204, + "rank": 203, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "HPAIWW", @@ -35353,7 +36142,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 205, + "rank": 204, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "HPAIWW", @@ -35380,7 +36169,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 206, + "rank": 205, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "HPAIWW", @@ -35407,7 +36196,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 207, + "rank": 206, "slot_uri": "GENEPIO:0101116", "alias": "genetic_target_name", "owner": "HPAIWW", @@ -35433,7 +36222,7 @@ "description": "The specific region or segment of a genetic sequence used for testing or analysis.", "title": "genetic target region", "from_schema": "https://example.com/hpai", - "rank": 208, + "rank": 207, "slot_uri": "GENEPIO:0101117", "alias": "genetic_target_region", "owner": "HPAIWW", @@ -35452,7 +36241,7 @@ "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", "title": "genetic target region reference genome", "from_schema": "https://example.com/hpai", - "rank": 209, + "rank": 208, "slot_uri": "GENEPIO:0101118", "alias": "genetic_target_region_reference_genome", "owner": "HPAIWW", @@ -35479,7 +36268,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 210, + "rank": 209, "slot_uri": "GENEPIO:0100962", "alias": "diagnostic_target_presence", "owner": "HPAIWW", @@ -35513,7 +36302,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 211, + "rank": 210, "slot_uri": "GENEPIO:0100963", "alias": "diagnostic_measurement_value", "owner": "HPAIWW", @@ -35540,7 +36329,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 212, + "rank": 211, "slot_uri": "GENEPIO:0100964", "alias": "diagnostic_measurement_unit", "owner": "HPAIWW", @@ -35574,7 +36363,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 213, + "rank": 212, "slot_uri": "GENEPIO:0100965", "alias": "diagnostic_measurement_method", "owner": "HPAIWW", @@ -35600,7 +36389,7 @@ "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold value", "from_schema": "https://example.com/hpai", - "rank": 214, + "rank": 213, "slot_uri": "GENEPIO:0101104", "alias": "diagnostic_testing_threshold_value", "owner": "HPAIWW", @@ -35619,7 +36408,7 @@ "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold units", "from_schema": "https://example.com/hpai", - "rank": 215, + "rank": 214, "slot_uri": "GENEPIO:0101105", "alias": "diagnostic_testing_threshold_units", "owner": "HPAIWW", @@ -35638,7 +36427,7 @@ "description": "Describe any details of the diagnsotic testing.", "title": "diagnostic testing details", "from_schema": "https://example.com/hpai", - "rank": 216, + "rank": 215, "slot_uri": "GENEPIO:0101106", "alias": "diagnostic_testing_details", "owner": "HPAIWW", @@ -35665,7 +36454,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 217, + "rank": 216, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "HPAIWW", @@ -35693,7 +36482,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 218, + "rank": 217, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "HPAIWW", @@ -35721,7 +36510,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 219, + "rank": 218, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "HPAIWW", @@ -35736,7 +36525,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -35756,7 +36545,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 220, + "rank": 219, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "HPAIWW", @@ -35792,7 +36581,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 221, + "rank": 220, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "HPAIWW", @@ -36141,789 +36930,784 @@ "rank": 64, "slot_group": "Environmental conditions and measurements" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "rank": 65, - "slot_group": "Environmental conditions and measurements" - }, "water_depth": { "name": "water_depth", - "rank": 66, + "rank": 65, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 67, + "rank": 66, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 68, + "rank": 67, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 69, + "rank": 68, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 70, + "rank": 69, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 71, + "rank": 70, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 72, + "rank": 71, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 73, + "rank": 72, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 74, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 73, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", - "rank": 75, + "rank": 74, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", - "rank": 76, + "rank": 75, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_value": { "name": "ambient_temperature_measurement_value", - "rank": 77, + "rank": 76, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_unit": { "name": "ambient_temperature_measurement_unit", - "rank": 78, + "rank": 77, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_value": { "name": "ph_measurement_value", - "rank": 79, + "rank": 78, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_method": { "name": "ph_measurement_method", - "rank": 80, + "rank": 79, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_value": { "name": "total_daily_flow_rate_measurement_value", - "rank": 81, + "rank": 80, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_unit": { "name": "total_daily_flow_rate_measurement_unit", - "rank": 82, + "rank": 81, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_method": { "name": "total_daily_flow_rate_measurement_method", - "rank": 83, + "rank": 82, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_value": { "name": "instantaneous_flow_rate_measurement_value", - "rank": 84, + "rank": 83, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_unit": { "name": "instantaneous_flow_rate_measurement_unit", - "rank": 85, + "rank": 84, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_method": { "name": "instantaneous_flow_rate_measurement_method", - "rank": 86, + "rank": 85, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_value": { "name": "turbidity_measurement_value", - "rank": 87, + "rank": 86, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_unit": { "name": "turbidity_measurement_unit", - "rank": 88, + "rank": 87, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_method": { "name": "turbidity_measurement_method", - "rank": 89, + "rank": 88, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_value": { "name": "dissolved_oxygen_measurement_value", - "rank": 90, + "rank": 89, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_unit": { "name": "dissolved_oxygen_measurement_unit", - "rank": 91, + "rank": 90, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_method": { "name": "dissolved_oxygen_measurement_method", - "rank": 92, + "rank": 91, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_value": { "name": "oxygen_reduction_potential_orp_measurement_value", - "rank": 93, + "rank": 92, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_unit": { "name": "oxygen_reduction_potential_orp_measurement_unit", - "rank": 94, + "rank": 93, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_method": { "name": "oxygen_reduction_potential_orp_measurement_method", - "rank": 95, + "rank": 94, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_value": { "name": "chemical_oxygen_demand_cod_measurement_value", - "rank": 96, + "rank": 95, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_unit": { "name": "chemical_oxygen_demand_cod_measurement_unit", - "rank": 97, + "rank": 96, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_method": { "name": "chemical_oxygen_demand_cod_measurement_method", - "rank": 98, + "rank": 97, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", - "rank": 99, + "rank": 98, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", - "rank": 100, + "rank": 99, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", - "rank": 101, + "rank": 100, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_value": { "name": "total_suspended_solids_tss_measurement_value", - "rank": 102, + "rank": 101, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_unit": { "name": "total_suspended_solids_tss_measurement_unit", - "rank": 103, + "rank": 102, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_method": { "name": "total_suspended_solids_tss_measurement_method", - "rank": 104, + "rank": 103, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_value": { "name": "total_dissolved_solids_tds_measurement_value", - "rank": 105, + "rank": 104, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_unit": { "name": "total_dissolved_solids_tds_measurement_unit", - "rank": 106, + "rank": 105, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_method": { "name": "total_dissolved_solids_tds_measurement_method", - "rank": 107, + "rank": 106, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_value": { "name": "total_solids_ts_measurement_value", - "rank": 108, + "rank": 107, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_unit": { "name": "total_solids_ts_measurement_unit", - "rank": 109, + "rank": 108, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_method": { "name": "total_solids_ts_measurement_method", - "rank": 110, + "rank": 109, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_value": { "name": "alkalinity_measurement_value", - "rank": 111, + "rank": 110, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_unit": { "name": "alkalinity_measurement_unit", - "rank": 112, + "rank": 111, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_method": { "name": "alkalinity_measurement_method", - "rank": 113, + "rank": 112, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_value": { "name": "conductivity_measurement_value", - "rank": 114, + "rank": 113, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_unit": { "name": "conductivity_measurement_unit", - "rank": 115, + "rank": 114, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_method": { "name": "conductivity_measurement_method", - "rank": 116, + "rank": 115, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_value": { "name": "salinity_measurement_value", - "rank": 117, + "rank": 116, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_unit": { "name": "salinity_measurement_unit", - "rank": 118, + "rank": 117, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_method": { "name": "salinity_measurement_method", - "rank": 119, + "rank": 118, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_value": { "name": "total_nitrogen_tn_measurement_value", - "rank": 120, + "rank": 119, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_unit": { "name": "total_nitrogen_tn_measurement_unit", - "rank": 121, + "rank": 120, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_method": { "name": "total_nitrogen_tn_measurement_method", - "rank": 122, + "rank": 121, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_value": { "name": "total_phosphorus_tp_measurement_value", - "rank": 123, + "rank": 122, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_unit": { "name": "total_phosphorus_tp_measurement_unit", - "rank": 124, + "rank": 123, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_method": { "name": "total_phosphorus_tp_measurement_method", - "rank": 125, + "rank": 124, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_indicator_": { "name": "fecal_contamination_indicator_", - "rank": 126, + "rank": 125, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_value": { "name": "fecal_contamination_value", - "rank": 127, + "rank": 126, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_unit": { "name": "fecal_contamination_unit", - "rank": 128, + "rank": 127, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_method": { "name": "fecal_contamination_method", - "rank": 129, + "rank": 128, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_value": { "name": "fecal_coliform_count_value", - "rank": 130, + "rank": 129, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_unit": { "name": "fecal_coliform_count_unit", - "rank": 131, + "rank": 130, "slot_group": "Environmental conditions and measurements" }, "fecal_coliform_count_method": { "name": "fecal_coliform_count_method", - "rank": 132, + "rank": 131, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_indicator": { "name": "urinary_contamination_indicator", - "rank": 133, + "rank": 132, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_value": { "name": "urinary_contamination_value", - "rank": 134, + "rank": 133, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_unit": { "name": "urinary_contamination_unit", - "rank": 135, + "rank": 134, "slot_group": "Environmental conditions and measurements" }, "urinary_contamination_method": { "name": "urinary_contamination_method", - "rank": 136, + "rank": 135, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_value_at_collection": { "name": "sample_temperature_value_at_collection", - "rank": 137, + "rank": 136, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_unit_at_collection": { "name": "sample_temperature_unit_at_collection", - "rank": 138, + "rank": 137, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_value_when_received": { "name": "sample_temperature_value_when_received", - "rank": 139, + "rank": 138, "slot_group": "Environmental conditions and measurements" }, "sample_temperature_unit_when_received": { "name": "sample_temperature_unit_when_received", - "rank": 140, + "rank": 139, "slot_group": "Environmental conditions and measurements" }, "library_id": { "name": "library_id", - "rank": 141, + "rank": 140, "slot_group": "Sequence information" }, "sequencing_assay_type": { "name": "sequencing_assay_type", - "rank": 142, + "rank": 141, "slot_group": "Sequence information" }, "sequencing_date": { "name": "sequencing_date", - "rank": 143, + "rank": 142, "slot_group": "Sequence information" }, "purpose_of_sequencing__": { "name": "purpose_of_sequencing__", - "rank": 144, + "rank": 143, "slot_group": "Sequence information" }, "purpose_of_sequencing_details": { "name": "purpose_of_sequencing_details", - "rank": 145, + "rank": 144, "slot_group": "Sequence information" }, "sequenced_by": { "name": "sequenced_by", - "rank": 146, + "rank": 145, "slot_group": "Sequence information" }, "sequenced_by_laboratory_name": { "name": "sequenced_by_laboratory_name", - "rank": 147, + "rank": 146, "slot_group": "Sequence information" }, "sequenced_by_contact_name": { "name": "sequenced_by_contact_name", - "rank": 148, + "rank": 147, "slot_group": "Sequence information" }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", - "rank": 149, + "rank": 148, "slot_group": "Sequence information" }, "sequence_submitted_by": { "name": "sequence_submitted_by", - "rank": 150, + "rank": 149, "slot_group": "Sequence information" }, "sequence_submitter_contact_email": { "name": "sequence_submitter_contact_email", - "rank": 151, + "rank": 150, "slot_group": "Sequence information" }, "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", - "rank": 152, - "slot_group": "Sample collection and processing" + "rank": 151, + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", - "rank": 153, - "slot_group": "Sample collection and processing" + "rank": 152, + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", - "rank": 154, - "slot_group": "Sample collection and processing" + "rank": 153, + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", - "rank": 155, + "rank": 154, "slot_group": "Sequence information" }, "sequencing_platform": { "name": "sequencing_platform", - "rank": 156, + "rank": 155, "slot_group": "Sequence information" }, "sequencing_instrument": { "name": "sequencing_instrument", - "rank": 157, + "rank": 156, "slot_group": "Sequence information" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 158, + "rank": 157, "slot_group": "Sequence information" }, "dna_fragment_length": { "name": "dna_fragment_length", - "rank": 159, + "rank": 158, "slot_group": "Sequence information" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 160, + "rank": 159, "slot_group": "Sequence information" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 161, + "rank": 160, "slot_group": "Sequence information" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 162, + "rank": 161, "slot_group": "Sequence information" }, "amplicon_size": { "name": "amplicon_size", - "rank": 163, + "rank": 162, "slot_group": "Sequence information" }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 164, + "rank": 163, "slot_group": "Sequence information" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 165, + "rank": 164, "slot_group": "Sequence information" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 166, + "rank": 165, "slot_group": "Sequence information" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - "rank": 167, + "rank": 166, "slot_group": "Sequence information" }, "fast5_filename": { "name": "fast5_filename", - "rank": 168, + "rank": 167, "slot_group": "Sequence information" }, "genome_sequence_file_name": { "name": "genome_sequence_file_name", - "rank": 169, + "rank": 168, "slot_group": "Sequence information" }, "assembly_filename": { "name": "assembly_filename", - "rank": 170, + "rank": 169, "slot_group": "Sequence information" }, "quality_control_method_name": { "name": "quality_control_method_name", - "rank": 171, + "rank": 170, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_method_version": { "name": "quality_control_method_version", - "rank": 172, + "rank": 171, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_determination": { "name": "quality_control_determination", - "rank": 173, + "rank": 172, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_issues": { "name": "quality_control_issues", - "rank": 174, + "rank": 173, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_details": { "name": "quality_control_details", - "rank": 175, + "rank": 174, "slot_group": "Bioinformatics and QC metrics" }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", - "rank": 176, + "rank": 175, "slot_group": "Bioinformatics and QC metrics" }, "dehosting_method": { "name": "dehosting_method", - "rank": 177, + "rank": 176, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_name": { "name": "sequence_assembly_software_name", - "rank": 178, + "rank": 177, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_version": { "name": "sequence_assembly_software_version", - "rank": 179, + "rank": 178, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "name": "consensus_sequence_software_name", - "rank": 180, + "rank": 179, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "name": "consensus_sequence_software_version", - "rank": 181, + "rank": 180, "slot_group": "Bioinformatics and QC metrics" }, "breadth_of_coverage_value": { "name": "breadth_of_coverage_value", - "rank": 182, + "rank": 181, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_value": { "name": "depth_of_coverage_value", - "rank": 183, + "rank": 182, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_threshold": { "name": "depth_of_coverage_threshold", - "rank": 184, + "rank": 183, "slot_group": "Bioinformatics and QC metrics" }, "genome_completeness": { "name": "genome_completeness", - "rank": 185, + "rank": 184, "slot_group": "Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "name": "number_of_base_pairs_sequenced", - "rank": 186, + "rank": 185, "slot_group": "Bioinformatics and QC metrics" }, "number_of_total_reads": { "name": "number_of_total_reads", - "rank": 187, + "rank": 186, "slot_group": "Bioinformatics and QC metrics" }, "number_of_unique_reads": { "name": "number_of_unique_reads", - "rank": 188, + "rank": 187, "slot_group": "Bioinformatics and QC metrics" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", - "rank": 189, + "rank": 188, "slot_group": "Bioinformatics and QC metrics" }, "number_of_contigs": { "name": "number_of_contigs", - "rank": 190, + "rank": 189, "slot_group": "Bioinformatics and QC metrics" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", - "rank": 191, + "rank": 190, "slot_group": "Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", - "rank": 192, + "rank": 191, "slot_group": "Bioinformatics and QC metrics" }, "n50": { "name": "n50", - "rank": 193, + "rank": 192, "slot_group": "Bioinformatics and QC metrics" }, "percent_read_contamination_": { "name": "percent_read_contamination_", - "rank": 194, + "rank": 193, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_length": { "name": "sequence_assembly_length", - "rank": 195, + "rank": 194, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 196, + "rank": 195, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 197, + "rank": 196, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 198, + "rank": 197, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 199, + "rank": 198, "slot_group": "Bioinformatics and QC metrics" }, "read_mapping_software_name": { "name": "read_mapping_software_name", - "rank": 200, + "rank": 199, "slot_group": "Taxonomic identification information" }, "read_mapping_software_version": { "name": "read_mapping_software_version", - "rank": 201, + "rank": 200, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_name": { "name": "taxonomic_reference_database_name", - "rank": 202, + "rank": 201, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_version": { "name": "taxonomic_reference_database_version", - "rank": 203, + "rank": 202, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_report_filename": { "name": "taxonomic_analysis_report_filename", - "rank": 204, + "rank": 203, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_date": { "name": "taxonomic_analysis_date", - "rank": 205, + "rank": 204, "slot_group": "Taxonomic identification information" }, "read_mapping_criteria": { "name": "read_mapping_criteria", - "rank": 206, + "rank": 205, "slot_group": "Taxonomic identification information" }, "genetic_target_name": { "name": "genetic_target_name", - "rank": 207, + "rank": 206, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region": { "name": "genetic_target_region", - "rank": 208, + "rank": 207, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region_reference_genome": { "name": "genetic_target_region_reference_genome", - "rank": 209, + "rank": 208, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_target_presence": { "name": "diagnostic_target_presence", - "rank": 210, + "rank": 209, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_value": { "name": "diagnostic_measurement_value", - "rank": 211, + "rank": 210, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_unit": { "name": "diagnostic_measurement_unit", - "rank": 212, + "rank": 211, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_method": { "name": "diagnostic_measurement_method", - "rank": 213, + "rank": 212, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_value": { "name": "diagnostic_testing_threshold_value", - "rank": 214, + "rank": 213, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_units": { "name": "diagnostic_testing_threshold_units", - "rank": 215, + "rank": 214, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_details": { "name": "diagnostic_testing_details", - "rank": 216, + "rank": 215, "slot_group": "Pathogen diagnostic testing" }, "prevalence_metrics": { "name": "prevalence_metrics", - "rank": 217, + "rank": 216, "slot_group": "Risk assessment information" }, "prevalence_metrics_details": { "name": "prevalence_metrics_details", - "rank": 218, + "rank": 217, "slot_group": "Risk assessment information" }, "stage_of_production": { "name": "stage_of_production", - "rank": 219, + "rank": 218, "slot_group": "Risk assessment information" }, "experimental_intervention": { "name": "experimental_intervention", - "rank": 220, + "rank": 219, "slot_group": "Risk assessment information" }, "experiment_intervention_details": { "name": "experiment_intervention_details", - "rank": 221, + "rank": 220, "slot_group": "Risk assessment information" } }, @@ -37598,7 +38382,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -38823,7 +39607,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -38896,39 +39680,6 @@ } ] }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", - "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." - ], - "examples": [ - { - "value": "12" - } - ], - "from_schema": "https://example.com/hpai", - "rank": 65, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", - "owner": "HPAIEnviro", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "slot_group": "Environmental conditions and measurements", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "water_depth": { "name": "water_depth", "description": "The depth of some water.", @@ -38942,7 +39693,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 66, + "rank": 65, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "HPAIEnviro", @@ -38967,7 +39718,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 67, + "rank": 66, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "HPAIEnviro", @@ -38999,7 +39750,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 68, + "rank": 67, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "HPAIEnviro", @@ -39024,7 +39775,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 69, + "rank": 68, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "HPAIEnviro", @@ -39056,7 +39807,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 70, + "rank": 69, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "HPAIEnviro", @@ -39081,7 +39832,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 71, + "rank": 70, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "HPAIEnviro", @@ -39113,7 +39864,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 72, + "rank": 71, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "HPAIEnviro", @@ -39138,7 +39889,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 73, + "rank": 72, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "HPAIEnviro", @@ -39157,22 +39908,22 @@ } ] }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "12" } ], "from_schema": "https://example.com/hpai", - "rank": 74, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 73, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "HPAIEnviro", "domain_of": [ "HPAI", @@ -39180,10 +39931,10 @@ "HPAIEnviro" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "recommended": true, "any_of": [ { - "range": "WeatherTypeMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -39203,7 +39954,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 75, + "rank": 74, "slot_uri": "GENEPIO:0100912", "alias": "precipitation_measurement_unit", "owner": "HPAIEnviro", @@ -39236,7 +39987,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 76, + "rank": 75, "slot_uri": "GENEPIO:0100913", "alias": "precipitation_measurement_method", "owner": "HPAIEnviro", @@ -39261,7 +40012,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 77, + "rank": 76, "slot_uri": "GENEPIO:0100935", "alias": "ambient_temperature_measurement_value", "owner": "HPAIEnviro", @@ -39286,7 +40037,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 78, + "rank": 77, "slot_uri": "GENEPIO:0100936", "alias": "ambient_temperature_measurement_unit", "owner": "HPAIEnviro", @@ -39318,7 +40069,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 79, + "rank": 78, "slot_uri": "GENEPIO:0001736", "alias": "ph_measurement_value", "owner": "HPAIEnviro", @@ -39343,7 +40094,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 80, + "rank": 79, "slot_uri": "GENEPIO:0100781", "alias": "ph_measurement_method", "owner": "HPAIEnviro", @@ -39368,7 +40119,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 81, + "rank": 80, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", "owner": "HPAIEnviro", @@ -39393,7 +40144,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 82, + "rank": 81, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", "owner": "HPAIEnviro", @@ -39425,7 +40176,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 83, + "rank": 82, "slot_uri": "GENEPIO:0100907", "alias": "total_daily_flow_rate_measurement_method", "owner": "HPAIEnviro", @@ -39450,7 +40201,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 84, + "rank": 83, "slot_uri": "GENEPIO:0100908", "alias": "instantaneous_flow_rate_measurement_value", "owner": "HPAIEnviro", @@ -39475,7 +40226,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 85, + "rank": 84, "slot_uri": "GENEPIO:0100909", "alias": "instantaneous_flow_rate_measurement_unit", "owner": "HPAIEnviro", @@ -39507,7 +40258,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 86, + "rank": 85, "slot_uri": "GENEPIO:0100910", "alias": "instantaneous_flow_rate_measurement_method", "owner": "HPAIEnviro", @@ -39532,7 +40283,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 87, + "rank": 86, "slot_uri": "GENEPIO:0100783", "alias": "turbidity_measurement_value", "owner": "HPAIEnviro", @@ -39558,7 +40309,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 88, + "rank": 87, "slot_uri": "GENEPIO:0100914", "alias": "turbidity_measurement_unit", "owner": "HPAIEnviro", @@ -39591,7 +40342,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 89, + "rank": 88, "slot_uri": "GENEPIO:0101013", "alias": "turbidity_measurement_method", "owner": "HPAIEnviro", @@ -39616,7 +40367,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 90, + "rank": 89, "slot_uri": "GENEPIO:0100915", "alias": "dissolved_oxygen_measurement_value", "owner": "HPAIEnviro", @@ -39641,7 +40392,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 91, + "rank": 90, "slot_uri": "GENEPIO:0100784", "alias": "dissolved_oxygen_measurement_unit", "owner": "HPAIEnviro", @@ -39673,7 +40424,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 92, + "rank": 91, "slot_uri": "GENEPIO:0100785", "alias": "dissolved_oxygen_measurement_method", "owner": "HPAIEnviro", @@ -39698,7 +40449,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 93, + "rank": 92, "slot_uri": "GENEPIO:0100917", "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "HPAIEnviro", @@ -39723,7 +40474,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 94, + "rank": 93, "slot_uri": "GENEPIO:0100786", "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "HPAIEnviro", @@ -39755,7 +40506,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 95, + "rank": 94, "slot_uri": "GENEPIO:0100787", "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "HPAIEnviro", @@ -39780,7 +40531,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 96, + "rank": 95, "slot_uri": "GENEPIO:0100788", "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "HPAIEnviro", @@ -39805,7 +40556,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 97, + "rank": 96, "slot_uri": "GENEPIO:0100789", "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "HPAIEnviro", @@ -39837,7 +40588,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 98, + "rank": 97, "slot_uri": "GENEPIO:0100790", "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "HPAIEnviro", @@ -39862,7 +40613,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 99, + "rank": 98, "slot_uri": "GENEPIO:0100791", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "HPAIEnviro", @@ -39887,7 +40638,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 100, + "rank": 99, "slot_uri": "GENEPIO:0100792", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "HPAIEnviro", @@ -39919,7 +40670,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 101, + "rank": 100, "slot_uri": "GENEPIO:0100793", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "HPAIEnviro", @@ -39944,7 +40695,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 102, + "rank": 101, "slot_uri": "GENEPIO:0100794", "alias": "total_suspended_solids_tss_measurement_value", "owner": "HPAIEnviro", @@ -39969,7 +40720,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 103, + "rank": 102, "slot_uri": "GENEPIO:0100795", "alias": "total_suspended_solids_tss_measurement_unit", "owner": "HPAIEnviro", @@ -40001,7 +40752,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 104, + "rank": 103, "slot_uri": "GENEPIO:0100796", "alias": "total_suspended_solids_tss_measurement_method", "owner": "HPAIEnviro", @@ -40026,7 +40777,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 105, + "rank": 104, "slot_uri": "GENEPIO:0100797", "alias": "total_dissolved_solids_tds_measurement_value", "owner": "HPAIEnviro", @@ -40051,7 +40802,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 106, + "rank": 105, "slot_uri": "GENEPIO:0100798", "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "HPAIEnviro", @@ -40083,7 +40834,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 107, + "rank": 106, "slot_uri": "GENEPIO:0100799", "alias": "total_dissolved_solids_tds_measurement_method", "owner": "HPAIEnviro", @@ -40108,7 +40859,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 108, + "rank": 107, "slot_uri": "GENEPIO:0100800", "alias": "total_solids_ts_measurement_value", "owner": "HPAIEnviro", @@ -40133,7 +40884,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 109, + "rank": 108, "slot_uri": "GENEPIO:0100801", "alias": "total_solids_ts_measurement_unit", "owner": "HPAIEnviro", @@ -40165,7 +40916,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 110, + "rank": 109, "slot_uri": "GENEPIO:0100802", "alias": "total_solids_ts_measurement_method", "owner": "HPAIEnviro", @@ -40190,7 +40941,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 111, + "rank": 110, "slot_uri": "GENEPIO:0100878", "alias": "alkalinity_measurement_value", "owner": "HPAIEnviro", @@ -40215,7 +40966,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 112, + "rank": 111, "slot_uri": "GENEPIO:0100879", "alias": "alkalinity_measurement_unit", "owner": "HPAIEnviro", @@ -40247,7 +40998,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 113, + "rank": 112, "slot_uri": "GENEPIO:0100880", "alias": "alkalinity_measurement_method", "owner": "HPAIEnviro", @@ -40272,7 +41023,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 114, + "rank": 113, "slot_uri": "GENEPIO:0100916", "alias": "conductivity_measurement_value", "owner": "HPAIEnviro", @@ -40297,7 +41048,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 115, + "rank": 114, "slot_uri": "GENEPIO:0100803", "alias": "conductivity_measurement_unit", "owner": "HPAIEnviro", @@ -40329,7 +41080,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 116, + "rank": 115, "slot_uri": "GENEPIO:0100804", "alias": "conductivity_measurement_method", "owner": "HPAIEnviro", @@ -40354,7 +41105,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 117, + "rank": 116, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", "owner": "HPAIEnviro", @@ -40379,7 +41130,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 118, + "rank": 117, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", "owner": "HPAIEnviro", @@ -40411,7 +41162,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 119, + "rank": 118, "slot_uri": "GENEPIO:0100807", "alias": "salinity_measurement_method", "owner": "HPAIEnviro", @@ -40436,7 +41187,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 120, + "rank": 119, "slot_uri": "GENEPIO:0100808", "alias": "total_nitrogen_tn_measurement_value", "owner": "HPAIEnviro", @@ -40461,7 +41212,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 121, + "rank": 120, "slot_uri": "GENEPIO:0100809", "alias": "total_nitrogen_tn_measurement_unit", "owner": "HPAIEnviro", @@ -40493,7 +41244,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 122, + "rank": 121, "slot_uri": "GENEPIO:0100810", "alias": "total_nitrogen_tn_measurement_method", "owner": "HPAIEnviro", @@ -40518,7 +41269,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 123, + "rank": 122, "slot_uri": "GENEPIO:0100811", "alias": "total_phosphorus_tp_measurement_value", "owner": "HPAIEnviro", @@ -40543,7 +41294,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 124, + "rank": 123, "slot_uri": "GENEPIO:0100812", "alias": "total_phosphorus_tp_measurement_unit", "owner": "HPAIEnviro", @@ -40555,7 +41306,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -40575,7 +41326,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 125, + "rank": 124, "slot_uri": "GENEPIO:0100813", "alias": "total_phosphorus_tp_measurement_method", "owner": "HPAIEnviro", @@ -40600,7 +41351,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 126, + "rank": 125, "slot_uri": "GENEPIO:0100814", "alias": "fecal_contamination_indicator_", "owner": "HPAIEnviro", @@ -40633,7 +41384,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 127, + "rank": 126, "slot_uri": "GENEPIO:0100815", "alias": "fecal_contamination_value", "owner": "HPAIEnviro", @@ -40659,7 +41410,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 128, + "rank": 127, "slot_uri": "GENEPIO:0100816", "alias": "fecal_contamination_unit", "owner": "HPAIEnviro", @@ -40692,7 +41443,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 129, + "rank": 128, "slot_uri": "GENEPIO:0100817", "alias": "fecal_contamination_method", "owner": "HPAIEnviro", @@ -40717,7 +41468,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 130, + "rank": 129, "slot_uri": "GENEPIO:0100818", "alias": "fecal_coliform_count_value", "owner": "HPAIEnviro", @@ -40742,7 +41493,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 131, + "rank": 130, "slot_uri": "GENEPIO:0100819", "alias": "fecal_coliform_count_unit", "owner": "HPAIEnviro", @@ -40774,7 +41525,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 132, + "rank": 131, "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "HPAIEnviro", @@ -40799,7 +41550,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 133, + "rank": 132, "slot_uri": "GENEPIO:0100837", "alias": "urinary_contamination_indicator", "owner": "HPAIEnviro", @@ -40831,7 +41582,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 134, + "rank": 133, "slot_uri": "GENEPIO:0100838", "alias": "urinary_contamination_value", "owner": "HPAIEnviro", @@ -40856,7 +41607,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 135, + "rank": 134, "slot_uri": "GENEPIO:0100839", "alias": "urinary_contamination_unit", "owner": "HPAIEnviro", @@ -40888,7 +41639,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 136, + "rank": 135, "slot_uri": "GENEPIO:0100840", "alias": "urinary_contamination_method", "owner": "HPAIEnviro", @@ -40913,7 +41664,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 137, + "rank": 136, "slot_uri": "GENEPIO:0100821", "alias": "sample_temperature_value_at_collection", "owner": "HPAIEnviro", @@ -40938,7 +41689,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 138, + "rank": 137, "slot_uri": "GENEPIO:0100822", "alias": "sample_temperature_unit_at_collection", "owner": "HPAIEnviro", @@ -40970,7 +41721,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 139, + "rank": 138, "slot_uri": "GENEPIO:0100823", "alias": "sample_temperature_value_when_received", "owner": "HPAIEnviro", @@ -40995,7 +41746,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 140, + "rank": 139, "slot_uri": "GENEPIO:0100824", "alias": "sample_temperature_unit_when_received", "owner": "HPAIEnviro", @@ -41027,7 +41778,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 141, + "rank": 140, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "HPAIEnviro", @@ -41054,7 +41805,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 142, + "rank": 141, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "HPAIEnviro", @@ -41084,7 +41835,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 143, + "rank": 142, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "HPAIEnviro", @@ -41111,7 +41862,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 144, + "rank": 143, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing__", "owner": "HPAIEnviro", @@ -41147,7 +41898,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 145, + "rank": 144, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "HPAIEnviro", @@ -41178,7 +41929,7 @@ "GISAID:sequenced_by", "BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 146, + "rank": 145, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "HPAIEnviro", @@ -41213,7 +41964,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 147, + "rank": 146, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "HPAIEnviro", @@ -41240,7 +41991,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 148, + "rank": 147, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "HPAIEnviro", @@ -41275,7 +42026,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 149, + "rank": 148, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "HPAIEnviro", @@ -41310,7 +42061,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 150, + "rank": 149, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "HPAIEnviro", @@ -41345,7 +42096,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 151, + "rank": 150, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "HPAIEnviro", @@ -41381,7 +42132,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 152, + "rank": 151, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "HPAIEnviro", @@ -41392,7 +42143,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -41408,7 +42159,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 153, + "rank": 152, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "HPAIEnviro", @@ -41419,7 +42170,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -41430,7 +42181,7 @@ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/hpai", - "rank": 154, + "rank": 153, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", "owner": "HPAIEnviro", @@ -41441,7 +42192,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -41458,7 +42209,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 155, + "rank": 154, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "HPAIEnviro", @@ -41485,7 +42236,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 156, + "rank": 155, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "HPAIEnviro", @@ -41519,7 +42270,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 157, + "rank": 156, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "HPAIEnviro", @@ -41553,7 +42304,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 158, + "rank": 157, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "HPAIEnviro", @@ -41580,7 +42331,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 159, + "rank": 158, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "HPAIEnviro", @@ -41607,7 +42358,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 160, + "rank": 159, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "HPAIEnviro", @@ -41634,7 +42385,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 161, + "rank": 160, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "HPAIEnviro", @@ -41661,7 +42412,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 162, + "rank": 161, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "HPAIEnviro", @@ -41688,7 +42439,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 163, + "rank": 162, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "HPAIEnviro", @@ -41715,7 +42466,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 164, + "rank": 163, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "HPAIEnviro", @@ -41742,7 +42493,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 165, + "rank": 164, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "HPAIEnviro", @@ -41769,7 +42520,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 166, + "rank": 165, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "HPAIEnviro", @@ -41796,7 +42547,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 167, + "rank": 166, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "HPAIEnviro", @@ -41823,7 +42574,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 168, + "rank": 167, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "HPAIEnviro", @@ -41850,7 +42601,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 169, + "rank": 168, "slot_uri": "GENEPIO:0101715", "alias": "genome_sequence_file_name", "owner": "HPAIEnviro", @@ -41877,7 +42628,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 170, + "rank": 169, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "HPAIEnviro", @@ -41904,7 +42655,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 171, + "rank": 170, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "HPAIEnviro", @@ -41931,7 +42682,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 172, + "rank": 171, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "HPAIEnviro", @@ -41958,7 +42709,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 173, + "rank": 172, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "HPAIEnviro", @@ -41993,7 +42744,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 174, + "rank": 173, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "HPAIEnviro", @@ -42028,7 +42779,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 175, + "rank": 174, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "HPAIEnviro", @@ -42055,7 +42806,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 176, + "rank": 175, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "HPAIEnviro", @@ -42090,7 +42841,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 177, + "rank": 176, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "HPAIEnviro", @@ -42125,7 +42876,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 178, + "rank": 177, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "HPAIEnviro", @@ -42159,7 +42910,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 179, + "rank": 178, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "HPAIEnviro", @@ -42193,7 +42944,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 180, + "rank": 179, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "HPAIEnviro", @@ -42227,7 +42978,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 181, + "rank": 180, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "HPAIEnviro", @@ -42261,7 +43012,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 182, + "rank": 181, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "HPAIEnviro", @@ -42288,7 +43039,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 183, + "rank": 182, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "HPAIEnviro", @@ -42315,7 +43066,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 184, + "rank": 183, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "HPAIEnviro", @@ -42342,7 +43093,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 185, + "rank": 184, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "HPAIEnviro", @@ -42369,7 +43120,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 186, + "rank": 185, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "HPAIEnviro", @@ -42396,7 +43147,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 187, + "rank": 186, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "HPAIEnviro", @@ -42423,7 +43174,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 188, + "rank": 187, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "HPAIEnviro", @@ -42450,7 +43201,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 189, + "rank": 188, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "HPAIEnviro", @@ -42477,7 +43228,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 190, + "rank": 189, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "HPAIEnviro", @@ -42504,7 +43255,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 191, + "rank": 190, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "HPAIEnviro", @@ -42531,7 +43282,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 192, + "rank": 191, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "HPAIEnviro", @@ -42558,7 +43309,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 193, + "rank": 192, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "HPAIEnviro", @@ -42585,7 +43336,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 194, + "rank": 193, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "HPAIEnviro", @@ -42612,7 +43363,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 195, + "rank": 194, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "HPAIEnviro", @@ -42639,7 +43390,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 196, + "rank": 195, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "HPAIEnviro", @@ -42666,7 +43417,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 197, + "rank": 196, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "HPAIEnviro", @@ -42693,7 +43444,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 198, + "rank": 197, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "HPAIEnviro", @@ -42720,7 +43471,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 199, + "rank": 198, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "HPAIEnviro", @@ -42747,7 +43498,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 200, + "rank": 199, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "HPAIEnviro", @@ -42774,7 +43525,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 201, + "rank": 200, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "HPAIEnviro", @@ -42801,7 +43552,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 202, + "rank": 201, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "HPAIEnviro", @@ -42828,7 +43579,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 203, + "rank": 202, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "HPAIEnviro", @@ -42855,7 +43606,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 204, + "rank": 203, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "HPAIEnviro", @@ -42882,7 +43633,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 205, + "rank": 204, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "HPAIEnviro", @@ -42909,7 +43660,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 206, + "rank": 205, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "HPAIEnviro", @@ -42936,7 +43687,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 207, + "rank": 206, "slot_uri": "GENEPIO:0101116", "alias": "genetic_target_name", "owner": "HPAIEnviro", @@ -42962,7 +43713,7 @@ "description": "The specific region or segment of a genetic sequence used for testing or analysis.", "title": "genetic target region", "from_schema": "https://example.com/hpai", - "rank": 208, + "rank": 207, "slot_uri": "GENEPIO:0101117", "alias": "genetic_target_region", "owner": "HPAIEnviro", @@ -42981,7 +43732,7 @@ "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", "title": "genetic target region reference genome", "from_schema": "https://example.com/hpai", - "rank": 209, + "rank": 208, "slot_uri": "GENEPIO:0101118", "alias": "genetic_target_region_reference_genome", "owner": "HPAIEnviro", @@ -43008,7 +43759,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 210, + "rank": 209, "slot_uri": "GENEPIO:0100962", "alias": "diagnostic_target_presence", "owner": "HPAIEnviro", @@ -43042,7 +43793,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 211, + "rank": 210, "slot_uri": "GENEPIO:0100963", "alias": "diagnostic_measurement_value", "owner": "HPAIEnviro", @@ -43069,7 +43820,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 212, + "rank": 211, "slot_uri": "GENEPIO:0100964", "alias": "diagnostic_measurement_unit", "owner": "HPAIEnviro", @@ -43103,7 +43854,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 213, + "rank": 212, "slot_uri": "GENEPIO:0100965", "alias": "diagnostic_measurement_method", "owner": "HPAIEnviro", @@ -43129,7 +43880,7 @@ "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold value", "from_schema": "https://example.com/hpai", - "rank": 214, + "rank": 213, "slot_uri": "GENEPIO:0101104", "alias": "diagnostic_testing_threshold_value", "owner": "HPAIEnviro", @@ -43148,7 +43899,7 @@ "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold units", "from_schema": "https://example.com/hpai", - "rank": 215, + "rank": 214, "slot_uri": "GENEPIO:0101105", "alias": "diagnostic_testing_threshold_units", "owner": "HPAIEnviro", @@ -43167,7 +43918,7 @@ "description": "Describe any details of the diagnsotic testing.", "title": "diagnostic testing details", "from_schema": "https://example.com/hpai", - "rank": 216, + "rank": 215, "slot_uri": "GENEPIO:0101106", "alias": "diagnostic_testing_details", "owner": "HPAIEnviro", @@ -43194,7 +43945,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 217, + "rank": 216, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "HPAIEnviro", @@ -43222,7 +43973,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 218, + "rank": 217, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "HPAIEnviro", @@ -43250,7 +44001,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 219, + "rank": 218, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "HPAIEnviro", @@ -43265,7 +44016,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -43285,7 +44036,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 220, + "rank": 219, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "HPAIEnviro", @@ -43321,7 +44072,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 221, + "rank": 220, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "HPAIEnviro", @@ -43613,27 +44364,27 @@ "host_common_name": { "name": "host_common_name", "rank": 53, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_scientific_name": { "name": "host_scientific_name", "rank": 54, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_ecotype": { "name": "host_ecotype", "rank": 55, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_breed": { "name": "host_breed", "rank": 56, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_food_production_name": { "name": "host_food_production_name", "rank": 57, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_age": { "name": "host_age", @@ -43648,12 +44399,12 @@ "host_age_bin": { "name": "host_age_bin", "rank": 60, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_disease": { "name": "host_disease", "rank": 61, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_health_state": { "name": "host_health_state", @@ -43833,17 +44584,17 @@ "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", "rank": 97, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", "rank": 98, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", "rank": 99, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", @@ -44852,7 +45603,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -45798,7 +46549,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -45838,7 +46589,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -45873,7 +46624,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_breed": { @@ -45901,7 +46652,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_food_production_name": { @@ -45928,7 +46679,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostFoodProductionNameMenu" @@ -46026,7 +46777,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostAgeBinMenu" @@ -46060,7 +46811,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostDiseaseMenu" @@ -47133,7 +47884,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -47160,7 +47911,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -47182,7 +47933,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -49006,7 +49757,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index 3bfe72a4..cac91b64 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -132,7 +132,6 @@ classes: - populated_area_type - sampling_weather_conditions - presampling_weather_conditions - - precipitation_measurement_value - water_depth - water_depth_units - sediment_depth @@ -141,7 +140,7 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - precipitation_measurement_value - precipitation_measurement_unit - precipitation_measurement_method - ambient_temperature_measurement_value @@ -490,19 +489,19 @@ classes: slot_group: Sample collection and processing host_common_name: rank: 67 - slot_group: Host information + slot_group: Host Information host_scientific_name: rank: 68 - slot_group: Host information + slot_group: Host Information host_ecotype: rank: 69 - slot_group: Host information + slot_group: Host Information host_breed: rank: 70 - slot_group: Host information + slot_group: Host Information host_food_production_name: rank: 71 - slot_group: Host information + slot_group: Host Information host_age: rank: 72 slot_group: Host Information @@ -511,10 +510,10 @@ classes: slot_group: Host Information host_age_bin: rank: 74 - slot_group: Host information + slot_group: Host Information host_disease: rank: 75 - slot_group: Host information + slot_group: Host Information host_health_state: rank: 76 slot_group: Host Information @@ -611,476 +610,473 @@ classes: presampling_weather_conditions: rank: 107 slot_group: Environmental conditions and measurements - precipitation_measurement_value: + water_depth: rank: 108 slot_group: Environmental conditions and measurements - water_depth: + water_depth_units: rank: 109 slot_group: Environmental conditions and measurements - water_depth_units: + sediment_depth: rank: 110 slot_group: Environmental conditions and measurements - sediment_depth: + sediment_depth_units: rank: 111 slot_group: Environmental conditions and measurements - sediment_depth_units: + air_temperature: rank: 112 slot_group: Environmental conditions and measurements - air_temperature: + air_temperature_units: rank: 113 slot_group: Environmental conditions and measurements - air_temperature_units: + water_temperature: rank: 114 slot_group: Environmental conditions and measurements - water_temperature: + water_temperature_units: rank: 115 slot_group: Environmental conditions and measurements - water_temperature_units: + precipitation_measurement_value: rank: 116 slot_group: Environmental conditions and measurements - weather_type: - rank: 117 - slot_group: Environmental conditions and measurements precipitation_measurement_unit: - rank: 118 + rank: 117 slot_group: Environmental conditions and measurements precipitation_measurement_method: - rank: 119 + rank: 118 slot_group: Environmental conditions and measurements ambient_temperature_measurement_value: - rank: 120 + rank: 119 slot_group: Environmental conditions and measurements ambient_temperature_measurement_unit: - rank: 121 + rank: 120 slot_group: Environmental conditions and measurements ph_measurement_value: - rank: 122 + rank: 121 slot_group: Environmental conditions and measurements ph_measurement_method: - rank: 123 + rank: 122 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_value: - rank: 124 + rank: 123 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_unit: - rank: 125 + rank: 124 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_method: - rank: 126 + rank: 125 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_value: - rank: 127 + rank: 126 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_unit: - rank: 128 + rank: 127 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_method: - rank: 129 + rank: 128 slot_group: Environmental conditions and measurements turbidity_measurement_value: - rank: 130 + rank: 129 slot_group: Environmental conditions and measurements turbidity_measurement_unit: - rank: 131 + rank: 130 slot_group: Environmental conditions and measurements turbidity_measurement_method: - rank: 132 + rank: 131 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_value: - rank: 133 + rank: 132 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_unit: - rank: 134 + rank: 133 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_method: - rank: 135 + rank: 134 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_value: - rank: 136 + rank: 135 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_unit: - rank: 137 + rank: 136 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_method: - rank: 138 + rank: 137 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_value: - rank: 139 + rank: 138 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_unit: - rank: 140 + rank: 139 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_method: - rank: 141 + rank: 140 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: - rank: 142 + rank: 141 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: - rank: 143 + rank: 142 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: - rank: 144 + rank: 143 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_value: - rank: 145 + rank: 144 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_unit: - rank: 146 + rank: 145 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_method: - rank: 147 + rank: 146 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_value: - rank: 148 + rank: 147 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_unit: - rank: 149 + rank: 148 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_method: - rank: 150 + rank: 149 slot_group: Environmental conditions and measurements total_solids_ts_measurement_value: - rank: 151 + rank: 150 slot_group: Environmental conditions and measurements total_solids_ts_measurement_unit: - rank: 152 + rank: 151 slot_group: Environmental conditions and measurements total_solids_ts_measurement_method: - rank: 153 + rank: 152 slot_group: Environmental conditions and measurements alkalinity_measurement_value: - rank: 154 + rank: 153 slot_group: Environmental conditions and measurements alkalinity_measurement_unit: - rank: 155 + rank: 154 slot_group: Environmental conditions and measurements alkalinity_measurement_method: - rank: 156 + rank: 155 slot_group: Environmental conditions and measurements conductivity_measurement_value: - rank: 157 + rank: 156 slot_group: Environmental conditions and measurements conductivity_measurement_unit: - rank: 158 + rank: 157 slot_group: Environmental conditions and measurements conductivity_measurement_method: - rank: 159 + rank: 158 slot_group: Environmental conditions and measurements salinity_measurement_value: - rank: 160 + rank: 159 slot_group: Environmental conditions and measurements salinity_measurement_unit: - rank: 161 + rank: 160 slot_group: Environmental conditions and measurements salinity_measurement_method: - rank: 162 + rank: 161 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_value: - rank: 163 + rank: 162 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_unit: - rank: 164 + rank: 163 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_method: - rank: 165 + rank: 164 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_value: - rank: 166 + rank: 165 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_unit: - rank: 167 + rank: 166 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_method: - rank: 168 + rank: 167 slot_group: Environmental conditions and measurements fecal_contamination_indicator_: - rank: 169 + rank: 168 slot_group: Environmental conditions and measurements fecal_contamination_value: - rank: 170 + rank: 169 slot_group: Environmental conditions and measurements fecal_contamination_unit: - rank: 171 + rank: 170 slot_group: Environmental conditions and measurements fecal_contamination_method: - rank: 172 + rank: 171 slot_group: Environmental conditions and measurements fecal_coliform_count_value: - rank: 173 + rank: 172 slot_group: Environmental conditions and measurements fecal_coliform_count_unit: - rank: 174 + rank: 173 slot_group: Environmental conditions and measurements fecal_coliform_count_method: - rank: 175 + rank: 174 slot_group: Environmental conditions and measurements urinary_contamination_indicator: - rank: 176 + rank: 175 slot_group: Environmental conditions and measurements urinary_contamination_value: - rank: 177 + rank: 176 slot_group: Environmental conditions and measurements urinary_contamination_unit: - rank: 178 + rank: 177 slot_group: Environmental conditions and measurements urinary_contamination_method: - rank: 179 + rank: 178 slot_group: Environmental conditions and measurements sample_temperature_value_at_collection: - rank: 180 + rank: 179 slot_group: Environmental conditions and measurements sample_temperature_unit_at_collection: - rank: 181 + rank: 180 slot_group: Environmental conditions and measurements sample_temperature_value_when_received: - rank: 182 + rank: 181 slot_group: Environmental conditions and measurements sample_temperature_unit_when_received: - rank: 183 + rank: 182 slot_group: Environmental conditions and measurements library_id: - rank: 184 + rank: 183 slot_group: Sequence information sequencing_assay_type: - rank: 185 + rank: 184 slot_group: Sequence information sequencing_date: - rank: 186 + rank: 185 slot_group: Sequence information purpose_of_sequencing__: - rank: 187 + rank: 186 slot_group: Sequence information purpose_of_sequencing_details: - rank: 188 + rank: 187 slot_group: Sequence information sequenced_by: - rank: 189 + rank: 188 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 190 + rank: 189 slot_group: Sequence information sequenced_by_contact_name: - rank: 191 + rank: 190 slot_group: Sequence information sequenced_by_contact_email: - rank: 192 + rank: 191 slot_group: Sequence information sequence_submitted_by: - rank: 193 + rank: 192 slot_group: Sequence information sequence_submitter_contact_email: - rank: 194 + rank: 193 slot_group: Sequence information nucleic_acid_extraction_method: - rank: 195 - slot_group: Sample collection and processing + rank: 194 + slot_group: Sequence information nucleic_acid_extraction_kit: - rank: 196 - slot_group: Sample collection and processing + rank: 195 + slot_group: Sequence information endogenous_control_details: - rank: 197 - slot_group: Sample collection and processing + rank: 196 + slot_group: Sequence information sequencing_project_name: - rank: 198 + rank: 197 slot_group: Sequence information sequencing_platform: - rank: 199 + rank: 198 slot_group: Sequence information sequencing_instrument: - rank: 200 + rank: 199 slot_group: Sequence information library_preparation_kit: - rank: 201 + rank: 200 slot_group: Sequence information dna_fragment_length: - rank: 202 + rank: 201 slot_group: Sequence information genomic_target_enrichment_method: - rank: 203 + rank: 202 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 204 + rank: 203 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 205 + rank: 204 slot_group: Sequence information amplicon_size: - rank: 206 + rank: 205 slot_group: Sequence information sequencing_flow_cell_version: - rank: 207 + rank: 206 slot_group: Sequence information sequencing_protocol: - rank: 208 + rank: 207 slot_group: Sequence information r1_fastq_filename: - rank: 209 + rank: 208 slot_group: Sequence information r2_fastq_filename: - rank: 210 + rank: 209 slot_group: Sequence information fast5_filename: - rank: 211 + rank: 210 slot_group: Sequence information genome_sequence_file_name: - rank: 212 + rank: 211 slot_group: Sequence information assembly_filename: - rank: 213 + rank: 212 slot_group: Sequence information quality_control_method_name: - rank: 214 + rank: 213 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 215 + rank: 214 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 216 + rank: 215 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 217 + rank: 216 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 218 + rank: 217 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 219 + rank: 218 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 220 + rank: 219 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 221 + rank: 220 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 222 + rank: 221 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 223 + rank: 222 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 224 + rank: 223 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 225 + rank: 224 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 226 + rank: 225 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 227 + rank: 226 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 228 + rank: 227 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 229 + rank: 228 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 230 + rank: 229 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 231 + rank: 230 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 232 + rank: 231 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 233 + rank: 232 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 234 + rank: 233 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 235 + rank: 234 slot_group: Bioinformatics and QC metrics n50: - rank: 236 + rank: 235 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 237 + rank: 236 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 238 + rank: 237 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 239 + rank: 238 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 240 + rank: 239 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 241 + rank: 240 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 242 + rank: 241 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 243 + rank: 242 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 244 + rank: 243 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 245 + rank: 244 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 246 + rank: 245 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 247 + rank: 246 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 248 + rank: 247 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 249 + rank: 248 slot_group: Taxonomic identification information genetic_target_name: - rank: 250 + rank: 249 slot_group: Pathogen diagnostic testing genetic_target_region: - rank: 251 + rank: 250 slot_group: Pathogen diagnostic testing genetic_target_region_reference_genome: - rank: 252 + rank: 251 slot_group: Pathogen diagnostic testing diagnostic_target_presence: - rank: 253 + rank: 252 slot_group: Pathogen diagnostic testing diagnostic_measurement_value: - rank: 254 + rank: 253 slot_group: Pathogen diagnostic testing diagnostic_measurement_unit: - rank: 255 + rank: 254 slot_group: Pathogen diagnostic testing diagnostic_measurement_method: - rank: 256 + rank: 255 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_value: - rank: 257 + rank: 256 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_units: - rank: 258 + rank: 257 slot_group: Pathogen diagnostic testing diagnostic_testing_details: - rank: 259 + rank: 258 slot_group: Pathogen diagnostic testing prevalence_metrics: - rank: 260 + rank: 259 slot_group: Risk assessment information prevalence_metrics_details: - rank: 261 + rank: 260 slot_group: Risk assessment information stage_of_production: - rank: 262 + rank: 261 slot_group: Risk assessment information experimental_intervention: - rank: 263 + rank: 262 slot_group: Risk assessment information experiment_intervention_details: - rank: 264 + rank: 263 slot_group: Risk assessment information HPAIFood: name: HPAIFood @@ -1432,13 +1428,13 @@ classes: slot_group: Sequence information nucleic_acid_extraction_method: rank: 68 - slot_group: Sample collection and processing + slot_group: Sequence information nucleic_acid_extraction_kit: rank: 69 - slot_group: Sample collection and processing + slot_group: Sequence information endogenous_control_details: rank: 70 - slot_group: Sample collection and processing + slot_group: Sequence information sequencing_project_name: rank: 71 slot_group: Sequence information @@ -1713,7 +1709,6 @@ classes: - populated_area_type - sampling_weather_conditions - presampling_weather_conditions - - precipitation_measurement_value - water_depth - water_depth_units - sediment_depth @@ -1722,7 +1717,7 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - precipitation_measurement_value - precipitation_measurement_unit - precipitation_measurement_method - ambient_temperature_measurement_value @@ -2063,476 +2058,473 @@ classes: presampling_weather_conditions: rank: 64 slot_group: Environmental conditions and measurements - precipitation_measurement_value: + water_depth: rank: 65 slot_group: Environmental conditions and measurements - water_depth: + water_depth_units: rank: 66 slot_group: Environmental conditions and measurements - water_depth_units: + sediment_depth: rank: 67 slot_group: Environmental conditions and measurements - sediment_depth: + sediment_depth_units: rank: 68 slot_group: Environmental conditions and measurements - sediment_depth_units: + air_temperature: rank: 69 slot_group: Environmental conditions and measurements - air_temperature: + air_temperature_units: rank: 70 slot_group: Environmental conditions and measurements - air_temperature_units: + water_temperature: rank: 71 slot_group: Environmental conditions and measurements - water_temperature: + water_temperature_units: rank: 72 slot_group: Environmental conditions and measurements - water_temperature_units: + precipitation_measurement_value: rank: 73 slot_group: Environmental conditions and measurements - weather_type: - rank: 74 - slot_group: Environmental conditions and measurements precipitation_measurement_unit: - rank: 75 + rank: 74 slot_group: Environmental conditions and measurements precipitation_measurement_method: - rank: 76 + rank: 75 slot_group: Environmental conditions and measurements ambient_temperature_measurement_value: - rank: 77 + rank: 76 slot_group: Environmental conditions and measurements ambient_temperature_measurement_unit: - rank: 78 + rank: 77 slot_group: Environmental conditions and measurements ph_measurement_value: - rank: 79 + rank: 78 slot_group: Environmental conditions and measurements ph_measurement_method: - rank: 80 + rank: 79 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_value: - rank: 81 + rank: 80 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_unit: - rank: 82 + rank: 81 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_method: - rank: 83 + rank: 82 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_value: - rank: 84 + rank: 83 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_unit: - rank: 85 + rank: 84 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_method: - rank: 86 + rank: 85 slot_group: Environmental conditions and measurements turbidity_measurement_value: - rank: 87 + rank: 86 slot_group: Environmental conditions and measurements turbidity_measurement_unit: - rank: 88 + rank: 87 slot_group: Environmental conditions and measurements turbidity_measurement_method: - rank: 89 + rank: 88 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_value: - rank: 90 + rank: 89 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_unit: - rank: 91 + rank: 90 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_method: - rank: 92 + rank: 91 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_value: - rank: 93 + rank: 92 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_unit: - rank: 94 + rank: 93 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_method: - rank: 95 + rank: 94 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_value: - rank: 96 + rank: 95 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_unit: - rank: 97 + rank: 96 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_method: - rank: 98 + rank: 97 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: - rank: 99 + rank: 98 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: - rank: 100 + rank: 99 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: - rank: 101 + rank: 100 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_value: - rank: 102 + rank: 101 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_unit: - rank: 103 + rank: 102 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_method: - rank: 104 + rank: 103 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_value: - rank: 105 + rank: 104 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_unit: - rank: 106 + rank: 105 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_method: - rank: 107 + rank: 106 slot_group: Environmental conditions and measurements total_solids_ts_measurement_value: - rank: 108 + rank: 107 slot_group: Environmental conditions and measurements total_solids_ts_measurement_unit: - rank: 109 + rank: 108 slot_group: Environmental conditions and measurements total_solids_ts_measurement_method: - rank: 110 + rank: 109 slot_group: Environmental conditions and measurements alkalinity_measurement_value: - rank: 111 + rank: 110 slot_group: Environmental conditions and measurements alkalinity_measurement_unit: - rank: 112 + rank: 111 slot_group: Environmental conditions and measurements alkalinity_measurement_method: - rank: 113 + rank: 112 slot_group: Environmental conditions and measurements conductivity_measurement_value: - rank: 114 + rank: 113 slot_group: Environmental conditions and measurements conductivity_measurement_unit: - rank: 115 + rank: 114 slot_group: Environmental conditions and measurements conductivity_measurement_method: - rank: 116 + rank: 115 slot_group: Environmental conditions and measurements salinity_measurement_value: - rank: 117 + rank: 116 slot_group: Environmental conditions and measurements salinity_measurement_unit: - rank: 118 + rank: 117 slot_group: Environmental conditions and measurements salinity_measurement_method: - rank: 119 + rank: 118 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_value: - rank: 120 + rank: 119 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_unit: - rank: 121 + rank: 120 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_method: - rank: 122 + rank: 121 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_value: - rank: 123 + rank: 122 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_unit: - rank: 124 + rank: 123 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_method: - rank: 125 + rank: 124 slot_group: Environmental conditions and measurements fecal_contamination_indicator_: - rank: 126 + rank: 125 slot_group: Environmental conditions and measurements fecal_contamination_value: - rank: 127 + rank: 126 slot_group: Environmental conditions and measurements fecal_contamination_unit: - rank: 128 + rank: 127 slot_group: Environmental conditions and measurements fecal_contamination_method: - rank: 129 + rank: 128 slot_group: Environmental conditions and measurements fecal_coliform_count_value: - rank: 130 + rank: 129 slot_group: Environmental conditions and measurements fecal_coliform_count_unit: - rank: 131 + rank: 130 slot_group: Environmental conditions and measurements fecal_coliform_count_method: - rank: 132 + rank: 131 slot_group: Environmental conditions and measurements urinary_contamination_indicator: - rank: 133 + rank: 132 slot_group: Environmental conditions and measurements urinary_contamination_value: - rank: 134 + rank: 133 slot_group: Environmental conditions and measurements urinary_contamination_unit: - rank: 135 + rank: 134 slot_group: Environmental conditions and measurements urinary_contamination_method: - rank: 136 + rank: 135 slot_group: Environmental conditions and measurements sample_temperature_value_at_collection: - rank: 137 + rank: 136 slot_group: Environmental conditions and measurements sample_temperature_unit_at_collection: - rank: 138 + rank: 137 slot_group: Environmental conditions and measurements sample_temperature_value_when_received: - rank: 139 + rank: 138 slot_group: Environmental conditions and measurements sample_temperature_unit_when_received: - rank: 140 + rank: 139 slot_group: Environmental conditions and measurements library_id: - rank: 141 + rank: 140 slot_group: Sequence information sequencing_assay_type: - rank: 142 + rank: 141 slot_group: Sequence information sequencing_date: - rank: 143 + rank: 142 slot_group: Sequence information purpose_of_sequencing__: - rank: 144 + rank: 143 slot_group: Sequence information purpose_of_sequencing_details: - rank: 145 + rank: 144 slot_group: Sequence information sequenced_by: - rank: 146 + rank: 145 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 147 + rank: 146 slot_group: Sequence information sequenced_by_contact_name: - rank: 148 + rank: 147 slot_group: Sequence information sequenced_by_contact_email: - rank: 149 + rank: 148 slot_group: Sequence information sequence_submitted_by: - rank: 150 + rank: 149 slot_group: Sequence information sequence_submitter_contact_email: - rank: 151 + rank: 150 slot_group: Sequence information nucleic_acid_extraction_method: - rank: 152 - slot_group: Sample collection and processing + rank: 151 + slot_group: Sequence information nucleic_acid_extraction_kit: - rank: 153 - slot_group: Sample collection and processing + rank: 152 + slot_group: Sequence information endogenous_control_details: - rank: 154 - slot_group: Sample collection and processing + rank: 153 + slot_group: Sequence information sequencing_project_name: - rank: 155 + rank: 154 slot_group: Sequence information sequencing_platform: - rank: 156 + rank: 155 slot_group: Sequence information sequencing_instrument: - rank: 157 + rank: 156 slot_group: Sequence information library_preparation_kit: - rank: 158 + rank: 157 slot_group: Sequence information dna_fragment_length: - rank: 159 + rank: 158 slot_group: Sequence information genomic_target_enrichment_method: - rank: 160 + rank: 159 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 161 + rank: 160 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 162 + rank: 161 slot_group: Sequence information amplicon_size: - rank: 163 + rank: 162 slot_group: Sequence information sequencing_flow_cell_version: - rank: 164 + rank: 163 slot_group: Sequence information sequencing_protocol: - rank: 165 + rank: 164 slot_group: Sequence information r1_fastq_filename: - rank: 166 + rank: 165 slot_group: Sequence information r2_fastq_filename: - rank: 167 + rank: 166 slot_group: Sequence information fast5_filename: - rank: 168 + rank: 167 slot_group: Sequence information genome_sequence_file_name: - rank: 169 + rank: 168 slot_group: Sequence information assembly_filename: - rank: 170 + rank: 169 slot_group: Sequence information quality_control_method_name: - rank: 171 + rank: 170 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 172 + rank: 171 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 173 + rank: 172 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 174 + rank: 173 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 175 + rank: 174 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 176 + rank: 175 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 177 + rank: 176 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 178 + rank: 177 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 179 + rank: 178 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 180 + rank: 179 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 181 + rank: 180 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 182 + rank: 181 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 183 + rank: 182 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 184 + rank: 183 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 185 + rank: 184 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 186 + rank: 185 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 187 + rank: 186 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 188 + rank: 187 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 189 + rank: 188 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 190 + rank: 189 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 191 + rank: 190 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 192 + rank: 191 slot_group: Bioinformatics and QC metrics n50: - rank: 193 + rank: 192 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 194 + rank: 193 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 195 + rank: 194 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 196 + rank: 195 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 197 + rank: 196 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 198 + rank: 197 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 199 + rank: 198 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 200 + rank: 199 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 201 + rank: 200 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 202 + rank: 201 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 203 + rank: 202 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 204 + rank: 203 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 205 + rank: 204 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 206 + rank: 205 slot_group: Taxonomic identification information genetic_target_name: - rank: 207 + rank: 206 slot_group: Pathogen diagnostic testing genetic_target_region: - rank: 208 + rank: 207 slot_group: Pathogen diagnostic testing genetic_target_region_reference_genome: - rank: 209 + rank: 208 slot_group: Pathogen diagnostic testing diagnostic_target_presence: - rank: 210 + rank: 209 slot_group: Pathogen diagnostic testing diagnostic_measurement_value: - rank: 211 + rank: 210 slot_group: Pathogen diagnostic testing diagnostic_measurement_unit: - rank: 212 + rank: 211 slot_group: Pathogen diagnostic testing diagnostic_measurement_method: - rank: 213 + rank: 212 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_value: - rank: 214 + rank: 213 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_units: - rank: 215 + rank: 214 slot_group: Pathogen diagnostic testing diagnostic_testing_details: - rank: 216 + rank: 215 slot_group: Pathogen diagnostic testing prevalence_metrics: - rank: 217 + rank: 216 slot_group: Risk assessment information prevalence_metrics_details: - rank: 218 + rank: 217 slot_group: Risk assessment information stage_of_production: - rank: 219 + rank: 218 slot_group: Risk assessment information experimental_intervention: - rank: 220 + rank: 219 slot_group: Risk assessment information experiment_intervention_details: - rank: 221 + rank: 220 slot_group: Risk assessment information HPAIEnviro: name: HPAIEnviro @@ -2607,7 +2599,6 @@ classes: - populated_area_type - sampling_weather_conditions - presampling_weather_conditions - - precipitation_measurement_value - water_depth - water_depth_units - sediment_depth @@ -2616,7 +2607,7 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - precipitation_measurement_value - precipitation_measurement_unit - precipitation_measurement_method - ambient_temperature_measurement_value @@ -2957,476 +2948,473 @@ classes: presampling_weather_conditions: rank: 64 slot_group: Environmental conditions and measurements - precipitation_measurement_value: + water_depth: rank: 65 slot_group: Environmental conditions and measurements - water_depth: + water_depth_units: rank: 66 slot_group: Environmental conditions and measurements - water_depth_units: + sediment_depth: rank: 67 slot_group: Environmental conditions and measurements - sediment_depth: + sediment_depth_units: rank: 68 slot_group: Environmental conditions and measurements - sediment_depth_units: + air_temperature: rank: 69 slot_group: Environmental conditions and measurements - air_temperature: + air_temperature_units: rank: 70 slot_group: Environmental conditions and measurements - air_temperature_units: + water_temperature: rank: 71 slot_group: Environmental conditions and measurements - water_temperature: + water_temperature_units: rank: 72 slot_group: Environmental conditions and measurements - water_temperature_units: + precipitation_measurement_value: rank: 73 slot_group: Environmental conditions and measurements - weather_type: - rank: 74 - slot_group: Environmental conditions and measurements precipitation_measurement_unit: - rank: 75 + rank: 74 slot_group: Environmental conditions and measurements precipitation_measurement_method: - rank: 76 + rank: 75 slot_group: Environmental conditions and measurements ambient_temperature_measurement_value: - rank: 77 + rank: 76 slot_group: Environmental conditions and measurements ambient_temperature_measurement_unit: - rank: 78 + rank: 77 slot_group: Environmental conditions and measurements ph_measurement_value: - rank: 79 + rank: 78 slot_group: Environmental conditions and measurements ph_measurement_method: - rank: 80 + rank: 79 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_value: - rank: 81 + rank: 80 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_unit: - rank: 82 + rank: 81 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_method: - rank: 83 + rank: 82 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_value: - rank: 84 + rank: 83 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_unit: - rank: 85 + rank: 84 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_method: - rank: 86 + rank: 85 slot_group: Environmental conditions and measurements turbidity_measurement_value: - rank: 87 + rank: 86 slot_group: Environmental conditions and measurements turbidity_measurement_unit: - rank: 88 + rank: 87 slot_group: Environmental conditions and measurements turbidity_measurement_method: - rank: 89 + rank: 88 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_value: - rank: 90 + rank: 89 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_unit: - rank: 91 + rank: 90 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_method: - rank: 92 + rank: 91 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_value: - rank: 93 + rank: 92 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_unit: - rank: 94 + rank: 93 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_method: - rank: 95 + rank: 94 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_value: - rank: 96 + rank: 95 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_unit: - rank: 97 + rank: 96 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_method: - rank: 98 + rank: 97 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: - rank: 99 + rank: 98 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: - rank: 100 + rank: 99 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: - rank: 101 + rank: 100 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_value: - rank: 102 + rank: 101 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_unit: - rank: 103 + rank: 102 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_method: - rank: 104 + rank: 103 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_value: - rank: 105 + rank: 104 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_unit: - rank: 106 + rank: 105 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_method: - rank: 107 + rank: 106 slot_group: Environmental conditions and measurements total_solids_ts_measurement_value: - rank: 108 + rank: 107 slot_group: Environmental conditions and measurements total_solids_ts_measurement_unit: - rank: 109 + rank: 108 slot_group: Environmental conditions and measurements total_solids_ts_measurement_method: - rank: 110 + rank: 109 slot_group: Environmental conditions and measurements alkalinity_measurement_value: - rank: 111 + rank: 110 slot_group: Environmental conditions and measurements alkalinity_measurement_unit: - rank: 112 + rank: 111 slot_group: Environmental conditions and measurements alkalinity_measurement_method: - rank: 113 + rank: 112 slot_group: Environmental conditions and measurements conductivity_measurement_value: - rank: 114 + rank: 113 slot_group: Environmental conditions and measurements conductivity_measurement_unit: - rank: 115 + rank: 114 slot_group: Environmental conditions and measurements conductivity_measurement_method: - rank: 116 + rank: 115 slot_group: Environmental conditions and measurements salinity_measurement_value: - rank: 117 + rank: 116 slot_group: Environmental conditions and measurements salinity_measurement_unit: - rank: 118 + rank: 117 slot_group: Environmental conditions and measurements salinity_measurement_method: - rank: 119 + rank: 118 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_value: - rank: 120 + rank: 119 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_unit: - rank: 121 + rank: 120 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_method: - rank: 122 + rank: 121 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_value: - rank: 123 + rank: 122 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_unit: - rank: 124 + rank: 123 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_method: - rank: 125 + rank: 124 slot_group: Environmental conditions and measurements fecal_contamination_indicator_: - rank: 126 + rank: 125 slot_group: Environmental conditions and measurements fecal_contamination_value: - rank: 127 + rank: 126 slot_group: Environmental conditions and measurements fecal_contamination_unit: - rank: 128 + rank: 127 slot_group: Environmental conditions and measurements fecal_contamination_method: - rank: 129 + rank: 128 slot_group: Environmental conditions and measurements fecal_coliform_count_value: - rank: 130 + rank: 129 slot_group: Environmental conditions and measurements fecal_coliform_count_unit: - rank: 131 + rank: 130 slot_group: Environmental conditions and measurements fecal_coliform_count_method: - rank: 132 + rank: 131 slot_group: Environmental conditions and measurements urinary_contamination_indicator: - rank: 133 + rank: 132 slot_group: Environmental conditions and measurements urinary_contamination_value: - rank: 134 + rank: 133 slot_group: Environmental conditions and measurements urinary_contamination_unit: - rank: 135 + rank: 134 slot_group: Environmental conditions and measurements urinary_contamination_method: - rank: 136 + rank: 135 slot_group: Environmental conditions and measurements sample_temperature_value_at_collection: - rank: 137 + rank: 136 slot_group: Environmental conditions and measurements sample_temperature_unit_at_collection: - rank: 138 + rank: 137 slot_group: Environmental conditions and measurements sample_temperature_value_when_received: - rank: 139 + rank: 138 slot_group: Environmental conditions and measurements sample_temperature_unit_when_received: - rank: 140 + rank: 139 slot_group: Environmental conditions and measurements library_id: - rank: 141 + rank: 140 slot_group: Sequence information sequencing_assay_type: - rank: 142 + rank: 141 slot_group: Sequence information sequencing_date: - rank: 143 + rank: 142 slot_group: Sequence information purpose_of_sequencing__: - rank: 144 + rank: 143 slot_group: Sequence information purpose_of_sequencing_details: - rank: 145 + rank: 144 slot_group: Sequence information sequenced_by: - rank: 146 + rank: 145 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 147 + rank: 146 slot_group: Sequence information sequenced_by_contact_name: - rank: 148 + rank: 147 slot_group: Sequence information sequenced_by_contact_email: - rank: 149 + rank: 148 slot_group: Sequence information sequence_submitted_by: - rank: 150 + rank: 149 slot_group: Sequence information sequence_submitter_contact_email: - rank: 151 + rank: 150 slot_group: Sequence information nucleic_acid_extraction_method: - rank: 152 - slot_group: Sample collection and processing + rank: 151 + slot_group: Sequence information nucleic_acid_extraction_kit: - rank: 153 - slot_group: Sample collection and processing + rank: 152 + slot_group: Sequence information endogenous_control_details: - rank: 154 - slot_group: Sample collection and processing + rank: 153 + slot_group: Sequence information sequencing_project_name: - rank: 155 + rank: 154 slot_group: Sequence information sequencing_platform: - rank: 156 + rank: 155 slot_group: Sequence information sequencing_instrument: - rank: 157 + rank: 156 slot_group: Sequence information library_preparation_kit: - rank: 158 + rank: 157 slot_group: Sequence information dna_fragment_length: - rank: 159 + rank: 158 slot_group: Sequence information genomic_target_enrichment_method: - rank: 160 + rank: 159 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 161 + rank: 160 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 162 + rank: 161 slot_group: Sequence information amplicon_size: - rank: 163 + rank: 162 slot_group: Sequence information sequencing_flow_cell_version: - rank: 164 + rank: 163 slot_group: Sequence information sequencing_protocol: - rank: 165 + rank: 164 slot_group: Sequence information r1_fastq_filename: - rank: 166 + rank: 165 slot_group: Sequence information r2_fastq_filename: - rank: 167 + rank: 166 slot_group: Sequence information fast5_filename: - rank: 168 + rank: 167 slot_group: Sequence information genome_sequence_file_name: - rank: 169 + rank: 168 slot_group: Sequence information assembly_filename: - rank: 170 + rank: 169 slot_group: Sequence information quality_control_method_name: - rank: 171 + rank: 170 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 172 + rank: 171 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 173 + rank: 172 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 174 + rank: 173 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 175 + rank: 174 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 176 + rank: 175 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 177 + rank: 176 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 178 + rank: 177 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 179 + rank: 178 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 180 + rank: 179 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 181 + rank: 180 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 182 + rank: 181 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 183 + rank: 182 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 184 + rank: 183 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 185 + rank: 184 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 186 + rank: 185 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 187 + rank: 186 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 188 + rank: 187 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 189 + rank: 188 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 190 + rank: 189 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 191 + rank: 190 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 192 + rank: 191 slot_group: Bioinformatics and QC metrics n50: - rank: 193 + rank: 192 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 194 + rank: 193 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 195 + rank: 194 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 196 + rank: 195 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 197 + rank: 196 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 198 + rank: 197 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 199 + rank: 198 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 200 + rank: 199 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 201 + rank: 200 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 202 + rank: 201 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 203 + rank: 202 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 204 + rank: 203 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 205 + rank: 204 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 206 + rank: 205 slot_group: Taxonomic identification information genetic_target_name: - rank: 207 + rank: 206 slot_group: Pathogen diagnostic testing genetic_target_region: - rank: 208 + rank: 207 slot_group: Pathogen diagnostic testing genetic_target_region_reference_genome: - rank: 209 + rank: 208 slot_group: Pathogen diagnostic testing diagnostic_target_presence: - rank: 210 + rank: 209 slot_group: Pathogen diagnostic testing diagnostic_measurement_value: - rank: 211 + rank: 210 slot_group: Pathogen diagnostic testing diagnostic_measurement_unit: - rank: 212 + rank: 211 slot_group: Pathogen diagnostic testing diagnostic_measurement_method: - rank: 213 + rank: 212 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_value: - rank: 214 + rank: 213 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_units: - rank: 215 + rank: 214 slot_group: Pathogen diagnostic testing diagnostic_testing_details: - rank: 216 + rank: 215 slot_group: Pathogen diagnostic testing prevalence_metrics: - rank: 217 + rank: 216 slot_group: Risk assessment information prevalence_metrics_details: - rank: 218 + rank: 217 slot_group: Risk assessment information stage_of_production: - rank: 219 + rank: 218 slot_group: Risk assessment information experimental_intervention: - rank: 220 + rank: 219 slot_group: Risk assessment information experiment_intervention_details: - rank: 221 + rank: 220 slot_group: Risk assessment information HPAIHost: name: HPAIHost @@ -3762,19 +3750,19 @@ classes: slot_group: Sample collection and processing host_common_name: rank: 53 - slot_group: Host information + slot_group: Host Information host_scientific_name: rank: 54 - slot_group: Host information + slot_group: Host Information host_ecotype: rank: 55 - slot_group: Host information + slot_group: Host Information host_breed: rank: 56 - slot_group: Host information + slot_group: Host Information host_food_production_name: rank: 57 - slot_group: Host information + slot_group: Host Information host_age: rank: 58 slot_group: Host Information @@ -3783,10 +3771,10 @@ classes: slot_group: Host Information host_age_bin: rank: 60 - slot_group: Host information + slot_group: Host Information host_disease: rank: 61 - slot_group: Host information + slot_group: Host Information host_health_state: rank: 62 slot_group: Host Information @@ -3894,13 +3882,13 @@ classes: slot_group: Sequence information nucleic_acid_extraction_method: rank: 97 - slot_group: Sample collection and processing + slot_group: Sequence information nucleic_acid_extraction_kit: rank: 98 - slot_group: Sample collection and processing + slot_group: Sequence information endogenous_control_details: rank: 99 - slot_group: Sample collection and processing + slot_group: Sequence information sequencing_project_name: rank: 100 slot_group: Sequence information @@ -4404,7 +4392,7 @@ slots: name: influenza_subtype title: influenza_subtype slot_uri: GENEPIO:0101108 - range: InfluenzaSubsubtypeMenu + range: InfluenzaSubtypeMenu multivalued: true required: true influenza_subtyping_scheme_name: @@ -5511,7 +5499,7 @@ slots: comments: Provide the populated area type from the pick list. slot_uri: GENEPIO:0100778 any_of: - - range: populated area type menu + - range: PopulatedAreaTypeMenu - range: NullValueMenu examples: - value: Urban area @@ -5540,19 +5528,6 @@ slots: multivalued: true examples: - value: Drizzle - precipitation_measurement_value: - name: precipitation_measurement_value - title: precipitation measurement value - description: The amount of water which has fallen during a precipitation process. - comments: Provide the quantity of precipitation in the area leading up to the - time of sample collection. - slot_uri: GENEPIO:0100911 - any_of: - - range: WhitespaceMinimizedString - - range: NullValueMenu - recommended: true - examples: - - value: '12' water_depth: name: water_depth title: water_depth @@ -5635,19 +5610,19 @@ slots: - range: NullValueMenu examples: - value: degree Celsius (C) [UO:0000027] - weather_type: - name: weather_type - title: weather_type - description: The state of the atmosphere at a place and time as regards heat, - dryness, sunshine, wind, rain, etc. - comments: Provide the weather conditions at the time of sample collection. - slot_uri: GENEPIO:0100442 + precipitation_measurement_value: + name: precipitation_measurement_value + title: precipitation measurement value + description: The amount of water which has fallen during a precipitation process. + comments: Provide the quantity of precipitation in the area leading up to the + time of sample collection. + slot_uri: GENEPIO:0100911 any_of: - - range: WeatherTypeMenu + - range: WhitespaceMinimizedString - range: NullValueMenu - multivalued: true + recommended: true examples: - - value: Rain [ENVO:01001564] + - value: '12' precipitation_measurement_unit: name: precipitation_measurement_unit title: precipitation measurement unit @@ -6154,7 +6129,7 @@ slots: comments: Provide the units of the measured TP. slot_uri: GENEPIO:0100812 any_of: - - range: TotalPhosphorusTPMeasurementUnitMenu + - range: TotalPhosphorpusTpMeasurementUnitMenu - range: NullValueMenu examples: - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) @@ -7209,7 +7184,7 @@ slots: comments: Provide the stage of food production as free text. slot_uri: GENEPIO:0100482 any_of: - - range: StageOfProductionMenu + - range: WhitespaceMinimizedString - range: NullValueMenu recommended: true examples: @@ -9534,9 +9509,9 @@ enums: Residual sample status unkown [GENEPIO:0101089]: text: Residual sample status unkown [GENEPIO:0101089] meaning: GENEPIO:0101089 - PurposeOfSampling: - name: PurposeOfSampling - title: purpose of sampling + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation [GENEPIO:0100001]: text: Cluster/Outbreak investigation [GENEPIO:0100001] @@ -9583,9 +9558,9 @@ enums: description: A sampling strategy in which individuals are sampled for surveillance investigations. meaning: GENEPIO:0100004 - PresamplingActivity: - name: PresamplingActivity - title: presampling activity + PresamplingActivityMenu: + name: PresamplingActivityMenu + title: presampling activity menu permissible_values: Addition of substances to food/water [GENEPIO:0100536]: text: Addition of substances to food/water [GENEPIO:0100536] @@ -9648,9 +9623,9 @@ enums: This includes any preparation intended for active immunological prophylaxis or treatment. meaning: NCIT:C15346 - SampleStorageDurationUnit: - name: SampleStorageDurationUnit - title: sample storage duration unit + SampleStorageDurationUnitMenu: + name: SampleStorageDurationUnitMenu + title: sample storage duration unit menu permissible_values: Second [UO:0000010]: text: Second [UO:0000010] @@ -9684,9 +9659,9 @@ enums: description: A time unit which is equal to 365 days, or 366 days during a leap year. meaning: UO:0000036 - SpecimenProcessing: - name: SpecimenProcessing - title: specimen processing + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Concentration [OBI:0600041]: text: Concentration [OBI:0600041] @@ -9707,9 +9682,9 @@ enums: text: Pooling specimens [OBI:0600016] description: Physical combination of several instances of like material. meaning: OBI:0600016 - ExperimentalSpecimenRoleType: - name: ExperimentalSpecimenRoleType - title: experimental specimen role type + ExperimentalSpecimenRoleTypeMenu: + name: ExperimentalSpecimenRoleTypeMenu + title: experimental specimen role type menu permissible_values: Positive experimental control [GENEPIO:0101018]: text: Positive experimental control [GENEPIO:0101018] @@ -10612,9 +10587,9 @@ enums: description: An age group that stratifies the age of a case to be greater than or equal to 100 years old. meaning: GENEPIO:0100059 - HostGender: - name: HostGender - title: host_gender + HostGenderMenu: + name: HostGenderMenu + title: host_gender menu permissible_values: Female [NCIT:C46110]: text: Female [NCIT:C46110] @@ -12198,18 +12173,32 @@ enums: permissible_values: <10 people: text: <10 people + description: An estimation of population size for a group smaller than 10 + people. 10 - 100 people: text: 10 - 100 people + description: An estimation of population size for a group smaller than 100 + people and larger than 10 people. 100 - 1,000 people: text: 100 - 1,000 people + description: An estimation of population size for a group smaller than 1,000 + people and larger than 100 people. 1,000 - 10,000 people: text: 1,000 - 10,000 people + description: An estimation of population size for a group smaller than 10,000 + people and larger than 1,000 people. 10,000 - 100,000 people: text: 10,000 - 100,000 people + description: An estimation of population size for a group smaller than 100,000 + people and larger than 10,000 people. 100,000 - 1,000,000 people: text: 100,000 - 1,000,000 people + description: An estimation of population size for a group smaller than 1,000,000 + people and larger than 100,000 people. 1,000,000+ people: text: 1,000,000+ people + description: An estimation of population size for a group larger than 1,000,000 + people. WaterCatchmentAreaHumanPopulationDensityUnitMenu: name: WaterCatchmentAreaHumanPopulationDensityUnitMenu title: water_catchment_area_human_population_density_unit menu @@ -12379,6 +12368,875 @@ enums: text: foot (ft) [UO:0010013] description: A non-SI unit of length which is approximately 0.3048 meters. meaning: UO:0010013 + WaterDepthUnitsMenu: + name: WaterDepthUnitsMenu + title: water_depth_units menu + permissible_values: + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m + meaning: UO:0000015 + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. + meaning: UO:0000008 + kilometer (km) [UO:0010066]: + text: kilometer (km) [UO:0010066] + description: A length unit which is equal to one thousand meters. + meaning: UO:0010066 + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. + meaning: UO:0010011 + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. + meaning: UO:0010013 + SedimentDepthUnitsMenu: + name: SedimentDepthUnitsMenu + title: sediment_depth_units menu + permissible_values: + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m + meaning: UO:0000015 + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. + meaning: UO:0000008 + kilometer (km) [UO:0010066]: + text: kilometer (km) [UO:0010066] + description: A length unit which is equal to one thousand meters. + meaning: UO:0010066 + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. + meaning: UO:0010011 + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. + meaning: UO:0010013 + AirTemperatureUnitsMenu: + name: AirTemperatureUnitsMenu + title: air_temperature_units menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + WaterTemperatureUnitsMenu: + name: WaterTemperatureUnitsMenu + title: water_temperature_units menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + SequencingPlatformMenu: + name: SequencingPlatformMenu + title: sequencing_platform menu + permissible_values: + Illumina [GENEPIO:0001923]: + text: Illumina [GENEPIO:0001923] + description: A sequencing platform provided by the Illumina company. + meaning: GENEPIO:0001923 + Pacific Biosciences [GENEPIO:0001927]: + text: Pacific Biosciences [GENEPIO:0001927] + description: A sequencing platform provided by the Pacific Biosciences company. + meaning: GENEPIO:0001927 + Ion Torrent [GENEPIO:0002683]: + text: Ion Torrent [GENEPIO:0002683] + description: A sequencing platform provided by the Ion Torrent company. + meaning: GENEPIO:0002683 + Oxford Nanopore Technologies [GENEPIO:0100986]: + text: Oxford Nanopore Technologies [GENEPIO:0100986] + description: An sequencing platform that is developing and selling nanopore + sequencing products and is based in the UK. + meaning: GENEPIO:0100986 + BGI Genomics [GENEPIO:0004324]: + text: BGI Genomics [GENEPIO:0004324] + description: A sequencing platform provided by the BGI Genomics company. + meaning: GENEPIO:0004324 + MGI [GENEPIO:0004325]: + text: MGI [GENEPIO:0004325] + description: A sequencing platform provided by the MGI company. + meaning: GENEPIO:0004325 + Roche LS454 [GENEPIO:0001926]: + text: Roche LS454 [GENEPIO:0001926] + description: A sequencing platform provided by the 454 Life Sciences company. + meaning: GENEPIO:0001926 + SOLiD sequencing [GENEPIO:0002684]: + text: SOLiD sequencing [GENEPIO:0002684] + description: A sequencing platform provided by Life Technologies Corporation. + meaning: GENEPIO:0002684 + Complete Genomics [GENEPIO:0001924]: + text: Complete Genomics [GENEPIO:0001924] + description: An in-house sequencing platform provided by Complete Genomics. + meaning: GENEPIO:0001924 + Helicos [GENEPIO:0002682]: + text: Helicos [GENEPIO:0002682] + description: A sequencing platform brand provided by Helicos corporation (now + defunct). + meaning: GENEPIO:0002682 + Applied Biosystems [GENEPIO:0100985]: + text: Applied Biosystems [GENEPIO:0100985] + description: A sequencing platform provided by ThermoFisher. + meaning: GENEPIO:0100985 + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing_instrument menu + permissible_values: + Illumina [GENEPIO:0100105]: + text: Illumina [GENEPIO:0100105] + description: A DNA sequencer manufactured by the Illumina corporation. + meaning: GENEPIO:0100105 + Illumina Genome Analyzer [GENEPIO:0100106]: + text: Illumina Genome Analyzer [GENEPIO:0100106] + description: A DNA sequencer manufactured by Solexa as one of its first sequencer + lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data + in a single run. + meaning: GENEPIO:0100106 + is_a: Illumina [GENEPIO:0100105] + Illumina Genome Analyzer II [OBI:0000703]: + text: Illumina Genome Analyzer II [OBI:0000703] + description: A DNA sequencer manufactured by the Illumina (Solexa) corporation, + which supports sequencing of single or paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0000703 + is_a: Illumina [GENEPIO:0100105] + Illumina Genome Analyzer IIx [OBI:0002000]: + text: Illumina Genome Analyzer IIx [OBI:0002000] + description: An Illumina Genome Analyzer II which is manufactured by the Illumina + corporation. It supports sequencing of single, long or short insert paired + end clone libraries relying on sequencing by synthesis technology. The Genome + Analyzer IIx is the most widely adopted next-generation sequencing platform + and proven and published across the broadest range of research applications. + meaning: OBI:0002000 + is_a: Illumina [GENEPIO:0100105] + Illumina HiScanSQ [GENEPIO:0100109]: + text: Illumina HiScanSQ [GENEPIO:0100109] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing + and microarray-based analyses as well as an "SQ Module" to support microfluidics. + meaning: GENEPIO:0100109 + is_a: Illumina [GENEPIO:0100105] + Illumina HiSeq [GENEPIO:0100110]: + text: Illumina HiSeq [GENEPIO:0100110] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + meaning: GENEPIO:0100110 + is_a: Illumina [GENEPIO:0100105] + Illumina HiSeq X [GENEPIO:0100111]: + text: Illumina HiSeq X [GENEPIO:0100111] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that enables sufficient depth and coverage + to produce the first 30x human genome for $1000. + meaning: GENEPIO:0100111 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X Five [GENEPIO:0100112]: + text: Illumina HiSeq X Five [GENEPIO:0100112] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing + Systems. + meaning: GENEPIO:0100112 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X Ten [GENEPIO:0100113]: + text: Illumina HiSeq X Ten [GENEPIO:0100113] + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. + meaning: GENEPIO:0100113 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 1000 [OBI:0002022]: + text: Illumina HiSeq 1000 [OBI:0002022] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0002022 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 1500 [GENEPIO:0100115]: + text: Illumina HiSeq 1500 [GENEPIO:0100115] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35-50 Gb per day. + meaning: GENEPIO:0100115 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 2000 [OBI:0002001]: + text: Illumina HiSeq 2000 [OBI:0002001] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. + meaning: OBI:0002001 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 2500 [OBI:0002002]: + text: Illumina HiSeq 2500 [OBI:0002002] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. + meaning: OBI:0002002 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 3000 [OBI:0002048]: + text: Illumina HiSeq 3000 [OBI:0002048] + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. + meaning: OBI:0002048 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 4000 [OBI:0002049]: + text: Illumina HiSeq 4000 [OBI:0002049] + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. + meaning: OBI:0002049 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina iSeq [GENEPIO:0100120]: + text: Illumina iSeq [GENEPIO:0100120] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight. + meaning: GENEPIO:0100120 + is_a: Illumina [GENEPIO:0100105] + Illumina iSeq 100 [GENEPIO:0100121]: + text: Illumina iSeq 100 [GENEPIO:0100121] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight and has an output capacity + between 144MB-1.2GB. + meaning: GENEPIO:0100121 + is_a: Illumina iSeq [GENEPIO:0100120] + Illumina NovaSeq [GENEPIO:0100122]: + text: Illumina NovaSeq [GENEPIO:0100122] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that has an output capacity of 6 Tb and + 20 billion reads in dual flow cell mode. + meaning: GENEPIO:0100122 + is_a: Illumina [GENEPIO:0100105] + Illumina NovaSeq 6000 [GENEPIO:0100123]: + text: Illumina NovaSeq 6000 [GENEPIO:0100123] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). + The sequencer utilizes synthesis technology and patterned flow cells to + optimize throughput and even spacing of sequencing clusters. + meaning: GENEPIO:0100123 + is_a: Illumina NovaSeq [GENEPIO:0100122] + Illumina MiniSeq [GENEPIO:0100124]: + text: Illumina MiniSeq [GENEPIO:0100124] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. + meaning: GENEPIO:0100124 + is_a: Illumina [GENEPIO:0100105] + Illumina MiSeq [OBI:0002003]: + text: Illumina MiSeq [OBI:0002003] + description: A DNA sequencer which is manufactured by the Illumina corporation. + Built upon sequencing by synthesis technology, the machine provides an end-to-end + solution (cluster generation, amplification, sequencing, and data analysis) + in a single machine. + meaning: OBI:0002003 + is_a: Illumina [GENEPIO:0100105] + Illumina NextSeq [GENEPIO:0100126]: + text: Illumina NextSeq [GENEPIO:0100126] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. + meaning: GENEPIO:0100126 + is_a: Illumina [GENEPIO:0100105] + Illumina NextSeq 500 [OBI:0002021]: + text: Illumina NextSeq 500 [OBI:0002021] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. + meaning: OBI:0002021 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 550 [GENEPIO:0100128]: + text: Illumina NextSeq 550 [GENEPIO:0100128] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. The 550 is an upgrade on the 500 model. + meaning: GENEPIO:0100128 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 1000 [GENEPIO:0004432]: + text: Illumina NextSeq 1000 [GENEPIO:0004432] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 + and P2 flow cells. + meaning: GENEPIO:0004432 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 2000 [GENEPIO:0100129]: + text: Illumina NextSeq 2000 [GENEPIO:0100129] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 30-360 Gb. + meaning: GENEPIO:0100129 + is_a: Illumina NextSeq [GENEPIO:0100126] + PacBio [GENEPIO:0100130]: + text: PacBio [GENEPIO:0100130] + description: A DNA sequencer manufactured by the Pacific Biosciences corporation. + meaning: GENEPIO:0100130 + PacBio RS [GENEPIO:0100131]: + text: PacBio RS [GENEPIO:0100131] + description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ + \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ + \ The RS was the first model made by the company." + meaning: GENEPIO:0100131 + is_a: PacBio [GENEPIO:0100130] + PacBio RS II [OBI:0002012]: + text: PacBio RS II [OBI:0002012] + description: A DNA sequencer which is manufactured by the Pacific Biosciences + corporation. Built upon single molecule real-time sequencing technology, + the machine is optimized for generation with long reads and high consensus + accuracy. + meaning: OBI:0002012 + is_a: PacBio [GENEPIO:0100130] + PacBio Sequel [GENEPIO:0100133]: + text: PacBio Sequel [GENEPIO:0100133] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation with long reads and high consensus + accuracy, and manufactured by the Pacific Biosciences corporation + meaning: GENEPIO:0100133 + is_a: PacBio [GENEPIO:0100130] + PacBio Sequel II [GENEPIO:0100134]: + text: PacBio Sequel II [GENEPIO:0100134] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation of highly accurate ("HiFi") long reads, + and which is manufactured by the Pacific Biosciences corporation. + meaning: GENEPIO:0100134 + is_a: PacBio [GENEPIO:0100130] + Ion Torrent [GENEPIO:0100135]: + text: Ion Torrent [GENEPIO:0100135] + description: A DNA sequencer manufactured by the Ion Torrent corporation. + meaning: GENEPIO:0100135 + Ion Torrent PGM [GENEPIO:0100136]: + text: Ion Torrent PGM [GENEPIO:0100136] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of 300 + MB - 1GB. + meaning: GENEPIO:0100136 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent Proton [GENEPIO:0100137]: + text: Ion Torrent Proton [GENEPIO:0100137] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of up to + 15 Gb. + meaning: GENEPIO:0100137 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent S5 XL [GENEPIO:0100138]: + text: Ion Torrent S5 XL [GENEPIO:0100138] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material while producing data faster than the S5 model. + meaning: GENEPIO:0100138 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent S5 [GENEPIO:0100139]: + text: Ion Torrent S5 [GENEPIO:0100139] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material. + meaning: GENEPIO:0100139 + is_a: Ion Torrent [GENEPIO:0100135] + Oxford Nanopore [GENEPIO:0100140]: + text: Oxford Nanopore [GENEPIO:0100140] + description: A DNA sequencer manufactured by the Oxford Nanopore corporation. + meaning: GENEPIO:0100140 + Oxford Nanopore Flongle [GENEPIO:0004433]: + text: Oxford Nanopore Flongle [GENEPIO:0004433] + description: An adapter for MinION or GridION DNA sequencers manufactured + by the Oxford Nanopore corporation that enables sequencing on smaller, single-use + flow cells. + meaning: GENEPIO:0004433 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore GridION [GENEPIO:0100141]: + text: Oxford Nanopore GridION [GENEPIO:0100141] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, that can run and analyze up to five individual flow cells producing + up to 150 Gb of data per run. The sequencer produces real-time results and + utilizes nanopore technology with the option of running the flow cells concurrently + or individual + meaning: GENEPIO:0100141 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore MinION [GENEPIO:0100142]: + text: Oxford Nanopore MinION [GENEPIO:0100142] + description: A portable DNA sequencer which is manufactured by the Oxford + Nanopore Technologies corporation, that uses consumable flow cells producing + up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time + results and utilizes nanopore technology with up to 512 nanopore channels + in the sensor array. + meaning: GENEPIO:0100142 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore PromethION [GENEPIO:0100143]: + text: Oxford Nanopore PromethION [GENEPIO:0100143] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, capable of running up to 48 flow cells and producing up to + 7.6 Tb of data per run. The sequencer produces real-time results and utilizes + Nanopore technology, with each flow cell allowing up to 3,000 nanopores + to be sequencing simultaneously. + meaning: GENEPIO:0100143 + is_a: Oxford Nanopore [GENEPIO:0100140] + BGI Genomics sequencing instrument [GENEPIO:0100144]: + text: BGI Genomics sequencing instrument [GENEPIO:0100144] + description: A DNA sequencer manufactured by the BGI Genomics corporation. + meaning: GENEPIO:0100144 + BGISEQ-500 [GENEPIO:0100145]: + text: BGISEQ-500 [GENEPIO:0100145] + description: A DNA sequencer manufactured by the BGI Genomics corporation + that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + meaning: GENEPIO:0100145 + is_a: BGI Genomics sequencing instrument [GENEPIO:0100144] + MGI sequencing instrument [GENEPIO:0100146]: + text: MGI sequencing instrument [GENEPIO:0100146] + description: A DNA sequencer manufactured by the MGI corporation. + meaning: GENEPIO:0100146 + MGISEQ-2000RS [GENEPIO:0100971]: + text: MGISEQ-2000RS [GENEPIO:0100971] + description: An MGI sequencing instrument model that utilises DNA nanoball + and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing + ad which is capable of medium to high throughput sequencing. + meaning: GENEPIO:0100971 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G99 [GENEPIO:0100972]: + text: MGI DNBSEQ-G99 [GENEPIO:0100972] + description: An MGI sequencing instrument model that utilises DNA nanoball + and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing + and which adopts triangular matrix signal spots on sequencing flow cell, + for low throughput at highspeeds. + meaning: GENEPIO:0100972 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G400 [GENEPIO:0100148]: + text: MGI DNBSEQ-G400 [GENEPIO:0100148] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB; 1440GB per run. + meaning: GENEPIO:0100148 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]: + text: MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB; 330GB per run, which enables faster sequencing than the + DNBSEQ-G400. + meaning: GENEPIO:0100149 + is_a: MGI DNBSEQ-G400 [GENEPIO:0100148] + MGI DNBSEQ-T7 [GENEPIO:0100147]: + text: MGI DNBSEQ-T7 [GENEPIO:0100147] + description: A high throughput DNA sequencer manufactured by the MGI corporation + with an output capacity of 1; 6TB of data per day. + meaning: GENEPIO:0100147 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-E25 [GENEPIO:0100973]: + text: MGI DNBSEQ-E25 [GENEPIO:0100973] + description: An MGI sequencing instrument model that is a compact and lightweight + standalone system which can bu used inside or outside the lab. + meaning: GENEPIO:0100973 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G50 [GENEPIO:0100150]: + text: MGI DNBSEQ-G50 [GENEPIO:0100150] + description: "A DNA sequencer manufactured by the MGI corporation with an\ + \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." + meaning: GENEPIO:0100150 + is_a: MGI sequencing instrument [GENEPIO:0100146] + 454 Genome Sequencer [GENEPIO:0001937]: + text: 454 Genome Sequencer [GENEPIO:0001937] + description: A DNA sequencer first manufactured by 454 Life Science Corporation + that conducts pyrosequencing. + meaning: GENEPIO:0001937 + 454 Genome Sequencer 20 [OBI:0000689]: + text: 454 Genome Sequencer 20 [OBI:0000689] + description: A DNA sequencer first manufactured by 454 Life Science Corporation + in 2005, and enables pyrosequencing to be performed. It comprises both optics + and fluidics subsystems, which are controlled by a computer subsystem. + meaning: OBI:0000689 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX [OBI:0000702]: + text: 454 Genome Sequencer FLX [OBI:0000702] + description: A DNA sequencer which was first manufactured by 454 Life Science + Corporation in 2008 and enables pyrosequencing to be performed. It comprises + both optics and fluidics subsystems, which are controlled by a computer + subsystem. It has the ability to sequence 400-600 million base pairs per + run with 400-500 base pair read lengths. + meaning: OBI:0000702 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX+ [GENEPIO:0100982]: + text: 454 Genome Sequencer FLX+ [GENEPIO:0100982] + description: A 454 Genome Sequencer that performs pyrosequencing and comprises + both optics and fluidics subsystems and can be used for longer reads when + used with the long-read Sequencing Kit XL+. + meaning: GENEPIO:0100982 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX Titanium [GENEPIO:0001936]: + text: 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] + description: A 454 Genome Sequencer that performs pyrosequencing and has enhanced + capacity and generates longer reads. + meaning: GENEPIO:0001936 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer Junior [GENEPIO:0001938]: + text: 454 Genome Sequencer Junior [GENEPIO:0001938] + description: A 454 Genome Sequencer that performs pyrosequencing and is more + compact. + meaning: GENEPIO:0001938 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + SOLiD System [OBI:0000696]: + text: SOLiD System [OBI:0000696] + description: A DNA sequencer which is manufactured by Applied Biosystems and + which enable DNA sequencing by ligation. + meaning: OBI:0000696 + SOLiD 5500 [GENEPIO:0001929]: + text: SOLiD 5500 [GENEPIO:0001929] + description: A DNA sequencer which is manufactured by Applied Biosystems and + utillizes sequencing by ligation technology and faster run times than the + SOLiD 4 series. + meaning: GENEPIO:0001929 + is_a: SOLiD System [OBI:0000696] + SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]: + text: SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] + description: A DNA sequencer which is manufactured by Applied Biosystems and + has two FlowChips for across 12 lanes and with a higher throughput than + the 5500 model. + meaning: GENEPIO:0001930 + is_a: SOLiD System [OBI:0000696] + SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]: + text: SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology and with a higher throughput + than SOLiD 5500xl Genetic Analyzer. + meaning: GENEPIO:0100984 + is_a: SOLiD System [OBI:0000696] + SOLiD 3 Plus System [OBI:0002007]: + text: SOLiD 3 Plus System [OBI:0002007] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology, the machine generates + greater than 1 billion mappable reads per run. + meaning: OBI:0002007 + is_a: SOLiD System [OBI:0000696] + SOLiD 4 System [OBI:0002024]: + text: SOLiD 4 System [OBI:0002024] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology with 100 Gb mappable + throughput. + meaning: OBI:0002024 + is_a: SOLiD System [OBI:0000696] + SOLiD 4hq System [GENEPIO:0001928]: + text: SOLiD 4hq System [GENEPIO:0001928] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology with 300 Gb mappable + throughput. + meaning: GENEPIO:0001928 + is_a: SOLiD System [OBI:0000696] + SOLiD PI System [GENEPIO:0001931]: + text: SOLiD PI System [GENEPIO:0001931] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology, the machine offers + 50Gb mappable throughput. + meaning: GENEPIO:0001931 + is_a: SOLiD System [OBI:0000696] + SOLiD System 2.0 [GENEPIO:0001932]: + text: SOLiD System 2.0 [GENEPIO:0001932] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. + meaning: GENEPIO:0001932 + is_a: SOLiD System [OBI:0000696] + SOLiD System 3.0 [GENEPIO:0001933]: + text: SOLiD System 3.0 [GENEPIO:0001933] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. + meaning: GENEPIO:0001933 + is_a: SOLiD System [OBI:0000696] + HeliScope Single Molecule Sequencer [OBI:0000717]: + text: HeliScope Single Molecule Sequencer [OBI:0000717] + description: A DNA sequencer manufacturer by Helicos Corporation to carry + out Single Molecule sequencing using reversible termination chemistry. + meaning: OBI:0000717 + Applied Biosystems sequencing instrument model [GENEPIO:0100974]: + text: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + description: A sequencing instrument model that is manufactured by Applied + Biosystems and which performs Sanger sequencing and fragment analysis by + capillary electrophoresis. + meaning: GENEPIO:0100974 + AB 310 Genetic Analyzer [GENEPIO:0100975]: + text: AB 310 Genetic Analyzer [GENEPIO:0100975] + description: An Applied Biosystems sequencing instrument model which utilises + a single capillary electrophoresis system to perform Sanger sequencing and + fragment analysis that is automated. + meaning: GENEPIO:0100975 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3130 Genetic Analyzer [GENEPIO:0100976]: + text: AB 3130 Genetic Analyzer [GENEPIO:0100976] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 4 capillaries. + meaning: GENEPIO:0100976 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3130xL Genetic Analyzer [GENEPIO:0100977]: + text: AB 3130xL Genetic Analyzer [GENEPIO:0100977] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 16 capillaries. + meaning: GENEPIO:0100977 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3500 Genetic Analyzer [GENEPIO:0100978]: + text: AB 3500 Genetic Analyzer [GENEPIO:0100978] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 8 capillaries, which can + run 96 well plates. + meaning: GENEPIO:0100978 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3500xL Genetic Analyzer [GENEPIO:0100979]: + text: AB 3500xL Genetic Analyzer [GENEPIO:0100979] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 24 capillaries, which + can run 384 well plates. + meaning: GENEPIO:0100979 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3730 Genetic Analyzer [GENEPIO:0100980]: + text: AB 3730 Genetic Analyzer [GENEPIO:0100980] + description: An Applied Biosystems sequencing instrument model which utilises + an 48 capillary array electrophoresis system for sequencing. + meaning: GENEPIO:0100980 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3730xL Genetic Analyzer [GENEPIO:0100981]: + text: AB 3730xL Genetic Analyzer [GENEPIO:0100981] + description: An Applied Biosystems sequencing instrument model which utilises + an 96 capillary array electrophoresis system for sequencing. + meaning: GENEPIO:0100981 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + GenomicTargetEnrichmentMethodMenu: + name: GenomicTargetEnrichmentMethodMenu + title: genomic_target_enrichment_method menu + permissible_values: + Hybrid selection method (bait-capture) [GENEPIO:0001950]: + text: Hybrid selection method (bait-capture) [GENEPIO:0001950] + description: Selection by hybridization in array or solution. + meaning: GENEPIO:0001950 + rRNA depletion method [GENEPIO:0101020]: + text: rRNA depletion method [GENEPIO:0101020] + description: Removal of background RNA for the purposes of enriching the genomic + target. + meaning: GENEPIO:0101020 + QualityControlDeterminationMenu: + name: QualityControlDeterminationMenu + title: quality_control_determination menu + permissible_values: + No quality control issues identified [GENEPIO:0100562]: + text: No quality control issues identified [GENEPIO:0100562] + description: A statement confirming that quality control processes were carried + out and no quality issues were detected. + meaning: GENEPIO:0100562 + Sequence passed quality control [GENEPIO:0100563]: + text: Sequence passed quality control [GENEPIO:0100563] + description: A statement confirming that quality control processes were carried + out and that the sequence met the assessment criteria. + meaning: GENEPIO:0100563 + Sequence failed quality control [GENEPIO:0100564]: + text: Sequence failed quality control [GENEPIO:0100564] + description: A statement confirming that quality control processes were carried + out and that the sequence did not meet the assessment criteria. + meaning: GENEPIO:0100564 + Minor quality control issues identified [GENEPIO:0100565]: + text: Minor quality control issues identified [GENEPIO:0100565] + description: A statement confirming that quality control processes were carried + out and that the sequence did not meet the assessment criteria, however + the issues detected were minor. + meaning: GENEPIO:0100565 + Sequence flagged for potential quality control issues [GENEPIO:0100566]: + text: Sequence flagged for potential quality control issues [GENEPIO:0100566] + description: A statement confirming that quality control processes were carried + out however it is unclear whether the sequence meets the assessment criteria + and the assessment requires review. + meaning: GENEPIO:0100566 + Quality control not performed [GENEPIO:0100567]: + text: Quality control not performed [GENEPIO:0100567] + description: A statement confirming that quality control processes have not + been carried out. + meaning: GENEPIO:0100567 + QualityControlIssuesMenu: + name: QualityControlIssuesMenu + title: quality_control_issues menu + permissible_values: + Low quality sequence [GENEPIO:0100568]: + text: Low quality sequence [GENEPIO:0100568] + description: Sequence data that does not meet quality control thresholds. + meaning: GENEPIO:0100568 + Sequence contaminated [GENEPIO:0100569]: + text: Sequence contaminated [GENEPIO:0100569] + description: Sequence data that contains reads from unintended targets (e.g. + other organisms, other samples) due to contamination so that it does not + faithfully represent the genetic information from the biological source. + meaning: GENEPIO:0100569 + Low average genome coverage [GENEPIO:0100570]: + text: Low average genome coverage [GENEPIO:0100570] + description: Sequence data in which the entire length of the genome is not + sufficiently sequenced (low breadth of coverage), or particular positions + of the genome are not sequenced a prescribed number of times (low depth + of coverage). + meaning: GENEPIO:0100570 + Low percent genome captured [GENEPIO:0100571]: + text: Low percent genome captured [GENEPIO:0100571] + description: Sequence data in which the entire length of the genome is not + sufficiently sequenced (low breadth of coverage). + meaning: GENEPIO:0100571 + Read lengths shorter than expected [GENEPIO:0100572]: + text: Read lengths shorter than expected [GENEPIO:0100572] + description: Average sequence read lengths that are below the expected size + range given a particular sequencing instrument, reagents and conditions. + meaning: GENEPIO:0100572 + Sequence amplification artifacts [GENEPIO:0100573]: + text: Sequence amplification artifacts [GENEPIO:0100573] + description: Sequence data containing errors generated during the PCR amplification + process during library generation (e.g. mutations, altered read distribution, + amplicon dropouts). + meaning: GENEPIO:0100573 + Low signal to noise ratio [GENEPIO:0100574]: + text: Low signal to noise ratio [GENEPIO:0100574] + description: Sequence data containing more errors or undetermined bases (noise) + than sequence representing the biological source (signal). + meaning: GENEPIO:0100574 + Low coverage of characteristic mutations [GENEPIO:0100575]: + text: Low coverage of characteristic mutations [GENEPIO:0100575] + description: Sequence data that contains a lower than expected number of mutations + that are usually observed in the reference sequence. + meaning: GENEPIO:0100575 + DiagnosticTargetPresenceMenu: + name: DiagnosticTargetPresenceMenu + title: diagnostic target presence menu + permissible_values: + diagnostic target present [GENEPIO:0100987]: + text: diagnostic target present [GENEPIO:0100987] + description: A quality inhering in a bearer by virtue of the bearer's existence. + meaning: GENEPIO:0100987 + diagnostic target absent [GENEPIO:0100988]: + text: diagnostic target absent [GENEPIO:0100988] + description: Aquality denoting the lack of an entity. + meaning: GENEPIO:0100988 + DiagnosticMeasurementUnitMenu: + name: DiagnosticMeasurementUnitMenu + title: diagnostic measurement unit menu + permissible_values: + gene copies per liter (GC/L): + text: gene copies per liter (GC/L) + description: A unit that measures the number of copies of a given gene within + a liter of a biological material. + cycle threshold (Ct) [GENEPIO:0100657]: + text: cycle threshold (Ct) [GENEPIO:0100657] + description: A data field which describes the cycle threshold (Ct) value result + from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) + test. + meaning: GENEPIO:0100657 + colony forming units per milliliter (CFU/mL) [UO:0000213]: + text: colony forming units per milliliter (CFU/mL) [UO:0000213] + description: A unit of microbial density that describes the number of colony + forming units within a milliliter of material. + meaning: UO:0000213 + colony forming units per 100 milliliter (CFU/100 mL): + text: colony forming units per 100 milliliter (CFU/100 mL) + description: A unit of microbial density that describes the number of colony + forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS): + text: colony forming units per grams total solids (CFU/gTS) + description: A unit of microbial density that describes the number of colony + forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL): + text: most probable number per milliliter (MPN/mL) + description: A unit of microbial density that describes the most probable + number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL): + text: most probable number per 100 milliliter (MPN/100 mL) + description: A unit of microbial density that describes the most probable + number of microbes within 100 milliliters of material. + DiagnosticMeasurementMethodMenu: + name: DiagnosticMeasurementMethodMenu + title: diagnostic measurement method menu + permissible_values: + Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]: + text: Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] + description: An assay, based on the PCR, that amplifies and simultaneously + quantifies a specific DNA molecule based on the use of complementary probes/primers. + It enables both detection and quantification (as absolute number of copies + or relative amount when normalized to DNA input or additional normalizing + genes) of one or more specific sequences in a DNA sample. + meaning: OBI:0000893 + Digital real time polymerase chain reaction (dPCR): + text: Digital real time polymerase chain reaction (dPCR) + description: A type of polymerase chain reaction technique in which the sample + is fractionated, within which individual PCR reactions occur in each fraction + Bacteria culture test: + text: Bacteria culture test + description: An assay to identify the presence of bacteria + ExperimentalInterventionMenu: + name: ExperimentalInterventionMenu + title: experimental_intervention menu + permissible_values: + Addition of substances to food/water [GENEPIO:0100536]: + text: Addition of substances to food/water [GENEPIO:0100536] + description: The addition of substances to food or water administered to an + individual or group of individuals. + meaning: GENEPIO:0100536 + Antimicrobial pre-treatment [GENEPIO:0100537]: + text: Antimicrobial pre-treatment [GENEPIO:0100537] + description: The administration of an antimicrobial agent to an individual + or its addition to a substance prior to some other event or activity. + meaning: GENEPIO:0100537 + Certified animal husbandry practices [GENEPIO:0100538]: + text: Certified animal husbandry practices [GENEPIO:0100538] + description: The implementation of animal husbandy practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100538 + Certified organic farming practices [GENEPIO:0100539]: + text: Certified organic farming practices [GENEPIO:0100539] + description: The implementation of organic farming practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100539 + Change in storage conditions [GENEPIO:0100540]: + text: Change in storage conditions [GENEPIO:0100540] + description: A change in the storage conditions of a material or a substance. + meaning: GENEPIO:0100540 + Cleaning/disinfection [GENEPIO:0100541]: + text: Cleaning/disinfection [GENEPIO:0100541] + description: A process of removing unwanted substances, such as dirt, infectious + agents, and other impurities, from an object or environment. + meaning: GENEPIO:0100541 + Extended downtime between activities [GENEPIO:0100542]: + text: Extended downtime between activities [GENEPIO:0100542] + description: A prolonged period of inactivity between processes or events. + meaning: GENEPIO:0100542 + Fertilizer pre-treatment [GENEPIO:0100543]: + text: Fertilizer pre-treatment [GENEPIO:0100543] + description: The addition of fertilizer to a material or environment prior + to some other event or activity. + meaning: GENEPIO:0100543 + Logistic slaughter [GENEPIO:0100545]: + text: Logistic slaughter [GENEPIO:0100545] + description: The logistical planning of events and processes upstream of the + immediate slaughter of an animal (which may include controlling transport + climate; traffic conditions, number of pick-up farms, as well as time and + distance during transport; queuing at the abattoir etc) that optimize operations + and reduce stress on the animal. + meaning: GENEPIO:0100545 + Microbial pre-treatment [GENEPIO:0100546]: + text: Microbial pre-treatment [GENEPIO:0100546] + description: The deliberate addition of microbes or a mixture of microbes + to an individual or substance prior to some other event or activity. + meaning: GENEPIO:0100546 + Probiotic pre-treatment [GENEPIO:0100547]: + text: Probiotic pre-treatment [GENEPIO:0100547] + description: The addition of a probiotic substance to an individual or material + prior to some other event or activity. + meaning: GENEPIO:0100547 + Vaccination [NCIT:C15346]: + text: Vaccination [NCIT:C15346] + description: Administration of vaccines to stimulate the host's immune response. + This includes any preparation intended for active immunological prophylaxis + or treatment. + meaning: NCIT:C15346 AirPressureMeasurementUnitMenu: name: AirPressureMeasurementUnitMenu title: air_pressure_measurement_unit menu @@ -12414,46 +13272,96 @@ enums: permissible_values: cubic meter per second (m^3/s): text: cubic meter per second (m^3/s) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one second. cubic meter per minute (m^3/min): text: cubic meter per minute (m^3/min) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one minute. cubic meter per hour (m^3/h): text: cubic meter per hour (m^3/h) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one hour. liter per second (L/s): text: liter per second (L/s) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one second. liter per minute (L/min): text: liter per minute (L/min) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one minute. liter per hour (L/h): text: liter per hour (L/h) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one hour. liter per day (L/day): text: liter per day (L/day) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one day. million gallons per day (MGD): text: million gallons per day (MGD) + description: A volumetric flow rate unit which is the measure of the volume + of one million gallons of matter crosses a given surface during the period + of time equal to one day. InstantaneousFlowRateMeasurementUnitMenu: name: InstantaneousFlowRateMeasurementUnitMenu title: instantaneous_flow_rate_measurement_unit menu permissible_values: cubic meter per second (m^3/s): text: cubic meter per second (m^3/s) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one second. cubic meter per minute (m^3/min): text: cubic meter per minute (m^3/min) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one minute. cubic meter per hour (m^3/h): text: cubic meter per hour (m^3/h) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one hour. liter per second (L/s): text: liter per second (L/s) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one second. liter per minute (L/min): text: liter per minute (L/min) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one minute. liter per hour (L/h): text: liter per hour (L/h) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one hour. liter per day (L/day): text: liter per day (L/day) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one day. million gallons per day (MGD): text: million gallons per day (MGD) + description: A volumetric flow rate unit which is the measure of the volume + of one million gallons of matter crosses a given surface during the period + of time equal to one day. TurbidityMeasurementUnitMenu: name: TurbidityMeasurementUnitMenu title: turbidity_measurement_unit menu permissible_values: nephelometric turbidity unit (NTU): text: nephelometric turbidity unit (NTU) + description: A measure of turbidity calculated by using a nephelometer to + compare how white light is scattered in a water sample. formazin nephelometric unit (FNU) [UO:0000318]: text: formazin nephelometric unit (FNU) [UO:0000318] description: A measure of turbidity calculated by comparing how infrared light @@ -12551,6 +13459,8 @@ enums: permissible_values: milliequivalent per liter (meq/L): text: milliequivalent per liter (meq/L) + description: A unit of ion concentration that represents chemical activity + per volume. milligram per liter (mg/L) [UO:0000273]: text: milligram per liter (mg/L) [UO:0000273] description: A non-SI unit of density that is equivalent to the SI metric @@ -12567,18 +13477,27 @@ enums: permissible_values: milliSiemen per centimeter (mS/cm): text: milliSiemen per centimeter (mS/cm) + description: A non-SI unit of electrical conductivity that is equivalent to + one tenth of a Siemen per meter (S/m). "microSiemen per centimeter (\u03BCS/cm)": text: "microSiemen per centimeter (\u03BCS/cm)" + description: A non-SI unit of electrical conductivity that is equivalent to + one ten thousandth of a Siemen per meter (S/m). Siemen per meter (S/m): text: Siemen per meter (S/m) + description: An SI unit of electrical conductivity that is equivalent to an + ampere per volt per meter (A/v/m). SalinityMeasurementUnitMenu: name: SalinityMeasurementUnitMenu title: salinity_measurement_unit menu permissible_values: practical salinity unit (PSU): text: practical salinity unit (PSU) + description: A unitless measure of salinity that is equivalent to per thousand. weight for weight (% w/w): text: weight for weight (% w/w) + description: A unitless comparison based on weight rather than volume, which + is equivalent to per hundred. parts per thousand [UO:0000168]: text: parts per thousand [UO:0000168] description: A dimensionless concentration notation which denotes the amount @@ -12606,12 +13525,16 @@ enums: meaning: UO:0000175 gram per total solids (g/gTS): text: gram per total solids (g/gTS) + description: A unitless comparison of the weight of a substance as a proportion + to the weight of total solids. TotalPhosphorpusTpMeasurementUnitMenu: name: TotalPhosphorpusTpMeasurementUnitMenu title: total_phosphorpus_(TP)_measurement_unit menu permissible_values: gram per total solids (g/gTS): text: gram per total solids (g/gTS) + description: A unitless comparison of the weight of a substance as a proportion + to the weight of total solids. orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]: text: orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] description: A substance unit which describes the weight of orthophosphate @@ -12665,8 +13588,12 @@ enums: permissible_values: log10 gene copies per 100 milliliter (log10 GC/100 mL): text: log10 gene copies per 100 milliliter (log10 GC/100 mL) + description: A unit that expresses on a logarithmic scale the number of copies + of a given gene within one hundred milliliters of a biological material. gene copies per liter (GC/L): text: gene copies per liter (GC/L) + description: A unit that measures the number of copies of a given gene within + a liter of a biological material. PCR quantification cycle [UO:0010077]: text: PCR quantification cycle [UO:0010077] description: A count unit of how many Polymerase Chain Reaction (PCR) cycles @@ -12675,6 +13602,8 @@ enums: meaning: UO:0010077 log10 gene copies per nanogram total DNA: text: log10 gene copies per nanogram total DNA + description: A unit that expresses on a logarithmic scale the number of copies + within a nanogram of deoxyribonucleic acid genetic material. UrinaryContaminationIndicatorMenu: name: UrinaryContaminationIndicatorMenu title: urinary_contamination_indicator menu @@ -12704,12 +13633,20 @@ enums: meaning: UO:0000213 colony forming units per 100 milliliter (CFU/100 mL): text: colony forming units per 100 milliliter (CFU/100 mL) + description: A unit of microbial density that describes the number of colony + forming units within 100 milliliters of material. colony forming units per grams total solids (CFU/gTS): text: colony forming units per grams total solids (CFU/gTS) + description: A unit of microbial density that describes the number of colony + forming units within a gram of total solids in waste material. most probable number per milliliter (MPN/mL): text: most probable number per milliliter (MPN/mL) + description: A unit of microbial density that describes the most probable + number of microbes within one milliliter of material. most probable number per 100 milliliter (MPN/100 mL): text: most probable number per 100 milliliter (MPN/100 mL) + description: A unit of microbial density that describes the most probable + number of microbes within 100 milliliters of material. SampleTemperatureUnitAtCollectionMenu: name: SampleTemperatureUnitAtCollectionMenu title: sample_temperature_unit_(at collection) menu diff --git a/web/templates/hpai/schema_enums.tsv b/web/templates/hpai/schema_enums.tsv index f742904b..fc1d4d9d 100644 --- a/web/templates/hpai/schema_enums.tsv +++ b/web/templates/hpai/schema_enums.tsv @@ -427,7 +427,7 @@ residual_sample_status menu ResidualSampleStatusMenu GENEPIO:0101087 Residual sa GENEPIO:0101089 Residual sample status unkown [GENEPIO:0101089] -purpose of sampling PurposeOfSampling GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. GENEPIO:0100002 Diagnostic testing [GENEPIO:0100002] A sampling strategy in which individuals are sampled in the context of diagnostic testing. GENEPIO:0100548 Environmental testing [GENEPIO:0100548] A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena. GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. @@ -436,7 +436,7 @@ purpose of sampling PurposeOfSampling GENEPIO:0100001 Cluster/Outbreak investiga GENEPIO:0100582 Survey study [GENEPIO:0100582] A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes. GENEPIO:0100004 Surveillance [GENEPIO:0100004] A sampling strategy in which individuals are sampled for surveillance investigations. -presampling activity PresamplingActivity GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. +presampling activity menu PresamplingActivityMenu GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. GENEPIO:0100537 Antimicrobial pre-treatment [GENEPIO:0100537] The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity. GENEPIO:0100538 Certified animal husbandry practices [GENEPIO:0100538] The implementation of animal husbandy practices that have been certified by an authorized organization. GENEPIO:0100894 Certified humane animal husbandry practices [GENEPIO:0100894] A certification organization in Washington DC that is dedicated to improving the lives of farm animals in food production from birth through slaughter. @@ -449,7 +449,7 @@ presampling activity PresamplingActivity GENEPIO:0100536 Addition of substances GENEPIO:0100547 Probiotic pre-treatment [GENEPIO:0100547] The addition of a probiotic substance to an individual or material prior to some other event or activity. NCIT:C15346 Vaccination [NCIT:C15346] Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. -sample storage duration unit SampleStorageDurationUnit UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. +sample storage duration unit menu SampleStorageDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. @@ -457,12 +457,12 @@ sample storage duration unit SampleStorageDurationUnit UO:0000010 Second [UO:000 UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. -specimen processing SpecimenProcessing OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. +specimen processing menu SpecimenProcessingMenu OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. -experimental specimen role type ExperimentalSpecimenRoleType GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. +experimental specimen role type menu ExperimentalSpecimenRoleTypeMenu GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. GENEPIO:0101123 Validation strain [GENEPIO:0101123] GENEPIO:0101124 Proficiency test isolate [GENEPIO:0101124] GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment @@ -635,7 +635,7 @@ host_age_bin menu HostAgeBinMenu GENEPIO:0100684 First winter [GENEPIO:0100684] GENEPIO:0100058 90 - 99 [GENEPIO:0100058] An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). GENEPIO:0100059 100+ [GENEPIO:0100059] An age group that stratifies the age of a case to be greater than or equal to 100 years old. -host_gender HostGender NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. +host_gender menu HostGenderMenu NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. NCIT:C46109 Male [NCIT:C46109] An individual who reports belonging to the cultural gender role distinction of male. GSSO:000132 Non-binary gender [GSSO:000132] Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. GSSO:004004 Transgender (assigned male at birth) [GSSO:004004] Having a feminine gender (identity) which is different from the sex one was assigned at birth. @@ -997,13 +997,13 @@ host_vaccination_status menu HostVaccinationStatusMenu GENEPIO:0100100 Fully Vac influenza_antiviral_treatment_administration menu InfluenzaAntiviralTreatmentAdministrationMenu GENEPIO:0101194 Influenza antiviral treatment administered [GENEPIO:0101194] GENEPIO:0101195 No influenza antiviral treatment administered [GENEPIO:0101195] -water_catchment_area_human_population_range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people - 10 - 100 people - 100 - 1,000 people - 1,000 - 10,000 people - 10,000 - 100,000 people - 100,000 - 1,000,000 people - 1,000,000+ people +water_catchment_area_human_population_range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people An estimation of population size for a group smaller than 10 people. + 10 - 100 people An estimation of population size for a group smaller than 100 people and larger than 10 people. + 100 - 1,000 people An estimation of population size for a group smaller than 1,000 people and larger than 100 people. + 1,000 - 10,000 people An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people. + 10,000 - 100,000 people An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people. + 100,000 - 1,000,000 people An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people. + 1,000,000+ people An estimation of population size for a group larger than 1,000,000 people. water_catchment_area_human_population_density_unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. @@ -1038,6 +1038,161 @@ precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu UO:0000016 UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. +water_depth_units menu WaterDepthUnitsMenu UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010066 kilometer (km) [UO:0010066] A length unit which is equal to one thousand meters. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +sediment_depth_units menu SedimentDepthUnitsMenu UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010066 kilometer (km) [UO:0010066] A length unit which is equal to one thousand meters. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +air_temperature_units menu AirTemperatureUnitsMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +water_temperature_units menu WaterTemperatureUnitsMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sequencing_platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. + GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. + GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. + GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. + GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. + GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. + GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. + GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. + GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. + GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). + GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. + + +sequencing_instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. + GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. + OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. + GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. + OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. + GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. + GENEPIO:0100972 MGI DNBSEQ-G99 [GENEPIO:0100972] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds. + GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. + GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. + GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. + GENEPIO:0100973 MGI DNBSEQ-E25 [GENEPIO:0100973] An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab. + GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. + OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. + OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. + GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. + GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. + OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. + GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. + GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. + GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. + OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. + GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. + GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. + GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. + GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. + GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. + GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. + GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. + GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. + GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. + GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. + GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. + +genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybrid selection method (bait-capture) [GENEPIO:0001950] Selection by hybridization in array or solution. + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. + +quality_control_determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. + +quality_control_issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. + +diagnostic target presence menu DiagnosticTargetPresenceMenu GENEPIO:0100987 diagnostic target present [GENEPIO:0100987] A quality inhering in a bearer by virtue of the bearer's existence. + GENEPIO:0100988 diagnostic target absent [GENEPIO:0100988] Aquality denoting the lack of an entity. + +diagnostic measurement unit menu DiagnosticMeasurementUnitMenu gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. + GENEPIO:0100657 cycle threshold (Ct) [GENEPIO:0100657] A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. + UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. + +diagnostic measurement method menu DiagnosticMeasurementMethodMenu OBI:0000893 Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + Digital real time polymerase chain reaction (dPCR) A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction + Bacteria culture test An assay to identify the presence of bacteria + +experimental_intervention menu ExperimentalInterventionMenu GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. + GENEPIO:0100537 Antimicrobial pre-treatment [GENEPIO:0100537] The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity. + GENEPIO:0100538 Certified animal husbandry practices [GENEPIO:0100538] The implementation of animal husbandy practices that have been certified by an authorized organization. + GENEPIO:0100539 Certified organic farming practices [GENEPIO:0100539] The implementation of organic farming practices that have been certified by an authorized organization. + GENEPIO:0100540 Change in storage conditions [GENEPIO:0100540] A change in the storage conditions of a material or a substance. + GENEPIO:0100541 Cleaning/disinfection [GENEPIO:0100541] A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment. + GENEPIO:0100542 Extended downtime between activities [GENEPIO:0100542] A prolonged period of inactivity between processes or events. + GENEPIO:0100543 Fertilizer pre-treatment [GENEPIO:0100543] The addition of fertilizer to a material or environment prior to some other event or activity. + GENEPIO:0100545 Logistic slaughter [GENEPIO:0100545] The logistical planning of events and processes upstream of the immediate slaughter of an animal (which may include controlling transport climate; traffic conditions, number of pick-up farms, as well as time and distance during transport; queuing at the abattoir etc) that optimize operations and reduce stress on the animal. + GENEPIO:0100546 Microbial pre-treatment [GENEPIO:0100546] The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity. + GENEPIO:0100547 Probiotic pre-treatment [GENEPIO:0100547] The addition of a probiotic substance to an individual or material prior to some other event or activity. + NCIT:C15346 Vaccination [NCIT:C15346] Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. + air_pressure_measurement_unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). bar UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). @@ -1045,25 +1200,25 @@ air_pressure_measurement_unit menu AirPressureMeasurementUnitMenu EFO:0005212 at ambient_temperature_measurement_unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. -total_daily_flow_rate_measurement_unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) - cubic meter per minute (m^3/min) - cubic meter per hour (m^3/h) - liter per second (L/s) - liter per minute (L/min) - liter per hour (L/h) - liter per day (L/day) - million gallons per day (MGD) - -instantaneous_flow_rate_measurement_unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) - cubic meter per minute (m^3/min) - cubic meter per hour (m^3/h) - liter per second (L/s) - liter per minute (L/min) - liter per hour (L/h) - liter per day (L/day) - million gallons per day (MGD) - -turbidity_measurement_unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) +total_daily_flow_rate_measurement_unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +instantaneous_flow_rate_measurement_unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +turbidity_measurement_unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample. UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. dissolved_oxygen_measurement_unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. @@ -1085,24 +1240,24 @@ total_dissolved_solids_(TDS)_measurement_unit menu TotalDissolvedSolidsTdsMeasur total_solids_(TS)_measurement_unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. -alkalinity_measurement_unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) +alkalinity_measurement_unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) A unit of ion concentration that represents chemical activity per volume. UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. -conductivity_measurement_unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) - microSiemen per centimeter (μS/cm) - Siemen per meter (S/m) +conductivity_measurement_unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m). + microSiemen per centimeter (μS/cm) A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m). + Siemen per meter (S/m) An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m). -salinity_measurement_unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) - weight for weight (% w/w) +salinity_measurement_unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) A unitless measure of salinity that is equivalent to per thousand. + weight for weight (% w/w) A unitless comparison based on weight rather than volume, which is equivalent to per hundred. UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. total_nitrogen_(TN)_measurement_unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - gram per total solids (g/gTS) + gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. -total_phosphorpus_(TP)_measurement_unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) +total_phosphorpus_(TP)_measurement_unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. @@ -1114,20 +1269,20 @@ fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:121 GENEPIO:0101002 F+ (male specific) coliphages A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. CHEBI:26756 Stercobilin Bile pigment found in fecal material. -fecal_contamination_unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) - gene copies per liter (GC/L) +fecal_contamination_unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material. + gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. - log10 gene copies per nanogram total DNA + log10 gene copies per nanogram total DNA A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material. urinary_contamination_indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. urinary_contamination_unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. fecal_coliform_count_unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. - colony forming units per 100 milliliter (CFU/100 mL) - colony forming units per grams total solids (CFU/gTS) - most probable number per milliliter (MPN/mL) - most probable number per 100 milliliter (MPN/100 mL) + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. sample_temperature_unit_(at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv index 334908f3..1d311bf3 100644 --- a/web/templates/hpai/schema_slots.tsv +++ b/web/templates/hpai/schema_slots.tsv @@ -22,7 +22,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPI HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100309 geo_loc_latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100310 geo_loc_longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype InfluenzaSubsubtypeMenu TRUE TRUE +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype InfluenzaSubtypeMenu TRUE TRUE HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101109 influenza_subtyping_scheme_name influenza_subtyping_scheme_name InfluenzaSubtypingSchemeNameMenu HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101110 virus_identifier virus_identifier WhitespaceMinimizedString @@ -68,16 +68,16 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPI HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria HPAI;HPAIHost GENEPIO:0001268 Host information -HPAI;HPAIHost Host information GENEPIO:0001386 host_(common_name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host -HPAI;HPAIHost Host information GENEPIO:0001387 host_(scientific_name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host -HPAI;HPAIHost Host information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety -HPAI;HPAIHost Host information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed -HPAI;HPAIHost Host information GENEPIO:0100452 host_(food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host +HPAI;HPAIHost Host Information GENEPIO:0001386 host_(common_name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host +HPAI;HPAIHost Host Information GENEPIO:0001387 host_(scientific_name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host +HPAI;HPAIHost Host Information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety +HPAI;HPAIHost Host Information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed +HPAI;HPAIHost Host Information GENEPIO:0100452 host_(food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host HPAI;HPAIHost Host Information GENEPIO:0001392 host_age host_age decimal NullValueMenu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age HPAI;HPAIHost Host Information GENEPIO:0001393 host_age_unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] -HPAI;HPAIHost Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age - host_gender host_gender -HPAI;HPAIHost Host information GENEPIO:0001391 host_disease host_disease HostDiseaseMenu NullValueMenu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease +HPAI;HPAIHost Host Information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host Information host_gender host_gender +HPAI;HPAIHost Host Information GENEPIO:0001391 host_disease host_disease HostDiseaseMenu NullValueMenu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease HPAI;HPAIHost Host Information GENEPIO:0001388 host_health_state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome @@ -115,10 +115,9 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100774 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100775 water_catchment_area_human_population_measurement_method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type populated area type menu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 @@ -127,7 +126,7 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100441 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type WeatherTypeMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 @@ -177,7 +176,7 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100808 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTNMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorusTPMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorpusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator_ FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 @@ -206,9 +205,9 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100471 se HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001165 sequence_submitter_contact_email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] @@ -277,7 +276,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:010 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0100478 Risk assessment information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production WhitespaceMinimizedString NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed \ No newline at end of file diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 64044c3a..a9115c15 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -1573,6 +1573,11 @@ "meaning": "GENEPIO:0100031", "is_a": "Filtration" }, + "Finger Prick": { + "text": "Finger Prick", + "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.", + "meaning": "GENEPIO:0100036" + }, "Lavage": { "text": "Lavage", "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid", @@ -1626,12 +1631,6 @@ "description": "The process of collecting specimen material using a swab collection device.", "meaning": "GENEPIO:0002117" }, - "Finger Prick": { - "text": "Finger Prick", - "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.", - "meaning": "GENEPIO:0100036", - "is_a": "Swabbing" - }, "Thoracentesis (chest tap)": { "text": "Thoracentesis (chest tap)", "description": "The removal of excess fluid via needle puncture from the thoracic cavity.", @@ -14465,7 +14464,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionMenu" + "range": "PriorMpoxInfectionMenu" }, { "range": "NullValueMenu" @@ -14491,7 +14490,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentMenu" + "range": "PriorMpoxAntiviralTreatmentMenu" }, { "range": "NullValueMenu" @@ -17261,7 +17260,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionMenu" + "range": "PriorMpoxInfectionMenu" }, { "range": "NullValueMenu" @@ -17329,7 +17328,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentMenu" + "range": "PriorMpoxAntiviralTreatmentMenu" }, { "range": "NullValueMenu" @@ -20256,7 +20255,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionInternationalMenu" + "range": "PriorMpoxInfectionInternationalMenu" }, { "range": "NullValueMenu" @@ -20279,7 +20278,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu" + "range": "PriorMpoxAntiviralTreatmentInternationalMenu" }, { "range": "NullValueMenu" @@ -23066,7 +23065,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionInternationalMenu" + "range": "PriorMpoxInfectionInternationalMenu" }, { "range": "NullValueMenu" @@ -23131,7 +23130,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu" + "range": "PriorMpoxAntiviralTreatmentInternationalMenu" }, { "range": "NullValueMenu" diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 4d3a318e..f9d2e8e3 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -591,7 +591,7 @@ classes: examples: - value: Prior infection any_of: - - range: PriorMonkeypoxInfectionMenu + - range: PriorMpoxInfectionMenu - range: NullValueMenu exact_mappings: - NML_LIMS:prior%20Monkeypox%20infection @@ -604,7 +604,7 @@ classes: examples: - value: Prior antiviral treatment any_of: - - range: PriorMonkeypoxAntiviralTreatmentMenu + - range: PriorMpoxAntiviralTreatmentMenu - range: NullValueMenu exact_mappings: - NML_LIMS:prior%20Monkeypox%20antiviral%20treatment @@ -1476,7 +1476,7 @@ classes: examples: - value: Prior infection [GENEPIO:0100037] any_of: - - range: PriorMonkeypoxInfectionInternationalMenu + - range: PriorMpoxInfectionInternationalMenu - range: NullValueMenu prior_mpox_infection_date: rank: 70 @@ -1487,7 +1487,7 @@ classes: examples: - value: Prior antiviral treatment [GENEPIO:0100037] any_of: - - range: PriorMonkeypoxAntiviralTreatmentInternationalMenu + - range: PriorMpoxAntiviralTreatmentInternationalMenu - range: NullValueMenu prior_antiviral_treatment_during_prior_mpox_infection: rank: 72 @@ -5293,6 +5293,12 @@ enums: air via an air filtration device. meaning: GENEPIO:0100031 is_a: Filtration + Finger Prick: + text: Finger Prick + description: A collecting specimen from organism process in which a skin site + free of surface arterial flow is pierced with a sterile lancet, after a + capillary blood droplet is formed a sample is captured in a capillary tupe. + meaning: GENEPIO:0100036 Lavage: text: Lavage description: A protocol application to separate cells and/or cellular secretions @@ -5348,13 +5354,6 @@ enums: description: The process of collecting specimen material using a swab collection device. meaning: GENEPIO:0002117 - Finger Prick: - text: Finger Prick - description: A collecting specimen from organism process in which a skin site - free of surface arterial flow is pierced with a sterile lancet, after a - capillary blood droplet is formed a sample is captured in a capillary tupe. - meaning: GENEPIO:0100036 - is_a: Swabbing Thoracentesis (chest tap): text: Thoracentesis (chest tap) description: The removal of excess fluid via needle puncture from the thoracic diff --git a/web/templates/mpox/schema_enums.tsv b/web/templates/mpox/schema_enums.tsv index 06cb850b..794fcfed 100644 --- a/web/templates/mpox/schema_enums.tsv +++ b/web/templates/mpox/schema_enums.tsv @@ -241,6 +241,7 @@ collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis A pren OBI:0002651 Needle Biopsy A biopsy that uses a hollow needle to extract cells. OBI:0302885 Filtration Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device GENEPIO:0100031 Air filtration A filtration process which removes solid particulates from the air via an air filtration device. + GENEPIO:0100036 Finger Prick A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. OBI:0600044 Lavage A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid GENEPIO:0100032 Bronchoalveolar lavage (BAL) The collection of bronchoalveolar lavage fluid (BAL) from the lungs. GENEPIO:0100033 Gastric Lavage The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. @@ -251,7 +252,6 @@ collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis A pren GENEPIO:0100034 Saline gargle (mouth rinse and gargle) A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device. GENEPIO:0100035 Scraping A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device. GENEPIO:0002117 Swabbing The process of collecting specimen material using a swab collection device. - GENEPIO:0100036 Finger Prick A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. NCIT:C15392 Thoracentesis (chest tap) The removal of excess fluid via needle puncture from the thoracic cavity. collection method international menu CollectionMethodInternationalMenu NCIT:C52009 Amniocentesis [NCIT:C52009] A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. Mpox_international diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 2cd58db4..738d420f 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -116,11 +116,11 @@ MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exp Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS Mpox;MpoxInternational Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information Mpox;MpoxInternational -Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMonkeypoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection Mpox -MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMonkeypoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] MpoxInternational +Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection Mpox +MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] MpoxInternational Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date Mpox;MpoxInternational -Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMonkeypoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment Mpox -MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMonkeypoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] MpoxInternational +Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment Mpox +MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] MpoxInternational Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection Mpox;MpoxInternational @@ -229,7 +229,6 @@ Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNam Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 Mpox Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 Mpox Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 Mpox - GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS Mpox;MpoxInternational Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS Mpox;MpoxInternational \ No newline at end of file diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index e6c15de8..1a4e3f05 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -304,27 +304,42 @@ "Not Applicable [GENEPIO:0001619]": { "text": "Not Applicable [GENEPIO:0001619]", "description": "A categorical choice recorded when a datum does not apply to a given context.", - "meaning": "GENEPIO:0001619" + "meaning": "GENEPIO:0001619", + "exact_mappings": [ + "NCBI_SRA:not%20applicable" + ] }, "Missing [GENEPIO:0001618]": { "text": "Missing [GENEPIO:0001618]", "description": "A categorical choice recorded when a datum is not included for an unknown reason.", - "meaning": "GENEPIO:0001618" + "meaning": "GENEPIO:0001618", + "exact_mappings": [ + "NCBI_SRA:missing" + ] }, "Not Collected [GENEPIO:0001620]": { "text": "Not Collected [GENEPIO:0001620]", "description": "A categorical choice recorded when a datum was not measured or collected.", - "meaning": "GENEPIO:0001620" + "meaning": "GENEPIO:0001620", + "exact_mappings": [ + "NCBI_SRA:not%20collected" + ] }, "Not Provided [GENEPIO:0001668]": { "text": "Not Provided [GENEPIO:0001668]", "description": "A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage.", - "meaning": "GENEPIO:0001668" + "meaning": "GENEPIO:0001668", + "exact_mappings": [ + "NCBI_SRA:not%20provided" + ] }, "Restricted Access [GENEPIO:0001810]": { "text": "Restricted Access [GENEPIO:0001810]", "description": "A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns.", - "meaning": "GENEPIO:0001810" + "meaning": "GENEPIO:0001810", + "exact_mappings": [ + "NCBI_SRA:restricted%20access" + ] } } }, @@ -2369,8 +2384,8 @@ } } }, - "environmental material menu": { - "name": "environmental material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", "title": "environmental material menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3475,57 +3490,90 @@ "Illumina [GENEPIO:0001923]": { "text": "Illumina [GENEPIO:0001923]", "description": "A sequencing platform provided by the Illumina company.", - "meaning": "GENEPIO:0001923" + "meaning": "GENEPIO:0001923", + "exact_mappings": [ + "NCBI_SRA:ILLUMINA" + ] }, "Pacific Biosciences [GENEPIO:0001927]": { "text": "Pacific Biosciences [GENEPIO:0001927]", "description": "A sequencing platform provided by the Pacific Biosciences company.", - "meaning": "GENEPIO:0001927" + "meaning": "GENEPIO:0001927", + "exact_mappings": [ + "NCBI_SRA:PACBIO_SMRT" + ] }, "Ion Torrent [GENEPIO:0002683]": { "text": "Ion Torrent [GENEPIO:0002683]", "description": "A sequencing platform provided by the Ion Torrent company.", - "meaning": "GENEPIO:0002683" + "meaning": "GENEPIO:0002683", + "exact_mappings": [ + "NCBI_SRA:ION_TORRENT" + ] }, "Oxford Nanopore Technologies [GENEPIO:0100986]": { "text": "Oxford Nanopore Technologies [GENEPIO:0100986]", "description": "An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK.", - "meaning": "GENEPIO:0100986" + "meaning": "GENEPIO:0100986", + "exact_mappings": [ + "NCBI_SRA:OXFORT_NANOPORE" + ] }, "BGI Genomics [GENEPIO:0004324]": { "text": "BGI Genomics [GENEPIO:0004324]", "description": "A sequencing platform provided by the BGI Genomics company.", - "meaning": "GENEPIO:0004324" + "meaning": "GENEPIO:0004324", + "exact_mappings": [ + "NCBI_SRA:BGISEQ" + ] }, "MGI [GENEPIO:0004325]": { "text": "MGI [GENEPIO:0004325]", "description": "A sequencing platform provided by the MGI company.", - "meaning": "GENEPIO:0004325" + "meaning": "GENEPIO:0004325", + "exact_mappings": [ + "NCBI_SRA:BGISEQ" + ] }, "Roche LS454 [GENEPIO:0001926]": { "text": "Roche LS454 [GENEPIO:0001926]", "description": "A sequencing platform provided by the 454 Life Sciences company.", - "meaning": "GENEPIO:0001926" + "meaning": "GENEPIO:0001926", + "exact_mappings": [ + "NCBI_SRA:_LS454" + ] }, "SOLiD sequencing [GENEPIO:0002684]": { "text": "SOLiD sequencing [GENEPIO:0002684]", "description": "A sequencing platform provided by Life Technologies Corporation.", - "meaning": "GENEPIO:0002684" + "meaning": "GENEPIO:0002684", + "exact_mappings": [ + "NCBI_SRA:ABI_SOLID" + ] }, "Complete Genomics [GENEPIO:0001924]": { "text": "Complete Genomics [GENEPIO:0001924]", "description": "An in-house sequencing platform provided by Complete Genomics.", - "meaning": "GENEPIO:0001924" + "meaning": "GENEPIO:0001924", + "exact_mappings": [ + "NCBI_SRA:COMPLETE_GENOMICS" + ] }, "Helicos [GENEPIO:0002682]": { "text": "Helicos [GENEPIO:0002682]", "description": "A sequencing platform brand provided by Helicos corporation (now defunct).", - "meaning": "GENEPIO:0002682" + "meaning": "GENEPIO:0002682", + "exact_mappings": [ + "NCBI_SRA:HELICOS" + ] }, "Applied Biosystems [GENEPIO:0100985]": { "text": "Applied Biosystems [GENEPIO:0100985]", "description": "A sequencing platform provided by ThermoFisher.", - "meaning": "GENEPIO:0100985" + "meaning": "GENEPIO:0100985", + "exact_mappings": [ + "NCBI_SRA:CAPILLARY" + ] } } }, @@ -3990,29 +4038,44 @@ "Amplicon sequencing assay [OBI:0002767]": { "text": "Amplicon sequencing assay [OBI:0002767]", "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", - "meaning": "OBI:0002767" + "meaning": "OBI:0002767", + "exact_mappings": [ + "NCBI_SRA:AMPLICON" + ] }, "16S ribosomal gene sequencing assay [OBI:0002763]": { "text": "16S ribosomal gene sequencing assay [OBI:0002763]", "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", "meaning": "OBI:0002763", - "is_a": "Amplicon sequencing assay [OBI:0002767]" + "is_a": "Amplicon sequencing assay [OBI:0002767]", + "exact_mappings": [ + "NCBI_SRA:AMPLICON" + ] }, "Whole genome sequencing assay [OBI:0002117]": { "text": "Whole genome sequencing assay [OBI:0002117]", "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", - "meaning": "OBI:0002117" + "meaning": "OBI:0002117", + "exact_mappings": [ + "NCBI_SRA:WGS" + ] }, "Whole metagenome sequencing assay [OBI:0002623]": { "text": "Whole metagenome sequencing assay [OBI:0002623]", "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", - "meaning": "OBI:0002623" + "meaning": "OBI:0002623", + "exact_mappings": [ + "NCBI_SRA:OTHER" + ] }, "Whole virome sequencing assay [OBI:0002768]": { "text": "Whole virome sequencing assay [OBI:0002768]", "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", "meaning": "OBI:0002768", - "is_a": "Whole metagenome sequencing assay [OBI:0002623]" + "is_a": "Whole metagenome sequencing assay [OBI:0002623]", + "exact_mappings": [ + "NCBI_SRA:OTHER" + ] } } }, @@ -4024,112 +4087,178 @@ "artic-v1 [GENEPIO:0100847]": { "text": "artic-v1 [GENEPIO:0100847]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0.", - "meaning": "GENEPIO:0100847" + "meaning": "GENEPIO:0100847", + "exact_mappings": [ + "NCBI_SRA:artic-v1" + ] }, "artic-v2 [GENEPIO:0100848]": { "text": "artic-v2 [GENEPIO:0100848]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0.", - "meaning": "GENEPIO:0100848" + "meaning": "GENEPIO:0100848", + "exact_mappings": [ + "NCBI_SRA:artic-v2" + ] }, "artic-v3 [GENEPIO:0100849]": { "text": "artic-v3 [GENEPIO:0100849]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0.", - "meaning": "GENEPIO:0100849" + "meaning": "GENEPIO:0100849", + "exact_mappings": [ + "NCBI_SRA:artic-v3" + ] }, "artic-v4 [GENEPIO:0100850]": { "text": "artic-v4 [GENEPIO:0100850]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0.", - "meaning": "GENEPIO:0100850" + "meaning": "GENEPIO:0100850", + "exact_mappings": [ + "NCBI_SRA:artic-v4" + ] }, "artic-v4.1 [GENEPIO:0100851]": { "text": "artic-v4.1 [GENEPIO:0100851]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0.", - "meaning": "GENEPIO:0100851" + "meaning": "GENEPIO:0100851", + "exact_mappings": [ + "NCBI_SRA:artic-v4.1" + ] }, "artic-v5.0.0_400 [GENEPIO:0100852]": { "text": "artic-v5.0.0_400 [GENEPIO:0100852]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100852" + "meaning": "GENEPIO:0100852", + "exact_mappings": [ + "NCBI_SRA:artic-v5.0.0_400" + ] }, "artic-v5.1.0_400 [GENEPIO:0100853]": { "text": "artic-v5.1.0_400 [GENEPIO:0100853]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100853" + "meaning": "GENEPIO:0100853", + "exact_mappings": [ + "NCBI_SRA:artic-v5.1.0_400" + ] }, "artic-v5.2.0_1200 [GENEPIO:0100854]": { "text": "artic-v5.2.0_1200 [GENEPIO:0100854]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100854" + "meaning": "GENEPIO:0100854", + "exact_mappings": [ + "NCBI_SRA:artic-v5.2.0_1200" + ] }, "artic-v5.2.0_400 [GENEPIO:0100855]": { "text": "artic-v5.2.0_400 [GENEPIO:0100855]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100855" + "meaning": "GENEPIO:0100855", + "exact_mappings": [ + "NCBI_SRA:artic-v5.2.0_400" + ] }, "artic-v5.3.2_400 [GENEPIO:0100856]": { "text": "artic-v5.3.2_400 [GENEPIO:0100856]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100856" + "meaning": "GENEPIO:0100856", + "exact_mappings": [ + "NCBI_SRA:artic-v5.3.2_400" + ] }, "eden-v1 [GENEPIO:0100857]": { "text": "eden-v1 [GENEPIO:0100857]", "description": "An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length.", - "meaning": "GENEPIO:0100857" + "meaning": "GENEPIO:0100857", + "exact_mappings": [ + "NCBI_SRA:eden-v1" + ] }, "midnight-bccdc-v1 [GENEPIO:0100858]": { "text": "midnight-bccdc-v1 [GENEPIO:0100858]", "description": "An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100858" + "meaning": "GENEPIO:0100858", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v1" + ] }, "midnight-bccdc-v2 [GENEPIO:0100859]": { "text": "midnight-bccdc-v2 [GENEPIO:0100859]", "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100859" + "meaning": "GENEPIO:0100859", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v2" + ] }, "midnight-bccdc-v3 [GENEPIO:0100860]": { "text": "midnight-bccdc-v3 [GENEPIO:0100860]", "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100860" + "meaning": "GENEPIO:0100860", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v3" + ] }, "midnight-bccdc-v4 [GENEPIO:0100861]": { "text": "midnight-bccdc-v4 [GENEPIO:0100861]", "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100861" + "meaning": "GENEPIO:0100861", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v4" + ] }, "midnight-ont-v3 [GENEPIO:0100862]": { "text": "midnight-ont-v3 [GENEPIO:0100862]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100862" + "meaning": "GENEPIO:0100862", + "exact_mappings": [ + "NCBI_SRA:midnight-ont-v3" + ] }, "midnight-v1 [GENEPIO:0100863]": { "text": "midnight-v1 [GENEPIO:0100863]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100863" + "meaning": "GENEPIO:0100863", + "exact_mappings": [ + "NCBI_SRA:midnight-v1" + ] }, "midnight-v2 [GENEPIO:0100864]": { "text": "midnight-v2 [GENEPIO:0100864]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100864" + "meaning": "GENEPIO:0100864", + "exact_mappings": [ + "NCBI_SRA:midnight-v2" + ] }, "varskip-vsl1a [GENEPIO:0100865]": { "text": "varskip-vsl1a [GENEPIO:0100865]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long.", - "meaning": "GENEPIO:0100865" + "meaning": "GENEPIO:0100865", + "exact_mappings": [ + "NCBI_SRA:varskip-vsl1a" + ] }, "varskip-vss1a [GENEPIO:0100866]": { "text": "varskip-vss1a [GENEPIO:0100866]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short.", - "meaning": "GENEPIO:0100866" + "meaning": "GENEPIO:0100866", + "exact_mappings": [ + "NCBI_SRA:varskip-vss1a" + ] }, "varskip-vss2a [GENEPIO:0100867]": { "text": "varskip-vss2a [GENEPIO:0100867]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a.", - "meaning": "GENEPIO:0100867" + "meaning": "GENEPIO:0100867", + "exact_mappings": [ + "NCBI_SRA:varskip-vss2a" + ] }, "varskip-vss2b [GENEPIO:0100868]": { "text": "varskip-vss2b [GENEPIO:0100868]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b.", - "meaning": "GENEPIO:0100868" + "meaning": "GENEPIO:0100868", + "exact_mappings": [ + "NCBI_SRA:varskip-vss2b" + ] } } }, @@ -4141,12 +4270,18 @@ "Hybridization capture [GENEPIO:0001950]": { "text": "Hybridization capture [GENEPIO:0001950]", "description": "Selection by hybridization in array or solution.", - "meaning": "GENEPIO:0001950" + "meaning": "GENEPIO:0001950", + "exact_mappings": [ + "NCBI_SRA:Hybrid%20Selection" + ] }, "rRNA depletion method [GENEPIO:0101020]": { "text": "rRNA depletion method [GENEPIO:0101020]", "description": "Removal of background RNA for the purposes of enriching the genomic target.", - "meaning": "GENEPIO:0101020" + "meaning": "GENEPIO:0101020", + "exact_mappings": [ + "NCBI_SRA:Other" + ] } } }, @@ -4158,32 +4293,50 @@ "No quality control issues identified [GENEPIO:0100562]": { "text": "No quality control issues identified [GENEPIO:0100562]", "description": "A statement confirming that quality control processes were carried out and no quality issues were detected.", - "meaning": "GENEPIO:0100562" + "meaning": "GENEPIO:0100562", + "exact_mappings": [ + "NCBI_SRA:no%20quality%20control%20issues%20identified" + ] }, "Sequence passed quality control [GENEPIO:0100563]": { "text": "Sequence passed quality control [GENEPIO:0100563]", "description": "A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", - "meaning": "GENEPIO:0100563" + "meaning": "GENEPIO:0100563", + "exact_mappings": [ + "NCBI_SRA:Sequence%20passed%20quality%20control" + ] }, "Sequence failed quality control [GENEPIO:0100564]": { "text": "Sequence failed quality control [GENEPIO:0100564]", "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", - "meaning": "GENEPIO:0100564" + "meaning": "GENEPIO:0100564", + "exact_mappings": [ + "NCBI_SRA:Sequence%20failed%20quality%20control" + ] }, "Minor quality control issues identified [GENEPIO:0100565]": { "text": "Minor quality control issues identified [GENEPIO:0100565]", "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", - "meaning": "GENEPIO:0100565" + "meaning": "GENEPIO:0100565", + "exact_mappings": [ + "NCBI_SRA:minor%20quality%20control%20issues%20identified" + ] }, "Sequence flagged for potential quality control issues [GENEPIO:0100566]": { "text": "Sequence flagged for potential quality control issues [GENEPIO:0100566]", "description": "A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", - "meaning": "GENEPIO:0100566" + "meaning": "GENEPIO:0100566", + "exact_mappings": [ + "NCBI_SRA:sequence%20flagged%20for%20potential%20quality%20control%20issues" + ] }, "Quality control not performed [GENEPIO:0100567]": { "text": "Quality control not performed [GENEPIO:0100567]", "description": "A statement confirming that quality control processes have not been carried out.", - "meaning": "GENEPIO:0100567" + "meaning": "GENEPIO:0100567", + "exact_mappings": [ + "NCBI_SRA:not%20performed" + ] } } }, @@ -4195,42 +4348,66 @@ "Low quality sequence [GENEPIO:0100568]": { "text": "Low quality sequence [GENEPIO:0100568]", "description": "Sequence data that does not meet quality control thresholds.", - "meaning": "GENEPIO:0100568" + "meaning": "GENEPIO:0100568", + "exact_mappings": [ + "NCBI_SRA:low%20quality%20sequence" + ] }, "Sequence contaminated [GENEPIO:0100569]": { "text": "Sequence contaminated [GENEPIO:0100569]", "description": "Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", - "meaning": "GENEPIO:0100569" + "meaning": "GENEPIO:0100569", + "exact_mappings": [ + "NCBI_SRA:sequenced%20contaminated" + ] }, "Low average genome coverage [GENEPIO:0100570]": { "text": "Low average genome coverage [GENEPIO:0100570]", "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", - "meaning": "GENEPIO:0100570" + "meaning": "GENEPIO:0100570", + "exact_mappings": [ + "NCBI_SRA:low%20average%20genome%20coverage" + ] }, "Low percent genome captured [GENEPIO:0100571]": { "text": "Low percent genome captured [GENEPIO:0100571]", "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", - "meaning": "GENEPIO:0100571" + "meaning": "GENEPIO:0100571", + "exact_mappings": [ + "NCBI_SRA:low%20%25%20genome%20captured" + ] }, "Read lengths shorter than expected [GENEPIO:0100572]": { "text": "Read lengths shorter than expected [GENEPIO:0100572]", "description": "Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", - "meaning": "GENEPIO:0100572" + "meaning": "GENEPIO:0100572", + "exact_mappings": [ + "NCBI_SRA:read%20lengths%20shorter%20than%20expected" + ] }, "Sequence amplification artifacts [GENEPIO:0100573]": { "text": "Sequence amplification artifacts [GENEPIO:0100573]", "description": "Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", - "meaning": "GENEPIO:0100573" + "meaning": "GENEPIO:0100573", + "exact_mappings": [ + "NCBI_SRA:sequence%20amplification%20artifacts" + ] }, "Low signal to noise ratio [GENEPIO:0100574]": { "text": "Low signal to noise ratio [GENEPIO:0100574]", "description": "Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", - "meaning": "GENEPIO:0100574" + "meaning": "GENEPIO:0100574", + "exact_mappings": [ + "NCBI_SRA:low%20signal%20to%20noise%20ratio" + ] }, "Low coverage of characteristic mutations [GENEPIO:0100575]": { "text": "Low coverage of characteristic mutations [GENEPIO:0100575]", "description": "Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", - "meaning": "GENEPIO:0100575" + "meaning": "GENEPIO:0100575", + "exact_mappings": [ + "NCBI_SRA:low%20coverage%20of%20characteristic%20mutations" + ] } } }, @@ -7838,7 +8015,7 @@ ], "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -11349,7 +11526,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -11400,7 +11577,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -15008,7 +15185,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -17154,7 +17331,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -17349,7 +17526,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -22209,7 +22386,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -29850,7 +30027,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index 277473ad..de8406e6 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -842,7 +842,7 @@ classes: examples: - value: E gene (orf4) any_of: - - range: GeneNameMenu + - range: GeneSymbolMenu - range: NullValueMenu diagnostic_target_presence_2: rank: 199 @@ -869,7 +869,7 @@ classes: examples: - value: E gene (orf4) any_of: - - range: GeneNameMenu + - range: GeneSymbolMenu - range: NullValueMenu diagnostic_target_presence_3: rank: 206 @@ -4389,7 +4389,7 @@ slots: comments: Provide the units of the measured TP. slot_uri: GENEPIO:0100812 any_of: - - range: TotalPhosphorusTpMeasurementUnitMenu + - range: TotalPhosphorpusTpMeasurementUnitMenu - range: NullValueMenu examples: - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) @@ -5604,27 +5604,37 @@ enums: description: A categorical choice recorded when a datum does not apply to a given context. meaning: GENEPIO:0001619 + exact_mappings: + - NCBI_SRA:not%20applicable Missing [GENEPIO:0001618]: text: Missing [GENEPIO:0001618] description: A categorical choice recorded when a datum is not included for an unknown reason. meaning: GENEPIO:0001618 + exact_mappings: + - NCBI_SRA:missing Not Collected [GENEPIO:0001620]: text: Not Collected [GENEPIO:0001620] description: A categorical choice recorded when a datum was not measured or collected. meaning: GENEPIO:0001620 + exact_mappings: + - NCBI_SRA:not%20collected Not Provided [GENEPIO:0001668]: text: Not Provided [GENEPIO:0001668] description: A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. meaning: GENEPIO:0001668 + exact_mappings: + - NCBI_SRA:not%20provided Restricted Access [GENEPIO:0001810]: text: Restricted Access [GENEPIO:0001810] description: A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. meaning: GENEPIO:0001810 + exact_mappings: + - NCBI_SRA:restricted%20access GeoLocNameCountryMenu: name: GeoLocNameCountryMenu title: geo_loc_name (country) menu @@ -8673,8 +8683,8 @@ enums: thrust from a jet engine, propeller, or rocket engine. meaning: ENVO:03501349 is_a: Transportation vehicle [ENVO:01000604] - environmental material menu: - name: environmental material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu title: environmental material menu permissible_values: Bar screen [ENVO:03501474]: @@ -9687,48 +9697,70 @@ enums: text: Illumina [GENEPIO:0001923] description: A sequencing platform provided by the Illumina company. meaning: GENEPIO:0001923 + exact_mappings: + - NCBI_SRA:ILLUMINA Pacific Biosciences [GENEPIO:0001927]: text: Pacific Biosciences [GENEPIO:0001927] description: A sequencing platform provided by the Pacific Biosciences company. meaning: GENEPIO:0001927 + exact_mappings: + - NCBI_SRA:PACBIO_SMRT Ion Torrent [GENEPIO:0002683]: text: Ion Torrent [GENEPIO:0002683] description: A sequencing platform provided by the Ion Torrent company. meaning: GENEPIO:0002683 + exact_mappings: + - NCBI_SRA:ION_TORRENT Oxford Nanopore Technologies [GENEPIO:0100986]: text: Oxford Nanopore Technologies [GENEPIO:0100986] description: An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. meaning: GENEPIO:0100986 + exact_mappings: + - NCBI_SRA:OXFORT_NANOPORE BGI Genomics [GENEPIO:0004324]: text: BGI Genomics [GENEPIO:0004324] description: A sequencing platform provided by the BGI Genomics company. meaning: GENEPIO:0004324 + exact_mappings: + - NCBI_SRA:BGISEQ MGI [GENEPIO:0004325]: text: MGI [GENEPIO:0004325] description: A sequencing platform provided by the MGI company. meaning: GENEPIO:0004325 + exact_mappings: + - NCBI_SRA:BGISEQ Roche LS454 [GENEPIO:0001926]: text: Roche LS454 [GENEPIO:0001926] description: A sequencing platform provided by the 454 Life Sciences company. meaning: GENEPIO:0001926 + exact_mappings: + - NCBI_SRA:_LS454 SOLiD sequencing [GENEPIO:0002684]: text: SOLiD sequencing [GENEPIO:0002684] description: A sequencing platform provided by Life Technologies Corporation. meaning: GENEPIO:0002684 + exact_mappings: + - NCBI_SRA:ABI_SOLID Complete Genomics [GENEPIO:0001924]: text: Complete Genomics [GENEPIO:0001924] description: An in-house sequencing platform provided by Complete Genomics. meaning: GENEPIO:0001924 + exact_mappings: + - NCBI_SRA:COMPLETE_GENOMICS Helicos [GENEPIO:0002682]: text: Helicos [GENEPIO:0002682] description: A sequencing platform brand provided by Helicos corporation (now defunct). meaning: GENEPIO:0002682 + exact_mappings: + - NCBI_SRA:HELICOS Applied Biosystems [GENEPIO:0100985]: text: Applied Biosystems [GENEPIO:0100985] description: A sequencing platform provided by ThermoFisher. meaning: GENEPIO:0100985 + exact_mappings: + - NCBI_SRA:CAPILLARY SequencingInstrumentMenu: name: SequencingInstrumentMenu title: sequencing instrument menu @@ -10249,6 +10281,8 @@ enums: description: A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. meaning: OBI:0002767 + exact_mappings: + - NCBI_SRA:AMPLICON 16S ribosomal gene sequencing assay [OBI:0002763]: text: 16S ribosomal gene sequencing assay [OBI:0002763] description: An amplicon sequencing assay in which the amplicon is derived @@ -10257,24 +10291,32 @@ enums: sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. meaning: OBI:0002763 + exact_mappings: + - NCBI_SRA:AMPLICON is_a: Amplicon sequencing assay [OBI:0002767] Whole genome sequencing assay [OBI:0002117]: text: Whole genome sequencing assay [OBI:0002117] description: A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. meaning: OBI:0002117 + exact_mappings: + - NCBI_SRA:WGS Whole metagenome sequencing assay [OBI:0002623]: text: Whole metagenome sequencing assay [OBI:0002623] description: A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. meaning: OBI:0002623 + exact_mappings: + - NCBI_SRA:OTHER Whole virome sequencing assay [OBI:0002768]: text: Whole virome sequencing assay [OBI:0002768] description: A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. meaning: OBI:0002768 + exact_mappings: + - NCBI_SRA:OTHER is_a: Whole metagenome sequencing assay [OBI:0002623] AmpliconPcrPrimerSchemeMenu: name: AmpliconPcrPrimerSchemeMenu @@ -10285,62 +10327,84 @@ enums: description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. meaning: GENEPIO:0100847 + exact_mappings: + - NCBI_SRA:artic-v1 artic-v2 [GENEPIO:0100848]: text: artic-v2 [GENEPIO:0100848] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. meaning: GENEPIO:0100848 + exact_mappings: + - NCBI_SRA:artic-v2 artic-v3 [GENEPIO:0100849]: text: artic-v3 [GENEPIO:0100849] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. meaning: GENEPIO:0100849 + exact_mappings: + - NCBI_SRA:artic-v3 artic-v4 [GENEPIO:0100850]: text: artic-v4 [GENEPIO:0100850] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. meaning: GENEPIO:0100850 + exact_mappings: + - NCBI_SRA:artic-v4 artic-v4.1 [GENEPIO:0100851]: text: artic-v4.1 [GENEPIO:0100851] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. meaning: GENEPIO:0100851 + exact_mappings: + - NCBI_SRA:artic-v4.1 artic-v5.0.0_400 [GENEPIO:0100852]: text: artic-v5.0.0_400 [GENEPIO:0100852] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100852 + exact_mappings: + - NCBI_SRA:artic-v5.0.0_400 artic-v5.1.0_400 [GENEPIO:0100853]: text: artic-v5.1.0_400 [GENEPIO:0100853] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100853 + exact_mappings: + - NCBI_SRA:artic-v5.1.0_400 artic-v5.2.0_1200 [GENEPIO:0100854]: text: artic-v5.2.0_1200 [GENEPIO:0100854] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100854 + exact_mappings: + - NCBI_SRA:artic-v5.2.0_1200 artic-v5.2.0_400 [GENEPIO:0100855]: text: artic-v5.2.0_400 [GENEPIO:0100855] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100855 + exact_mappings: + - NCBI_SRA:artic-v5.2.0_400 artic-v5.3.2_400 [GENEPIO:0100856]: text: artic-v5.3.2_400 [GENEPIO:0100856] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100856 + exact_mappings: + - NCBI_SRA:artic-v5.3.2_400 eden-v1 [GENEPIO:0100857]: text: eden-v1 [GENEPIO:0100857] description: An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. meaning: GENEPIO:0100857 + exact_mappings: + - NCBI_SRA:eden-v1 midnight-bccdc-v1 [GENEPIO:0100858]: text: midnight-bccdc-v1 [GENEPIO:0100858] description: An amplicon strategy which is for SARS-CoV-2 and based on the @@ -10348,6 +10412,8 @@ enums: adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100858 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v1 midnight-bccdc-v2 [GENEPIO:0100859]: text: midnight-bccdc-v2 [GENEPIO:0100859] description: An amplicon strategy which targets SARS-CoV-2 and is based on @@ -10355,6 +10421,8 @@ enums: and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100859 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v2 midnight-bccdc-v3 [GENEPIO:0100860]: text: midnight-bccdc-v3 [GENEPIO:0100860] description: An amplicon strategy which targets SARS-CoV-2 and is based on @@ -10362,6 +10430,8 @@ enums: and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100860 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v3 midnight-bccdc-v4 [GENEPIO:0100861]: text: midnight-bccdc-v4 [GENEPIO:0100861] description: An amplicon strategy which targets SARS-CoV-2 and is based on @@ -10369,48 +10439,64 @@ enums: and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100861 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v4 midnight-ont-v3 [GENEPIO:0100862]: text: midnight-ont-v3 [GENEPIO:0100862] description: An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100862 + exact_mappings: + - NCBI_SRA:midnight-ont-v3 midnight-v1 [GENEPIO:0100863]: text: midnight-v1 [GENEPIO:0100863] description: An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100863 + exact_mappings: + - NCBI_SRA:midnight-v1 midnight-v2 [GENEPIO:0100864]: text: midnight-v2 [GENEPIO:0100864] description: An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100864 + exact_mappings: + - NCBI_SRA:midnight-v2 varskip-vsl1a [GENEPIO:0100865]: text: varskip-vsl1a [GENEPIO:0100865] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. meaning: GENEPIO:0100865 + exact_mappings: + - NCBI_SRA:varskip-vsl1a varskip-vss1a [GENEPIO:0100866]: text: varskip-vss1a [GENEPIO:0100866] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. meaning: GENEPIO:0100866 + exact_mappings: + - NCBI_SRA:varskip-vss1a varskip-vss2a [GENEPIO:0100867]: text: varskip-vss2a [GENEPIO:0100867] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. meaning: GENEPIO:0100867 + exact_mappings: + - NCBI_SRA:varskip-vss2a varskip-vss2b [GENEPIO:0100868]: text: varskip-vss2b [GENEPIO:0100868] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. meaning: GENEPIO:0100868 + exact_mappings: + - NCBI_SRA:varskip-vss2b GenomicTargetEnrichmentMethodMenu: name: GenomicTargetEnrichmentMethodMenu title: genomic target enrichment method menu @@ -10419,11 +10505,15 @@ enums: text: Hybridization capture [GENEPIO:0001950] description: Selection by hybridization in array or solution. meaning: GENEPIO:0001950 + exact_mappings: + - NCBI_SRA:Hybrid%20Selection rRNA depletion method [GENEPIO:0101020]: text: rRNA depletion method [GENEPIO:0101020] description: Removal of background RNA for the purposes of enriching the genomic target. meaning: GENEPIO:0101020 + exact_mappings: + - NCBI_SRA:Other QualityControlDeterminationMenu: name: QualityControlDeterminationMenu title: quality control determination menu @@ -10433,33 +10523,45 @@ enums: description: A statement confirming that quality control processes were carried out and no quality issues were detected. meaning: GENEPIO:0100562 + exact_mappings: + - NCBI_SRA:no%20quality%20control%20issues%20identified Sequence passed quality control [GENEPIO:0100563]: text: Sequence passed quality control [GENEPIO:0100563] description: A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. meaning: GENEPIO:0100563 + exact_mappings: + - NCBI_SRA:Sequence%20passed%20quality%20control Sequence failed quality control [GENEPIO:0100564]: text: Sequence failed quality control [GENEPIO:0100564] description: A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. meaning: GENEPIO:0100564 + exact_mappings: + - NCBI_SRA:Sequence%20failed%20quality%20control Minor quality control issues identified [GENEPIO:0100565]: text: Minor quality control issues identified [GENEPIO:0100565] description: A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. meaning: GENEPIO:0100565 + exact_mappings: + - NCBI_SRA:minor%20quality%20control%20issues%20identified Sequence flagged for potential quality control issues [GENEPIO:0100566]: text: Sequence flagged for potential quality control issues [GENEPIO:0100566] description: A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. meaning: GENEPIO:0100566 + exact_mappings: + - NCBI_SRA:sequence%20flagged%20for%20potential%20quality%20control%20issues Quality control not performed [GENEPIO:0100567]: text: Quality control not performed [GENEPIO:0100567] description: A statement confirming that quality control processes have not been carried out. meaning: GENEPIO:0100567 + exact_mappings: + - NCBI_SRA:not%20performed QualityControlIssuesMenu: name: QualityControlIssuesMenu title: quality control issues menu @@ -10468,12 +10570,16 @@ enums: text: Low quality sequence [GENEPIO:0100568] description: Sequence data that does not meet quality control thresholds. meaning: GENEPIO:0100568 + exact_mappings: + - NCBI_SRA:low%20quality%20sequence Sequence contaminated [GENEPIO:0100569]: text: Sequence contaminated [GENEPIO:0100569] description: Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. meaning: GENEPIO:0100569 + exact_mappings: + - NCBI_SRA:sequenced%20contaminated Low average genome coverage [GENEPIO:0100570]: text: Low average genome coverage [GENEPIO:0100570] description: Sequence data in which the entire length of the genome is not @@ -10481,32 +10587,44 @@ enums: of the genome are not sequenced a prescribed number of times (low depth of coverage). meaning: GENEPIO:0100570 + exact_mappings: + - NCBI_SRA:low%20average%20genome%20coverage Low percent genome captured [GENEPIO:0100571]: text: Low percent genome captured [GENEPIO:0100571] description: Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). meaning: GENEPIO:0100571 + exact_mappings: + - NCBI_SRA:low%20%25%20genome%20captured Read lengths shorter than expected [GENEPIO:0100572]: text: Read lengths shorter than expected [GENEPIO:0100572] description: Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. meaning: GENEPIO:0100572 + exact_mappings: + - NCBI_SRA:read%20lengths%20shorter%20than%20expected Sequence amplification artifacts [GENEPIO:0100573]: text: Sequence amplification artifacts [GENEPIO:0100573] description: Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). meaning: GENEPIO:0100573 + exact_mappings: + - NCBI_SRA:sequence%20amplification%20artifacts Low signal to noise ratio [GENEPIO:0100574]: text: Low signal to noise ratio [GENEPIO:0100574] description: Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). meaning: GENEPIO:0100574 + exact_mappings: + - NCBI_SRA:low%20signal%20to%20noise%20ratio Low coverage of characteristic mutations [GENEPIO:0100575]: text: Low coverage of characteristic mutations [GENEPIO:0100575] description: Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. meaning: GENEPIO:0100575 + exact_mappings: + - NCBI_SRA:low%20coverage%20of%20characteristic%20mutations GeneSymbolMenu: name: GeneSymbolMenu title: gene symbol menu diff --git a/web/templates/wastewater/schema_enums.tsv b/web/templates/wastewater/schema_enums.tsv index 222799e6..6f123a56 100644 --- a/web/templates/wastewater/schema_enums.tsv +++ b/web/templates/wastewater/schema_enums.tsv @@ -1,10 +1,10 @@ -title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_NCBI_SRA EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. - GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. - GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. - GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. - GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. +null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. not applicable + GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. missing + GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. not collected + GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. not provided + GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. restricted access geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] @@ -403,7 +403,7 @@ environmental site menu EnvironmentalSiteMenu ENVO:01001481 Correctional facilit ENVO:01000608 Boat [ENVO:01000608] A boat is a watercraft of any size which is able to float or plane on water. ENVO:03501349 Airplane [ENVO:03501349] An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine. -environmental material menu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater +environmental material menu EnvironmentalMaterialMenu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence ENVO:03501456 Wastewater sediment [ENVO:03501456] A sediment which is removed from waste water during a waste water treatment process. @@ -612,17 +612,17 @@ purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surv GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. -sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. - GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. - GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. - GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. - GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. - GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. - GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. - GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. - GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. - GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). - GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. +sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. ILLUMINA + GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. PACBIO_SMRT + GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. ION_TORRENT + GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. OXFORT_NANOPORE + GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. BGISEQ + GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. BGISEQ + GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. _LS454 + GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. ABI_SOLID + GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. COMPLETE_GENOMICS + GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). HELICOS + GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. CAPILLARY sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. @@ -701,53 +701,53 @@ sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GE GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. -sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. - OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. - OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. - OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. - OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. - -amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. - GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. - GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. - GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. - GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. - GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. - GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. - GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. - GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. - GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. - GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. - GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. - GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. - GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. - -genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. - GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. - -quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. - GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. - GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. - GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. - GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. - GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. - -quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. - GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. - GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). - GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). - GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. - GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). - GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). - GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. +sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. AMPLICON + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. AMPLICON + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. WGS + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. OTHER + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. OTHER + +amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. artic-v1 + GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. artic-v2 + GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. artic-v3 + GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. artic-v4 + GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. artic-v4.1 + GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. artic-v5.0.0_400 + GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. artic-v5.1.0_400 + GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. artic-v5.2.0_1200 + GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. artic-v5.2.0_400 + GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. artic-v5.3.2_400 + GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. eden-v1 + GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v1 + GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v2 + GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v3 + GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v4 + GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-ont-v3 + GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-v1 + GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-v2 + GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. varskip-vsl1a + GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. varskip-vss1a + GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. varskip-vss2a + GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. varskip-vss2b + +genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. Hybrid Selection + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. Other + +quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. no quality control issues identified + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. Sequence passed quality control + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. Sequence failed quality control + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. minor quality control issues identified + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. sequence flagged for potential quality control issues + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. not performed + +quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. low quality sequence + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. sequenced contaminated + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). low average genome coverage + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). low % genome captured + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. read lengths shorter than expected + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). sequence amplification artifacts + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). low signal to noise ratio + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. low coverage of characteristic mutations gene symbol menu GeneSymbolMenu GENEPIO:0100151 E gene (orf4) [GENEPIO:0100151] GENEPIO:0100152 M gene (orf5) [GENEPIO:0100152] diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index bddf02b9..299a4b05 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -1,263 +1,263 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ -WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml -WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 -WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 -WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. -WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 -WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf -WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information -WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 -WastewaterAMR GENEPIO:0100479 AMR detection information -WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier -WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 -WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) -WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 -WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc -WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 2 gene_symbol_2 GeneNameMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 3 gene_symbol_3 GeneNameMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors Authors -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance Additional Comments \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ +WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml +WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 +WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. +WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorpusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 +WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf +WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information +WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +WastewaterAMR GENEPIO:0100479 AMR detection information +WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier +WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 +WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) +WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 +WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc +WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 2 gene_symbol_2 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 3 gene_symbol_3 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance \ No newline at end of file