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nfdi4plants_ontology_OBSOLETE.obo
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format-version: 1.2
data-version: init/2020-12-01
saved-by: muehlhaus
default-namespace: NFDI4PSO
remark: This ontology is obsolete and has been replaced with dpbo.obo
remark: coverage: Missing Terms for the DataPLANT end-point repository templates
remark: creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de>
remark: creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de>
ontology: nfdi4pso
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-9021-3197 xsd:string
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-1476-2121 xsd:string
property_value: http://purl.org/dc/elements/1.1/title "The DataPlant Ontology" xsd:string
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))\n\n\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/NFDI4PSO_1000119> \"\"^^xsd:string)\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/NFDI4PSO_1000120> \"\"^^xsd:string)\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/NFDI4PSO_1000126> \"\"^^xsd:string)\n)
treat-xrefs-as-equivalent: OBI
treat-xrefs-as-equivalent: EFO
treat-xrefs-as-equivalent: GENEPIO
treat-xrefs-as-equivalent: CHMO
treat-xrefs-as-equivalent: NCIT
treat-xrefs-as-equivalent: PSO
treat-xrefs-as-equivalent: CHEBI
treat-xrefs-as-equivalent: SIO
treat-xrefs-as-equivalent: ENVO
treat-xrefs-as-equivalent: ERO
treat-xrefs-as-equivalent: MS
treat-xrefs-as-equivalent: PATO
treat-xrefs-as-equivalent: UO
treat-xrefs-as-equivalent: OME
treat-xrefs-as-equivalent: EDAM
treat-xrefs-as-equivalent: dc
treat-xrefs-as-equivalent: SCTID
[Term]
id: NFDI4PSO:0000001
name: growth plot design
def: "A plan specification that states how treatments are allocated to the experimental units. It refers to the conceptual framework within which the experiment is conducted" []
synonym: "Experimental Randomisation" RELATED []
disjoint_from: NFDI4PSO:0000002 ! Read Alignment Software
is_obsolete: true
[Term]
id: NFDI4PSO:0000002
name: Read Alignment Software
def: "The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478" []
comment: “We might need to add the relationship with the class referenced above”
is_obsolete: true
[Term]
id: NFDI4PSO:0000003
name: Read Alignment Software Version
def: "The version of the read alignment software (NFDI4PSO:0000002)." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000004
name: Read Alignment Software Parameters
def: "The parameters of the read alignment software (NFDI4PSO:0000002)." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000005
name: Humidity Day
def: "This term defines the relative humidity of the air at daytime, it is a specialised concept of http://purl.obolibrary.org/obo/PECO_0007197" []
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"
is_obsolete: true
[Term]
id: NFDI4PSO:0000006
name: Humidity Night
def: "This term defines the relative humidity of the air at nighttime, it is a specialised concept of http://purl.obolibrary.org/obo/PECO_0007197”" []
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"
is_obsolete: true
[Term]
id: NFDI4PSO:0000007
name: Temperature Day
def: "This term defines the air temperature at daytime, it is a specialised concept of http://purl.obolibrary.org/obo/ENVO_09200001" []
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
is_obsolete: true
[Term]
id: NFDI4PSO:0000008
name: Temperature Night
def: "This term defines the air temperature at nighttime, it is a specialised concept of http://purl.obolibrary.org/obo/ENVO_09200001”" []
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
is_obsolete: true
[Term]
id: NFDI4PSO:0000009
name: Sample Collection Method
def: "Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ”" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000010
name: Metabolism quenching method
def: "Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000011
name: Sample storage
def: "The method used for sample storage. Should include the temperature of the sample. May include the medium (freezer or liquid nitrogen) and/or additional processing (freeze-drying) of the sample”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000012
name: Bio entity
def: "The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000013
name: Biosource amount
def: "The amount (typically in milligram) of material from which a bio entity (NFDI4PSO:0000012) is extracted.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000014
name: Extraction Kit
def: "The name of the commercial kit used for extraction of a bio entity (NFDI4PSO:0000012). Should include the company name.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000015
name: Library layout
def: "Determines the choice of DNA sequencing strategy, in which a single read is initiated from each end (paired-end) or one end (single-end) of DNA fragment”" []
comment: “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423"
is_obsolete: true
[Term]
id: NFDI4PSO:0000016
name: Library RNA amount
def: "Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000017
name: Base-calling Software
def: "The name of the software used for base-calling." []
comment: Alternative: http://edamontology.org/operation_3185
xref: EDAM:operation_3185
is_obsolete: true
[Term]
id: NFDI4PSO:0000018
name: Base-calling Software Version
def: "The version of the Base-calling Software (NFDI4PSO:0000017).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000019
name: Base-calling Software Parameters
def: "The parameters of the Base-calling Software (NFDI4PSO:0000017).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000020
name: Library strand
def: "Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (NFDI4PSO:0000015)”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000021
name: Raw data file format
def: "File format of the raw data file”" []
comment: “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915"
is_obsolete: true
[Term]
id: NFDI4PSO:0000022
name: Raw data file checksum
def: "Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000023
name: Data filtering software
def: "Name of the software applied for data filtering" []
comment: “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)”
is_obsolete: true
[Term]
id: NFDI4PSO:0000024
name: Data filtering software version
def: "The version of the data filtering software (NFDI4PSO:0000023).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000025
name: Data filtering Software Parameters
def: "The parameters of the data filtering software (NFDI4PSO:0000023).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000026
name: Genome reference sequence
def: "Name and version of the genome reference.”" []
comment: “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644”
is_obsolete: true
[Term]
id: NFDI4PSO:0000027
name: Processed data file format
def: "File format of the processed data file”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000028
name: Processed data file name
def: "Name of the processed data file”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000029
name: Processed data file checksum
def: "Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000030
name: Organism
def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." []
xref: OBI:0100026
is_obsolete: true
[Term]
id: NFDI4PSO:0000031
name: Genotype
def: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." []
xref: EFO:0000513
is_obsolete: true
[Term]
id: NFDI4PSO:0000032
name: Organism part
def: "The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm)." []
xref: EFO:0000635
is_obsolete: true
[Term]
id: NFDI4PSO:0000033
name: Plant age
def: "A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting)." []
comment: “This is a specialization of http://www.ebi.ac.uk/efo/EFO_0000246"
is_obsolete: true
[Term]
id: NFDI4PSO:0000034
name: Time point
def: "Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point." []
xref: EFO:0000724
is_obsolete: true
[Term]
id: NFDI4PSO:0000035
name: Library strategy
def: "Sequencing technique intended for a next generation sequencing library." []
xref: GENEPIO:0001973
is_obsolete: true
[Term]
id: NFDI4PSO:0000036
name: Library Selection
def: "The method used to select for or against, enrich, or screen the material being sequenced." []
xref: GENEPIO:0001940
is_obsolete: true
[Term]
id: NFDI4PSO:0000037
name: Library preparation kit
def: "Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids." []
xref: GENEPIO:0000085
is_obsolete: true
[Term]
id: NFDI4PSO:0000038
name: Library preparation kit version
def: "The version identifier of a packaged kit tailored for specific sequencing workflows." []
xref: GENEPIO:0000149
is_obsolete: true
[Term]
id: NFDI4PSO:0000039
name: Adapter sequence
def: "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters." []
xref: GENEPIO:0000083
is_obsolete: true
[Term]
id: NFDI4PSO:0000040
name: Next generation sequencing instrument model
def: "Model name or number of next generation sequencing instrument" []
xref: EFO:0003739
is_obsolete: true
[Term]
id: NFDI4PSO:0000041
name: Growth day length
def: "The time (e.g. hours of light) of the light regime in a growth experiment (e.g. 12hr light /12hr dark, 12/12, short day, long day)" []
comment: “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078"
is_obsolete: true
[Term]
id: NFDI4PSO:0000042
name: Biological replicate
def: "Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2')" []
comment: “Similar to http://purl.obolibrary.org/obo/MS_1001809"
is_obsolete: true
[Term]
id: NFDI4PSO:0000043
name: MS sample post-extraction
def: "Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000044
name: MS sample resuspension
def: "Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000045
name: MS sample type
def: "Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000046
name: Chromatography instrument model
def: "Company name, and instrument name or serial number of the chromatography instrument" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000048
is_obsolete: true
[Term]
id: NFDI4PSO:0000047
name: Chromatography autosampler model
def: "Company name, and name or serial number of the chromatography autosampler model" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000555
is_obsolete: true
[Term]
id: NFDI4PSO:0000048
name: Chromatography column model
def: "Company name, and name or serial number of the chromatography column" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000049
name: Chromatography guard column model
def: "Company name, and name or serial number of the chromatography guard column" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000614
is_obsolete: true
[Term]
id: NFDI4PSO:0000050
name: Extraction buffer
def: "Chemical buffer, solvent or solution used to extract a component from a biological sample." []
comment: “related to http://purl.obolibrary.org/obo/OBI_0302884. DB"
is_obsolete: true
[Term]
id: NFDI4PSO:0000051
name: Extraction buffer volume
def: "Volume of the buffer (NFDI4PSO:0000050) used during extraction." []
comment: related to http://purl.obolibrary.org/obo/OBI_0302884
is_obsolete: true
[Term]
id: NFDI4PSO:0000052
name: MS derivatization
def: "Derivatization for metabolomics mass spectrometry." []
xref: CHMO:0001485
is_obsolete: true
[Term]
id: NFDI4PSO:0000053
name: Chromatography column type
def: "Type of chromatography column (NFDI4PSO:0000048)" []
xref: CHMO:0001000
is_obsolete: true
[Term]
id: NFDI4PSO:0000054
name: Extraction method
def: "Method or kit that was used to extract DNA or RNA" []
comment: “More general than NFDI4PSO:0000014, because not everyone uses a kit for RNA/DNA extraction"
is_obsolete: true
[Term]
id: NFDI4PSO:0000055
name: Library source
def: "Type of source material that is being sequenced" []
xref: GENEPIO:0001965
is_obsolete: true
[Term]
id: NFDI4PSO:0000056
name: Library DNA amount
def: "Amount of DNA (microgram) used as starting material for library construction" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000057
name: Next generation sequencing platform
def: "Name of the company that produces next generation sequencing instruments" []
xref: GENEPIO:0000071
is_obsolete: true
[Term]
id: NFDI4PSO:0000058
name: Read length
def: "Numbers of base pairs per read" []
xref: GENEPIO:0000076
is_obsolete: true
[Term]
id: NFDI4PSO:0000059
name: Sequence assembly method
def: "Strategy that was used to assemble reads into contigs" []
comment: “Just two options should be possible: de-novo assembly or mapping"
xref: GENEPIO:0000090
is_obsolete: true
[Term]
id: NFDI4PSO:0000060
name: Sequence assembly algorithm version
def: "The version of the sequence assembly algorithm (OBI_0001522)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000061
name: Genome status
def: "Status of the genome sequence that is uploaded" []
comment: “Just two options should be possible: full or partial"
is_obsolete: true
[Term]
id: NFDI4PSO:0000062
name: RNA quality check
def: "Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000063
name: BioProject Accession Number
def: "The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345." []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C175890
is_obsolete: true
[Term]
id: NFDI4PSO:0000064
name: Sample type
def: "Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C70713
is_obsolete: true
[Term]
id: NFDI4PSO:0000065
name: Isolate
def: "A specific individual microbe and its genetically identical progeny separated on a single occasion from a sample taken from a host or culture system. [Definition Source: NCI]" []
xref: NCIT:C53471
is_obsolete: true
[Term]
id: NFDI4PSO:0000066
name: Cultivar
def: "A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species." []
comment: “[Definition Source: http://www.ebi.ac.uk/efo/EFO_0005136]"
xref: EFO:0005136
is_obsolete: true
[Term]
id: NFDI4PSO:0000067
name: Ecotype
def: "A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler" []
comment: “[Definition Source: http://www.ebi.ac.uk/efo/EFO_0000434]"
xref: EFO:0000434
is_obsolete: true
[Term]
id: NFDI4PSO:0000068
name: Cell line
def: "A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [Definition Source: NCI][attribution: On-line Medical Dictionary]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]"
xref: NCIT:C16403
is_obsolete: true
[Term]
id: NFDI4PSO:0000069
name: Cell type
def: "The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. [Definition Source: NCI]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C12508]"
xref: NCIT:C12508
is_obsolete: true
[Term]
id: NFDI4PSO:0000070
name: Developmental Stage
def: "A general term that usually refers to named landmark events during development of an organism. [Definition Source: NCI]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C43531]"
xref: NCIT:C43531
is_obsolete: true
[Term]
id: NFDI4PSO:0000071
name: Plant disease
def: "A biotic plant stress caused by exposure to an environment containing a biological stress agent." []
comment: “[Definition Source: http://purl.obolibrary.org/obo/PSO_0000013]"
xref: PSO:0000013
[Term]
id: NFDI4PSO:0000072
name: Plant disease stage
def: "Stage of plant disease (NFDI4PSO:0000071) at the time of sampling." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000073
name: Phenotype
def: "Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C16977
is_obsolete: true
[Term]
id: NFDI4PSO:0000074
name: Geogaphic Area
def: "Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg 'Canada: Vancouver' or 'Germany: halfway down Zugspitze, Alps'" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C16632
is_obsolete: true
[Term]
id: NFDI4PSO:0000075
name: Sample Collection Date
def: "The date on which the sample was collected" []
xref: NCIT:C81286
is_obsolete: true
[Term]
id: NFDI4PSO:0000076
name: Sample Collected By
def: "Indicates the person, group, or institution who performed the collection act. [Definition Source: NCI]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C45262"
xref: NCIT:C45262
is_obsolete: true
[Term]
id: NFDI4PSO:0000077
name: Metabolite Assignment File
def: "metabolite assignment file (MAF) as required by MetaboLights to describe metabolites analyzed during a metabolomics assay. Details see: https://www.ebi.ac.uk/metabolights/guides/MAF/Title" []
comment: “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title"
is_obsolete: true
[Term]
id: NFDI4PSO:0000078
name: BioSample Accession Number
def: "BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]!" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C175889
is_obsolete: true
[Term]
id: NFDI4PSO:0000079
name: label
def: "A role played by a part of a molecular entity distinguishable by the observer but not by the system and used to identify a tracer." []
xref: CHEBI:35209
is_obsolete: true
[Term]
id: NFDI4PSO:0000080
name: mobile phase
def: "A fluid that percolates through or along the stationary bed in chromatography." []
xref: CHMO:0000995
is_obsolete: true
[Term]
id: NFDI4PSO:0000081
name: Chromatography gradient
def: "Settings of the gradient used during (e.g. liquid, gas or ion) chromatography" []
comment: "term was previously !elution!"
is_obsolete: true
[Term]
id: NFDI4PSO:0000082
name: rRNA depletion
def: "Method used for rRNA depletion during construction of the sequencing library." []
comment: "see also http://purl.obolibrary.org/obo/NCIT_C18685"
is_obsolete: true
[Term]
id: NFDI4PSO:0002000
name: alias
def: "Unique identificator for a study. This is used to link experiments to the study." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002001
name: study_abstract
def: "Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002002
name: title
def: "Title of the study as would be used in a publication." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002003
name: latitude
def: "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system." []
xref: SIO:000319
is_obsolete: true
[Term]
id: NFDI4PSO:0002004
name: longitude
def: "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system." []
xref: SIO:000318
is_obsolete: true
[Term]
id: NFDI4PSO:0002005
name: project name
def: "Name of the project within which the experiment was organized." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002006
name: sequencing method
def: "Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002007
name: investigation type
def: "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium" []
is_obsolete: true
[Term]
id: NFDI4PSO:0002008
name: environment (feature)
def: "Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
xref: ENVO:01000813
is_obsolete: true
[Term]
id: NFDI4PSO:0002009
name: environment (material)
def: "The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
xref: ENVO:00010483
is_obsolete: true
[Term]
id: NFDI4PSO:0002010
name: plant-associated environmental package
def: "MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported" []
is_obsolete: true
[Term]
id: NFDI4PSO:0010000
name: ENA
def: "The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data." []
comment: https://www.ebi.ac.uk/ena/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:33:08Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010002
name: BIOSAMPLE
def: "The BioSample database contains descriptions of biological source materials used in experimental assays." []
comment: https://www.ncbi.nlm.nih.gov/biosample/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:33:08Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010004
name: BIOPROJECT
def: "A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project." []
comment: https://www.ncbi.nlm.nih.gov/bioproject/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:58:37Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010005
name: GENBANK
def: "GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis." []
comment: https://www.ncbi.nlm.nih.gov/genbank/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:59:49Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010006
name: SRA
def: "Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis." []
comment: https://www.ncbi.nlm.nih.gov/sra/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T09:02:27Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010007
name: PGP
def: "Plant Genomics & Phenomics Research Data Repository" []
comment: https://edal-pgp.ipk-gatersleben.de
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T09:03:35Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010008
name: BIA
def: "The BioImage Archive (BIA) stores and distributes biological images that are useful to life sciences researchers. It also provides data archiving services to the broader bioimaging database community including added-value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR." []
comment: https://www.ebi.ac.uk/bioimage-archive/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T09:04:46Z xsd:dateTime
created_by: Dominik Brilhaus[Term]
is_obsolete: true
[Term]
id: NFDI4PSO:0010009
name: Biosource material state
def: "The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay." []
comment: "Relates to NFDI4PSO:0000013 ! Biosource amount"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010010
name: Fresh material
def: "Fresh (non-dry) biosource material" []
comment: "Relates to https://cropontology.org/rdf/CO_347:0000193 ! Plant FW - Measurement"
is_a: NFDI4PSO:0010009
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010011
name: Dry material
def: "Dry biosource material" []
comment: "Relates to https://cropontology.org/rdf/CO_347:0000196 ! Plant DW - Measurement"
is_a: NFDI4PSO:0010009
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010012
name: Internal standard
def: "Internal standard added in known amount to an analytical sample" []
comment: "Similar to http://purl.obolibrary.org/obo/MSIO_0000005 ! internal standard role"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010013
name: Sample volume
def: "Volume taken from the sample to be assayed (measured)." []
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010014
name: Chromatography injection volume
def: "Volume of the sample injected during chromatography" []
comment: "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577 ! injection volume setting"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010015
name: Chromatography injection mode
def: "This is to specify split / splitless runs during e.g. gas-chromatography." []
comment: "Compare to http://purl.obolibrary.org/obo/OBI_0000525 ! splitless GC injector"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:1000000
name: _NotUse_TemplateTerm
def: "This is a helper term, since I was unable to properly handle custom `property_value` tags with Protege... Dominik" []
comment: "For property values that are not ontology terms themselves, but literals/strings, add `xsd:string`"
property_value: ER_target NFDI4PSO:1000099
property_value: ER_target "Put name of ER here" xsd:string
property_value: ER_target_term "Put name of ER target term for which this term should be selectable" xsd:string
property_value: UserInstruction "This could be a place for detailed user instructions in SWATE templates" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000003
name: RNA-Seq
def: "placeholder def of RNA-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000004
name: miRNA-Seq
def: "placeholder def of miRNA-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000005
name: ncRNA-Seq
def: "placeholder def of ncRNA-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000006
name: RNA-Seq (size fractionation)
def: "placeholder def of RNA-Seq (size fractionation)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000007
name: RNA-Seq (CAGE)
def: "placeholder def of RNA-Seq (CAGE)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000008
name: RNA-Seq (RACE)
def: "placeholder def of RNA-Seq (RACE)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000009
name: ssRNA-seq
def: "placeholder def of ssRNA-seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000010
name: ChIP-Seq
def: "placeholder def of ChIP-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000011
name: MNase-Seq
def: "placeholder def of MNase-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000012
name: MBD-Seq
def: "placeholder def of MBD-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000013
name: MRE-Seq
def: "placeholder def of MRE-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000014
name: Bisulfite-Seq
def: "placeholder def of Bisulfite-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000015
name: Bisulfite-Seq (reduced representation)
def: "placeholder def of Bisulfite-Seq (reduced representation)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000016
name: MeDIP-Seq
def: "placeholder def of MeDIP-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000017
name: DNase-Hypersensitivity
def: "placeholder def of DNase-Hypersensitivity" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000018
name: Tn-Seq
def: "placeholder def of Tn-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000019
name: FAIRE-seq
def: "placeholder def of FAIRE-seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string