diff --git a/docs/image_data_type.md b/docs/image_data_type.md index c8c3198..568faf8 100644 --- a/docs/image_data_type.md +++ b/docs/image_data_type.md @@ -2,21 +2,22 @@ [BioSamples](http://www.ebi.ac.uk/biosamples) takes sample records with a set of attributes. Each attribute has a name and a value. It can also have 'Units', or a 'Term Source' and a 'Term Source ID'. The Term Source and ID allow us to refer to entries in other databases or ontologies. This is fully described on the [BioSamples help pages](http://www.ebi.ac.uk/biosamples/help/st_scd.html). The following section describes the expectations for each data type within IMAGE. -### date +### number -Dates should be reported in an [ISO 8601](https://en.wikipedia.org/wiki/ISO_8601) format, YYYY-MM-DD for dates or YYYY-MM for months. To ensure clarity, the format must be reported as the 'units'. +A number, with units specified. BioSamples recommends that units are given without abbreviations. Terms defined in the [UO](http://www.ebi.ac.uk/ols/ontologies/uo) are encouraged to be used. For example, a birth weight could have a value of 1.3 and the units specified as '[kilogram](http://www.ebi.ac.uk/ols/ontologies/uo/terms?short_form=UO_0000009)' . -### NCBI taxon ID +### text -A species name and identifier from the [NCBI Taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy). For example, [human](http://www.ncbi.nlm.nih.gov/taxonomy/9606) would be described in the term with value of 'Homo sapiens', term source as 'NCBI Taxonomy' and term source ID as 9606. +Text, using US English spellings. No check on this type. -### number +### limited value -A number, with units specified. BioSamples recommends that units are given without abbreviations. Terms defined in the [UO](http://www.ebi.ac.uk/ols/ontologies/uo) are encouraged to be used. For example, a birth weight could have a value of 1.3 and the units specified as '[kilogram](http://www.ebi.ac.uk/ols/ontologies/uo/terms?short_form=UO_0000009)' . +Text type, but the allowed values are limited which either defined in the allowed values or point to other samples. Samples can be referred to in two ways. If the sample you need to reference is in the submission, use the sample name. If +the sample was already submitted, use the BioSample ID (e.g. SAMEA2821491). -### text +### date -Text, using US English spellings. +Dates should be reported in an [ISO 8601](https://en.wikipedia.org/wiki/ISO_8601) format, YYYY-MM-DD for dates or YYYY-MM for months. To ensure clarity, the format must be reported as the 'units'. ### URI @@ -30,10 +31,8 @@ A URI, such as 'http://www.imageh2020.eu/'. Depending on the context, http, ftp Digital Object Identifier (DOI) can unambiguously point to one publication, which can be resolved [here](http://www.doi.org/). -### ontology term +### ontology id A reference to an ontology term. The attribute value should be the term label. The term source should be the ontology used, and the term source ID should be an ID from that ontology. For example, cerebral cortex could be described with an ontology term from 'UBERON' with ontology ID of 'UBERON:0000956' and the attribute value is 'cerebral cortex'. Though in the experiment submission, direct links to ontologies cannot be submitted as attributes. The use of ontology terms is still encouraged by setting the attribute value to exactly match the term name in the ontology. +A special case is taxonomy. A species name and identifier from the [NCBI Taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy). For example, [human](http://www.ncbi.nlm.nih.gov/taxonomy/9606) would be described in the term with value of 'Homo sapiens', term source as 'NCBI Taxonomy' and term source ID as 9606. -### sample - -Samples can be referred to in two ways. If the sample you need to reference is in the submission, use the sample name. If the sample was already submitted, use the BioSample ID (e.g. SAMEA2821491). diff --git a/docs/image_data_type.pdf b/docs/image_data_type.pdf index f24f661..47989ce 100644 Binary files a/docs/image_data_type.pdf and b/docs/image_data_type.pdf differ diff --git a/docs/image_experiment_metadata.pdf b/docs/image_experiment_metadata.pdf index 5d50691..c44a6ca 100644 Binary files a/docs/image_experiment_metadata.pdf and b/docs/image_experiment_metadata.pdf differ diff --git a/docs/image_sample_metadata.md b/docs/image_sample_metadata.md index 546dbb0..61c4b58 100644 --- a/docs/image_sample_metadata.md +++ b/docs/image_sample_metadata.md @@ -28,11 +28,11 @@ Mandatory: * `Submission title` (*text*) A descriptive title for the submission * `Material` (*ontology_id*) type of the sample, either animal(organism) or sample (specimen from organism) Allowed values are: - * [Organism](http://purl.obolibrary.org/obo/OBI_0100026) - * [Specimen from organism](http://purl.obolibrary.org/obo/OBI_0001479) + * [organism](http://purl.obolibrary.org/obo/OBI_0100026) + * [specimen from organism](http://purl.obolibrary.org/obo/OBI_0001479) * `Person last name` (*text*) the last name of the submitter or contact for these samples, multiple persons can be provided - * `Person email` (*uri_value*) email of contact person + * `Person email` (*uri*) email of contact person * `Person affiliation` (*text*) affiliation of person * `Person role` (*text*) the role (type of the contribution) made by the person * `Organization name` (*text*) Organization name, multiple can be supplied, but at least one must be the name of the gene bank @@ -40,7 +40,7 @@ Mandatory: * `Gene bank name` (*text*) The name of the gene bank that the data of this submission belongs to, ideally use the value stored in EUGENA * `Gene bank country` (*limited value*) Country in which the gene bank resides, particularly important when different countries use the same database infrastructure, e.g. CryoWeb. The controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary * `Data source type` (*limited value*) the type of the data source the current Inject tool can handle Allowed values are: - * CyroWeb + * CryoWeb * CRB-Anim * Template @@ -52,15 +52,30 @@ Recommended: * `Submission description` (*text*) A brief description of the submission * `Person first name` (*text*) the first name of the submitter or contact for these samples, multiple persons can be provided * `Organization address` (*text*) The address of the organisation, multiple can be supplied - * `Organization country` (*text*) Country in which organization resides, the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary Allowed values are: - * the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary + * `Organization country` (*text*) Country in which organization resides, the organization list is maintained at https://github.com/cnr-ibba/IMAGE-InjectTool/blob/devel/django-data/image/image_app/management/commands/organization_list.csv Allowed values are: + * [France](http://purl.obolibrary.org/obo/NCIT_C16592) + * [Egypt](http://purl.obolibrary.org/obo/NCIT_C16530) + * [Colombia](http://purl.obolibrary.org/obo/NCIT_C16449) + * [Switzerland](http://purl.obolibrary.org/obo/NCIT_C17181) + * [Netherlands](http://purl.obolibrary.org/obo/NCIT_C16903) + * [Germany](http://purl.obolibrary.org/obo/NCIT_C16636) + * [Italy](http://purl.obolibrary.org/obo/NCIT_C16761) + * [Hungary](http://purl.obolibrary.org/obo/NCIT_C16699) + * [Morocco](http://purl.obolibrary.org/obo/NCIT_C16878) + * [Spain](http://purl.obolibrary.org/obo/NCIT_C17152) + * [Argentina](http://purl.obolibrary.org/obo/NCIT_C16305) + * [Sweden](http://purl.obolibrary.org/obo/NCIT_C17180) + * [United Kingdom](http://purl.obolibrary.org/obo/NCIT_C17233) + * [Poland](http://purl.obolibrary.org/obo/NCIT_C17002) + * [Portugal](http://purl.obolibrary.org/obo/NCIT_C17006) + * [Austria](http://purl.obolibrary.org/obo/NCIT_C16312) Optional: * `Description` (*text*) A brief description of the sample * `Person initial` (*text*) the initial of the submitter or contact for these samples, multiple persons can be provided - * `Organization uri` (*uri_value*) the websites of orgnization, multiple can be supplied + * `Organization uri` (*uri*) the websites of orgnization, multiple can be supplied * `Publication DOI` (*doi*) Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication ### Animal @@ -89,7 +104,7 @@ Recommended: Optional: - * `Child of` (*BioSample ID or Alternative animal ID*) Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted + * `Child of` (*text*) Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted ### Sample @@ -116,7 +131,7 @@ Recommended: * `Collection place longitude` (*number*) longitude of the place where the sample was collected * `Developmental stage` (*ontology_id*) developmental stage of the animal from which the specimen is collected * `Physiological stage` (*ontology_id*) physiological stage of the animal from which the specimen is collected - * `Availability` (*uri_value or text*) Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts. Allowed values are: + * `Availability` (*text*) Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts. Allowed values are: * no longer available * mailto:a.valid@email diff --git a/docs/image_sample_metadata.pdf b/docs/image_sample_metadata.pdf index a66e20e..fe8dc12 100644 Binary files a/docs/image_sample_metadata.pdf and b/docs/image_sample_metadata.pdf differ diff --git a/rulesets/sample_ruleset.json b/rulesets/sample_ruleset.json index eab482d..c3844e1 100644 --- a/rulesets/sample_ruleset.json +++ b/rulesets/sample_ruleset.json @@ -1,451 +1,573 @@ { - "name" : "IMAGE sample metadata rules", - "further_details_iri" : "https://github.com/bioinformatics-ptp/IMAGE-metadata/blob/master/README.md", "description" : "Validation rules for the IMAGE project.", "rule_groups" : [ { "name" : "standard", "rules" : [ { - "Allow Multiple" : "no", - "Description" : "the id used in the original data source to identify the record", - "Example" : "SAMEA4450075, ANIMAL:::ID:::132713,SAMPLE:::ID:::19483", "Required" : "mandatory", + "Allow Multiple" : "no", "Name" : "Data source ID", - "Type" : "text" + "Example" : "SAMEA4450075, ANIMAL:::ID:::132713,SAMPLE:::ID:::19483", + "Type" : "text", + "Description" : "the id used in the original data source to identify the record" }, { + "Description" : "the other identifier used in the orignal data source, e.g. accession, secondary id etc.", "Type" : "limited value", - "Name" : "Alternative id", - "Required" : "mandatory", "Example" : "Siems_0722_393449", + "Name" : "Alternative id", "Allow Multiple" : "no", - "Description" : "the other identifier used in the orignal data source, e.g. accession, secondary id etc." + "Required" : "mandatory" }, { "Description" : "A brief description of the sample", - "Allow Multiple" : "no", + "Type" : "text", + "Name" : "Description", "Example" : "Pig sperm sample from 3 year old duroc", "Required" : "optional", - "Type" : "text", - "Name" : "Description" + "Allow Multiple" : "no" }, { - "Example" : "IMAGE", - "Description" : "All samples are stated to be part of the IMAGE project, while still belonging to each individual gene bank. This tag is required to identify them in public databases", "Allow Multiple" : "no", + "Required" : "mandatory", + "Example" : "IMAGE", "Name" : "Project", "Type" : "text", + "Description" : "All samples are stated to be part of the IMAGE project, while still belonging to each individual gene bank. This tag is required to identify them in public databases", "Valid values" : [ "IMAGE" - ], - "Required" : "mandatory" + ] }, { - "Type" : "text", - "Name" : "Submission title", + "Allow Multiple" : "no", "Required" : "mandatory", "Example" : "German National Sperm Bank", - "Allow Multiple" : "no", + "Name" : "Submission title", + "Type" : "text", "Description" : "A descriptive title for the submission" }, { + "Name" : "Submission description", "Example" : "A collection of cattle samples from local breeding stocks", + "Required" : "recommended", "Allow Multiple" : "no", "Description" : "A brief description of the submission", - "Type" : "text", - "Name" : "Submission description", - "Required" : "recommended" + "Type" : "text" }, { - "Name" : "Material", + "Example" : "Specimen from Organism", + "Type" : "ontology_id", "Valid terms" : [ { - "term" : "OBI_0100026", + "ontology_name" : "OBI", "term_iri" : "http://purl.obolibrary.org/obo/OBI_0100026", "include_root" : 1, "allow_descendants" : 0, - "ontology_name" : "OBI" + "term" : "OBI_0100026" }, { "term" : "OBI_0001479", + "ontology_name" : "OBI", "term_iri" : "http://purl.obolibrary.org/obo/OBI_0001479", "include_root" : 1, - "allow_descendants" : 0, - "ontology_name" : "OBI" + "allow_descendants" : 0 } ], - "Example" : "Specimen from Organism", "Description" : "type of the sample, either animal(organism) or sample (specimen from organism)", - "Type" : "ontology_id", - "Valid values" : [ - "Organism", - "Specimen from organism" - ], "Required" : "mandatory", - "Allow Multiple" : "no" + "Allow Multiple" : "no", + "Name" : "Material", + "Valid values" : [ + "organism", + "specimen from organism" + ] }, { - "Required" : "mandatory", + "Description" : "the last name of the submitter or contact for these samples, multiple persons can be provided", "Type" : "text", + "Example" : "Harrison", "Name" : "Person last name", - "Description" : "the last name of the submitter or contact for these samples, multiple persons can be provided", "Allow Multiple" : "yes", - "Example" : "Harrison" + "Required" : "mandatory" }, { - "Example" : "W", - "Description" : "the initial of the submitter or contact for these samples, multiple persons can be provided", + "Required" : "optional", "Allow Multiple" : "yes", - "Type" : "text", "Name" : "Person initial", - "Required" : "optional" + "Example" : "W", + "Type" : "text", + "Description" : "the initial of the submitter or contact for these samples, multiple persons can be provided" }, { - "Required" : "recommended", - "Name" : "Person first name", + "Description" : "the first name of the submitter or contact for these samples, multiple persons can be provided", "Type" : "text", + "Example" : "Peter", + "Name" : "Person first name", "Allow Multiple" : "yes", - "Description" : "the first name of the submitter or contact for these samples, multiple persons can be provided", - "Example" : "Peter" + "Required" : "recommended" }, { - "Allow Multiple" : "yes", + "Type" : "uri", "Description" : "email of contact person", - "Example" : "mailto:peter@ebi.ac.uk", + "Allow Multiple" : "yes", "Required" : "mandatory", - "Name" : "Person email", - "Type" : "uri_value" + "Example" : "mailto:peter@ebi.ac.uk", + "Name" : "Person email" }, { - "Required" : "mandatory", - "Type" : "text", "Name" : "Person affiliation", - "Description" : "affiliation of person", + "Example" : "EMBL-EBI", + "Required" : "mandatory", "Allow Multiple" : "yes", - "Example" : "EMBL-EBI" + "Description" : "affiliation of person", + "Type" : "text" }, { + "Type" : "text", "Valid terms" : [ { - "ontology_name" : "\"\"EFO", - "allow_descendants" : 1, "term" : "\"\"EFO_0002012", + "allow_descendants" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/\"\"EFO_0002012", "include_root" : 0, - "term_iri" : "http://purl.obolibrary.org/obo/\"\"EFO_0002012" + "ontology_name" : "\"\"EFO" } ], - "Allow Multiple" : "yes", "Description" : "the role (type of the contribution) made by the person", - "Example" : "Submitter", "Required" : "mandatory", + "Allow Multiple" : "yes", "Name" : "Person role", - "Type" : "text" + "Example" : "Submitter" }, { - "Allow Multiple" : "yes", - "Description" : "Organization name, multiple can be supplied, but at least one must be the name of the gene bank", + "Name" : "Organization name", "Example" : "EMBL-EBI", "Required" : "mandatory", - "Type" : "text", - "Name" : "Organization name" + "Allow Multiple" : "yes", + "Description" : "Organization name, multiple can be supplied, but at least one must be the name of the gene bank", + "Type" : "text" }, { - "Required" : "recommended", - "Type" : "text", "Name" : "Organization address", + "Example" : "European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, UK", + "Required" : "recommended", "Allow Multiple" : "yes", "Description" : "The address of the organisation, multiple can be supplied", - "Example" : "European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, UK" + "Type" : "text" }, { + "Name" : "Organization uri", "Example" : "www.ebi.ac.uk", - "Description" : "the websites of orgnization, multiple can be supplied", + "Required" : "optional", "Allow Multiple" : "yes", - "Type" : "uri_value", - "Name" : "Organization uri", - "Required" : "optional" + "Description" : "the websites of orgnization, multiple can be supplied", + "Type" : "uri" }, { - "Required" : "recommended", "Valid values" : [ - "the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary" + "France", + "Egypt", + "Colombia", + "Switzerland", + "Netherlands", + "Germany", + "Italy", + "Hungary", + "Morocco", + "Spain", + "Argentina", + "Sweden", + "United Kingdom", + "Poland", + "Portugal", + "Austria" ], - "Type" : "text", "Name" : "Organization country", - "Description" : "Country in which organization resides, the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary", "Allow Multiple" : "yes", + "Required" : "recommended", + "Valid terms" : [ + { + "term" : "NCIT_C16592", + "allow_descendants" : 0, + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16592", + "ontology_name" : "NCIT" + }, + { + "term" : "NCIT_C16530", + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16530", + "include_root" : 1, + "allow_descendants" : 0, + "ontology_name" : "NCIT" + }, + { + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16449", + "term" : "NCIT_C16449" + }, + { + "term" : "NCIT_C17181", + "allow_descendants" : 0, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C17181", + "include_root" : 1, + "ontology_name" : "NCIT" + }, + { + "allow_descendants" : 0, + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16903", + "ontology_name" : "NCIT", + "term" : "NCIT_C16903" + }, + { + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16636", + "include_root" : 1, + "term" : "NCIT_C16636" + }, + { + "term" : "NCIT_C16761", + "ontology_name" : "NCIT", + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16761", + "include_root" : 1, + "allow_descendants" : 0 + }, + { + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16699", + "include_root" : 1, + "term" : "NCIT_C16699" + }, + { + "term" : "NCIT_C16878", + "ontology_name" : "NCIT", + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16878", + "allow_descendants" : 0 + }, + { + "term" : "NCIT_C17152", + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C17152", + "allow_descendants" : 0, + "ontology_name" : "NCIT" + }, + { + "term" : "NCIT_C16305", + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16305", + "include_root" : 1, + "allow_descendants" : 0, + "ontology_name" : "NCIT" + }, + { + "term" : "NCIT_C17180", + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C17180" + }, + { + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C17233", + "term" : "NCIT_C17233" + }, + { + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C17002", + "include_root" : 1, + "allow_descendants" : 0, + "ontology_name" : "NCIT", + "term" : "NCIT_C17002" + }, + { + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C17006", + "include_root" : 1, + "term" : "NCIT_C17006" + }, + { + "term" : "NCIT_C16312", + "ontology_name" : "NCIT", + "allow_descendants" : 0, + "include_root" : 1, + "term_iri" : "http://purl.obolibrary.org/obo/NCIT_C16312" + } + ], + "Description" : "Country in which organization resides, the organization list is maintained at https://github.com/cnr-ibba/IMAGE-InjectTool/blob/devel/django-data/image/image_app/management/commands/organization_list.csv", + "Type" : "text", "Example" : "United Kingdom" }, { "Type" : "ontology_id", - "Name" : "Organization role", - "Required" : "mandatory", - "Example" : "Submitter", - "Allow Multiple" : "yes", "Description" : "the role of the organization, e.g. biobank, funder", "Valid terms" : [ { - "ontology_name" : "\"\"EFO", "allow_descendants" : 1, - "term" : "\"\"EFO_0002012", + "include_root" : 0, "term_iri" : "http://purl.obolibrary.org/obo/\"\"EFO_0002012", - "include_root" : 0 + "ontology_name" : "\"\"EFO", + "term" : "\"\"EFO_0002012" } - ] + ], + "Required" : "mandatory", + "Allow Multiple" : "yes", + "Name" : "Organization role", + "Example" : "Submitter" }, { - "Example" : "doi://10.1139/o09-005", - "Description" : "Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication", - "Allow Multiple" : "no", - "Type" : "doi", "Name" : "Publication DOI", - "Required" : "optional" + "Example" : "doi:10.1139/o09-005", + "Required" : "optional", + "Allow Multiple" : "no", + "Description" : "Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication", + "Type" : "doi" }, { - "Required" : "mandatory", + "Example" : "CryoWeb", "Name" : "Gene bank name", - "Type" : "text", "Allow Multiple" : "no", + "Required" : "mandatory", "Description" : "The name of the gene bank that the data of this submission belongs to, ideally use the value stored in EUGENA", - "Example" : "CryoWeb" + "Type" : "text" }, { - "Allow Multiple" : "no", "Description" : "Country in which the gene bank resides, particularly important when different countries use the same database infrastructure, e.g. CryoWeb. The controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary", + "Type" : "limited value", "Example" : "Italy", - "Required" : "mandatory", "Name" : "Gene bank country", - "Type" : "limited value" + "Allow Multiple" : "no", + "Required" : "mandatory" }, { - "Example" : "CryoWeb", - "Description" : "the type of the data source the current Inject tool can handle", - "Allow Multiple" : "no", - "Name" : "Data source type", "Type" : "limited value", - "Required" : "mandatory", "Valid values" : [ - "CyroWeb", + "CryoWeb", "CRB-Anim", "Template" - ] + ], + "Description" : "the type of the data source the current Inject tool can handle", + "Allow Multiple" : "no", + "Required" : "mandatory", + "Example" : "CryoWeb", + "Name" : "Data source type" }, { - "Example" : "2018-04-27, version 1.5", + "Required" : "mandatory", "Allow Multiple" : "no", - "Description" : "the version of the data source, suggested to be either the dump date or the version number used by the source", - "Type" : "text", "Name" : "Data source version", - "Required" : "mandatory" + "Example" : "2018-04-27, version 1.5", + "Type" : "text", + "Description" : "the version of the data source, suggested to be either the dump date or the version number used by the source" }, { - "Example" : "Sus scrofa", - "Description" : "the species of the sample record", - "Allow Multiple" : "no", "Valid terms" : [ { + "term" : "\"\"NCBITaxon_1", "ontology_name" : "\"\"NCBITaxon", - "allow_descendants" : 1, "include_root" : 0, "term_iri" : "http://purl.obolibrary.org/obo/\"\"NCBITaxon_1", - "term" : "\"\"NCBITaxon_1" + "allow_descendants" : 1 } ], + "Description" : "the species of the sample record", "Type" : "ontology_id", "Name" : "Species", - "Required" : "mandatory" + "Example" : "Sus scrofa", + "Required" : "mandatory", + "Allow Multiple" : "no" } ] }, { - "name" : "organism", - "condition" : { - "attribute_value_match" : { - "Material" : "Organism" - } - }, "rules" : [ { - "Type" : "BioSample ID or Alternative animal ID", - "Name" : "Child of", "Required" : "optional", + "Allow Multiple" : "max 2", + "Name" : "Child of", "Example" : "SAMEA4450075 or 11", - "Description" : "Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted", - "Allow Multiple" : "max 2" + "Type" : "text", + "Description" : "Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted" }, { + "Description" : "the breed information contained in the original data source, could be a local language or breed variation", "Type" : "text", - "Name" : "Supplied breed", - "Required" : "mandatory", "Example" : "Bunte Bentheimer", + "Name" : "Supplied breed", "Allow Multiple" : "no", - "Description" : "the breed information contained in the original data source, could be a local language or breed variation" + "Required" : "mandatory" }, { "Example" : "Germany", - "Description" : "the country where the breed locates, the country name should be in the INSDC list", - "Allow Multiple" : "no", - "Type" : "text", "Name" : "EFABIS Breed country", - "Required" : "mandatory" + "Allow Multiple" : "no", + "Required" : "mandatory", + "Description" : "the country where the breed locates, the country name should be in the INSDC list", + "Type" : "text" }, { + "Required" : "recommended", + "Allow Multiple" : "no", + "Name" : "Mapped breed", + "Example" : "LBO_0000347", + "Type" : "ontology_id", + "Description" : "If possible breed will be mapped to a standardised breed ontology, both supplied and mapped breed will be available to end users", "Valid terms" : [ { "term" : "\"\"LBO_0000000", - "include_root" : 0, "term_iri" : "http://purl.obolibrary.org/obo/\"\"LBO_0000000", - "ontology_name" : "\"\"LBO", - "allow_descendants" : 1 + "include_root" : 0, + "allow_descendants" : 1, + "ontology_name" : "\"\"LBO" } - ], - "Example" : "LBO_0000347", - "Description" : "If possible breed will be mapped to a standardised breed ontology, both supplied and mapped breed will be available to end users", - "Allow Multiple" : "no", - "Name" : "Mapped breed", - "Type" : "ontology_id", - "Required" : "recommended" + ] }, { "Valid terms" : [ { - "ontology_name" : "PATO", - "allow_descendants" : 0, - "term" : "PATO_0000384", "include_root" : 1, - "term_iri" : "http://purl.obolibrary.org/obo/PATO_0000384" - }, - { + "term_iri" : "http://purl.obolibrary.org/obo/PATO_0000384", "allow_descendants" : 0, "ontology_name" : "PATO", + "term" : "PATO_0000384" + }, + { "term_iri" : "http://purl.obolibrary.org/obo/PATO_0000383", "include_root" : 1, + "allow_descendants" : 0, + "ontology_name" : "PATO", "term" : "PATO_0000383" } ], "Description" : "the sex of the animal", - "Allow Multiple" : "no", + "Type" : "ontology_id", "Example" : "PATO:0000384 (male)", - "Required" : "mandatory", "Name" : "Sex", - "Type" : "ontology_id" + "Allow Multiple" : "no", + "Required" : "mandatory" }, { - "Name" : "Birth location", - "Type" : "text", "Required" : "recommended", + "Allow Multiple" : "no", + "Name" : "Birth location", "Example" : "Germany", - "Description" : "name of the place where the animal was given birth", - "Allow Multiple" : "no" + "Type" : "text", + "Description" : "name of the place where the animal was given birth" }, { "Example" : "47.86591", - "Description" : "the longitude of the place where the animal was given birth in decimal degrees", - "Allow Multiple" : "no", - "Type" : "number", "Name" : "Birth location longitude", + "Allow Multiple" : "no", "Required" : "recommended", "Valid units" : [ "decimal degrees" - ] + ], + "Description" : "the longitude of the place where the animal was given birth in decimal degrees", + "Type" : "number" }, { - "Example" : "12.19115", - "Description" : "the latitude of the place where the animal was given birth in decimal degrees", - "Allow Multiple" : "no", - "Type" : "number", "Name" : "Birth location latitude", - "Required" : "recommended", + "Example" : "12.19115", "Valid units" : [ "decimal degrees" - ] + ], + "Required" : "recommended", + "Allow Multiple" : "no", + "Description" : "the latitude of the place where the animal was given birth in decimal degrees", + "Type" : "number" }, { - "Allow Multiple" : "no", - "Name" : "Birth location accuracy", - "Type" : "limited value", - "Required" : "mandatory", "Valid values" : [ "missing geographic information", "country level", "region level", "precise coordinates", "unknown accuracy level" - ] + ], + "Type" : "limited value", + "Name" : "Birth location accuracy", + "Required" : "mandatory", + "Allow Multiple" : "no" } - ] - }, - { - "name" : "specimen from organism", + ], + "name" : "organism", "condition" : { "attribute_value_match" : { - "Material" : "Specimen from Organism" + "Material" : "Organism" } - }, + } + }, + { "rules" : [ { - "Name" : "Derived from", "Type" : "text", - "Required" : "mandatory", - "Example" : "SAMEA4450079", "Description" : "The data source id or alternative id of the animal from which the sample was collected", - "Allow Multiple" : "no" + "Required" : "mandatory", + "Allow Multiple" : "no", + "Name" : "Derived from", + "Example" : "SAMEA4450079" }, { - "Required" : "recommended", "Type" : "uri", - "Name" : "Specimen collection protocol", "Description" : "A URL link to the protocol used to collect this sample", "Allow Multiple" : "no", - "Example" : "ftp://ftp.faang.ebi.ac.uk/ftp/protocols/samples/WUR_SOP_animal_sampling_20160405.pdf" + "Required" : "recommended", + "Example" : "ftp://ftp.faang.ebi.ac.uk/ftp/protocols/samples/WUR_SOP_animal_sampling_20160405.pdf", + "Name" : "Specimen collection protocol" }, { - "Required" : "mandatory", - "Type" : "date", "Name" : "Collection date", + "Example" : "17/01/1992", + "Required" : "mandatory", "Valid units" : [ "YYYY-MM-DD", "YYYY-MM", "YYYY" ], - "Description" : "Date when the sample was collected", "Allow Multiple" : "no", - "Example" : "1992-01-17" + "Description" : "Date when the sample was collected", + "Type" : "date" }, { + "Example" : "47.86591", + "Name" : "Collection place latitude", + "Allow Multiple" : "no", + "Required" : "recommended", "Valid units" : [ "decimal degrees" ], - "Name" : "Collection place latitude", - "Type" : "number", - "Required" : "recommended", - "Example" : "47.86591", - "Allow Multiple" : "no", - "Description" : "latitude of the place where the sample was collected" + "Description" : "latitude of the place where the sample was collected", + "Type" : "number" }, { + "Description" : "longitude of the place where the sample was collected", + "Type" : "number", + "Name" : "Collection place longitude", + "Example" : "12.19115", "Valid units" : [ "decimal degrees" ], "Required" : "recommended", - "Name" : "Collection place longitude", - "Type" : "number", - "Allow Multiple" : "no", - "Description" : "longitude of the place where the sample was collected", - "Example" : "12.19115" + "Allow Multiple" : "no" }, { + "Allow Multiple" : "no", "Required" : "mandatory", - "Type" : "text", + "Example" : "Germany", "Name" : "Collection place", - "Description" : "name of the place where the sample was collected", - "Allow Multiple" : "no", - "Example" : "Germany" + "Type" : "text", + "Description" : "name of the place where the sample was collected" }, { - "Allow Multiple" : "no", + "Name" : "Collection place accuracy", "Required" : "mandatory", + "Allow Multiple" : "no", "Valid values" : [ "missing geographic information", "country level", @@ -453,82 +575,96 @@ "precise coordinates", "unknown accuracy level" ], - "Name" : "Collection place accuracy", "Type" : "limited value" }, { - "Required" : "mandatory", - "Name" : "Organism part", - "Type" : "ontology_id", + "Description" : "Ontology for organism part where the specimen was taken from", "Valid terms" : [ { "term" : "UBERON_0001062", + "allow_descendants" : 1, "term_iri" : "http://purl.obolibrary.org/obo/UBERON_0001062", "include_root" : 0, - "ontology_name" : "UBERON", - "allow_descendants" : 1 + "ontology_name" : "UBERON" } ], - "Allow Multiple" : "no", - "Description" : "Ontology for organism part where the specimen was taken from", - "Example" : "UBERON_0001968 (semen)" + "Type" : "ontology_id", + "Name" : "Organism part", + "Example" : "UBERON_0001968 (semen)", + "Required" : "mandatory", + "Allow Multiple" : "no" }, { "Type" : "ontology_id", - "Name" : "Developmental stage", - "Required" : "recommended", - "Example" : "EFO_0001272 (adult)", "Description" : "developmental stage of the animal from which the specimen is collected", - "Allow Multiple" : "no", "Valid terms" : [ { - "allow_descendants" : 1, - "ontology_name" : "EFO", - "include_root" : 0, + "term" : "EFO_0000399", "term_iri" : "http://purl.obolibrary.org/obo/EFO_0000399", - "term" : "EFO_0000399" + "include_root" : 0, + "allow_descendants" : 1, + "ontology_name" : "EFO" } - ] - }, - { - "Type" : "ontology_id", - "Name" : "Physiological stage", + ], "Required" : "recommended", - "Example" : "PATO_0001701 (mature)", "Allow Multiple" : "no", - "Description" : "physiological stage of the animal from which the specimen is collected", + "Name" : "Developmental stage", + "Example" : "EFO_0001272 (adult)" + }, + { "Valid terms" : [ { + "ontology_name" : "PATO", + "allow_descendants" : 1, "term_iri" : "http://purl.obolibrary.org/obo/PATO_0000261", "include_root" : 0, - "term" : "PATO_0000261", - "allow_descendants" : 1, - "ontology_name" : "PATO" + "term" : "PATO_0000261" } - ] + ], + "Description" : "physiological stage of the animal from which the specimen is collected", + "Type" : "ontology_id", + "Example" : "PATO_0001701 (mature)", + "Name" : "Physiological stage", + "Allow Multiple" : "no", + "Required" : "recommended" }, { - "Description" : "Animal age at the point of collection.", + "Required" : "optional", + "Valid units" : [ + "minutes", + "hours", + "days", + "weeks", + "months", + "years", + "minute", + "hour", + "day", + "week", + "month", + "year" + ], "Allow Multiple" : "no", + "Name" : "Animal age at collection", "Example" : "3 years", - "Required" : "optional", "Type" : "number", - "Name" : "Animal age at collection" + "Description" : "Animal age at the point of collection." }, { - "Example" : "mailto:vdc-internal@ebi.ac.uk", - "Description" : "Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts.", "Allow Multiple" : "no", - "Type" : "uri_value or text", - "Name" : "Availability", "Required" : "recommended", + "Example" : "mailto:vdc-internal@ebi.ac.uk", + "Name" : "Availability", + "Type" : "text", + "Description" : "Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts.", "Valid values" : [ "no longer available", "mailto:a.valid@email" ] }, { - "Required" : "recommended", + "Type" : "text", + "Description" : "How the sample was stored. Temperatures are in degree Celsius. 'Frozen, vapor phase' refers to storing samples above liquid nitrogen in the vapor", "Valid values" : [ "ambient temperature", "cut slide", @@ -542,15 +678,13 @@ "paraffin block at ambient temperatures (+15 to +30 degrees Celsius)", "freeze dried" ], - "Type" : "text", - "Name" : "Sample storage", + "Required" : "recommended", "Allow Multiple" : "no", - "Description" : "How the sample was stored. Temperatures are in degree Celsius. 'Frozen, vapor phase' refers to storing samples above liquid nitrogen in the vapor" + "Name" : "Sample storage" }, { - "Allow Multiple" : "no", + "Type" : "text", "Description" : "How the sample was prepared for storage", - "Required" : "recommended", "Valid values" : [ "cryopreservation in liquid nitrogen (dead tissue)", "cryopreservation in dry ice (dead tissue)", @@ -562,12 +696,12 @@ "freeze dried (vaiable for reproduction)", "freeze dried" ], - "Name" : "Sample storage processing", - "Type" : "text" + "Allow Multiple" : "no", + "Required" : "recommended", + "Name" : "Sample storage processing" }, { - "Name" : "Sampling to preparation interval", - "Type" : "number", + "Allow Multiple" : "no", "Required" : "optional", "Valid units" : [ "minutes", @@ -583,11 +717,20 @@ "month", "year" ], - "Description" : "How long between the sample being taken and the assay experiment preperations commencing. If sample preperations were then left in intermediate stages after preperation commenced, for example as sheared chromatin, then this should be made clear in your protocols", - "Allow Multiple" : "no" + "Name" : "Sampling to preparation interval", + "Type" : "number", + "Description" : "How long between the sample being taken and the assay experiment preperations commencing. If sample preperations were then left in intermediate stages after preperation commenced, for example as sheared chromatin, then this should be made clear in your protocols" } - ] + ], + "name" : "specimen from organism", + "condition" : { + "attribute_value_match" : { + "Material" : "Specimen from Organism" + } + } } - ] + ], + "further_details_iri" : "https://github.com/bioinformatics-ptp/IMAGE-metadata/blob/master/README.md", + "name" : "IMAGE sample metadata rules" } diff --git a/rulesets/sample_ruleset.md b/rulesets/sample_ruleset.md index 546dbb0..61c4b58 100644 --- a/rulesets/sample_ruleset.md +++ b/rulesets/sample_ruleset.md @@ -28,11 +28,11 @@ Mandatory: * `Submission title` (*text*) A descriptive title for the submission * `Material` (*ontology_id*) type of the sample, either animal(organism) or sample (specimen from organism) Allowed values are: - * [Organism](http://purl.obolibrary.org/obo/OBI_0100026) - * [Specimen from organism](http://purl.obolibrary.org/obo/OBI_0001479) + * [organism](http://purl.obolibrary.org/obo/OBI_0100026) + * [specimen from organism](http://purl.obolibrary.org/obo/OBI_0001479) * `Person last name` (*text*) the last name of the submitter or contact for these samples, multiple persons can be provided - * `Person email` (*uri_value*) email of contact person + * `Person email` (*uri*) email of contact person * `Person affiliation` (*text*) affiliation of person * `Person role` (*text*) the role (type of the contribution) made by the person * `Organization name` (*text*) Organization name, multiple can be supplied, but at least one must be the name of the gene bank @@ -40,7 +40,7 @@ Mandatory: * `Gene bank name` (*text*) The name of the gene bank that the data of this submission belongs to, ideally use the value stored in EUGENA * `Gene bank country` (*limited value*) Country in which the gene bank resides, particularly important when different countries use the same database infrastructure, e.g. CryoWeb. The controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary * `Data source type` (*limited value*) the type of the data source the current Inject tool can handle Allowed values are: - * CyroWeb + * CryoWeb * CRB-Anim * Template @@ -52,15 +52,30 @@ Recommended: * `Submission description` (*text*) A brief description of the submission * `Person first name` (*text*) the first name of the submitter or contact for these samples, multiple persons can be provided * `Organization address` (*text*) The address of the organisation, multiple can be supplied - * `Organization country` (*text*) Country in which organization resides, the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary Allowed values are: - * the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary + * `Organization country` (*text*) Country in which organization resides, the organization list is maintained at https://github.com/cnr-ibba/IMAGE-InjectTool/blob/devel/django-data/image/image_app/management/commands/organization_list.csv Allowed values are: + * [France](http://purl.obolibrary.org/obo/NCIT_C16592) + * [Egypt](http://purl.obolibrary.org/obo/NCIT_C16530) + * [Colombia](http://purl.obolibrary.org/obo/NCIT_C16449) + * [Switzerland](http://purl.obolibrary.org/obo/NCIT_C17181) + * [Netherlands](http://purl.obolibrary.org/obo/NCIT_C16903) + * [Germany](http://purl.obolibrary.org/obo/NCIT_C16636) + * [Italy](http://purl.obolibrary.org/obo/NCIT_C16761) + * [Hungary](http://purl.obolibrary.org/obo/NCIT_C16699) + * [Morocco](http://purl.obolibrary.org/obo/NCIT_C16878) + * [Spain](http://purl.obolibrary.org/obo/NCIT_C17152) + * [Argentina](http://purl.obolibrary.org/obo/NCIT_C16305) + * [Sweden](http://purl.obolibrary.org/obo/NCIT_C17180) + * [United Kingdom](http://purl.obolibrary.org/obo/NCIT_C17233) + * [Poland](http://purl.obolibrary.org/obo/NCIT_C17002) + * [Portugal](http://purl.obolibrary.org/obo/NCIT_C17006) + * [Austria](http://purl.obolibrary.org/obo/NCIT_C16312) Optional: * `Description` (*text*) A brief description of the sample * `Person initial` (*text*) the initial of the submitter or contact for these samples, multiple persons can be provided - * `Organization uri` (*uri_value*) the websites of orgnization, multiple can be supplied + * `Organization uri` (*uri*) the websites of orgnization, multiple can be supplied * `Publication DOI` (*doi*) Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication ### Animal @@ -89,7 +104,7 @@ Recommended: Optional: - * `Child of` (*BioSample ID or Alternative animal ID*) Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted + * `Child of` (*text*) Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted ### Sample @@ -116,7 +131,7 @@ Recommended: * `Collection place longitude` (*number*) longitude of the place where the sample was collected * `Developmental stage` (*ontology_id*) developmental stage of the animal from which the specimen is collected * `Physiological stage` (*ontology_id*) physiological stage of the animal from which the specimen is collected - * `Availability` (*uri_value or text*) Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts. Allowed values are: + * `Availability` (*text*) Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts. Allowed values are: * no longer available * mailto:a.valid@email diff --git a/rulesets/sample_ruleset.txt b/rulesets/sample_ruleset.txt index 9fddd8b..07e2a9b 100644 --- a/rulesets/sample_ruleset.txt +++ b/rulesets/sample_ruleset.txt @@ -5,26 +5,26 @@ standard Description text optional no Pig sperm sample from 3 year old duroc standard Project text mandatory no """IMAGE""" IMAGE "All samples are stated to be part of the ""IMAGE"" project, while still belonging to each individual gene bank. This tag is required to identify them in public databases" standard Submission title text mandatory no German National Sperm Bank A descriptive title for the submission standard Submission description text recommended no A collection of cattle samples from local breeding stocks A brief description of the submission -standard Material ontology_id mandatory no """Organism"",""Specimen from organism""" """OBI_0100026"",""OBI_0001479""" Specimen from Organism "type of the sample, either animal(organism) or sample (specimen from organism)" +standard Material ontology_id mandatory no """organism"",""specimen from organism""" """OBI_0100026"",""OBI_0001479""" Specimen from Organism "type of the sample, either animal(organism) or sample (specimen from organism)" standard Person last name text mandatory yes Harrison "the last name of the submitter or contact for these samples, multiple persons can be provided" standard Person initial text optional yes W "the initial of the submitter or contact for these samples, multiple persons can be provided" standard Person first name text recommended yes Peter "the first name of the submitter or contact for these samples, multiple persons can be provided" -standard Person email uri_value mandatory yes mailto:peter@ebi.ac.uk email of contact person +standard Person email uri mandatory yes mailto:peter@ebi.ac.uk email of contact person standard Person affiliation text mandatory yes EMBL-EBI affiliation of person standard Person role text mandatory yes "descendants of ""EFO_0002012""" Submitter the role (type of the contribution) made by the person standard Organization name text mandatory yes EMBL-EBI "Organization name, multiple can be supplied, but at least one must be the name of the gene bank" standard Organization address text recommended yes "European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, UK" "The address of the organisation, multiple can be supplied" -standard Organization uri uri_value optional yes www.ebi.ac.uk "the websites of orgnization, multiple can be supplied" -standard Organization country text recommended yes the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary United Kingdom "Country in which organization resides, the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary" +standard Organization uri uri optional yes www.ebi.ac.uk "the websites of orgnization, multiple can be supplied" +standard Organization country text recommended yes """France"",""Egypt"",""Colombia"",""Switzerland"",""Netherlands"",""Germany"",""Italy"",""Hungary"",""Morocco"",""Spain"",""Argentina"",""Sweden"",""United Kingdom"",""Poland"",""Portugal"",""Austria""" """NCIT_C16592"",""NCIT_C16530"",""NCIT_C16449"",""NCIT_C17181"",""NCIT_C16903"",""NCIT_C16636"",""NCIT_C16761"",""NCIT_C16699"",""NCIT_C16878"",""NCIT_C17152"",""NCIT_C16305"",""NCIT_C17180"",""NCIT_C17233"",""NCIT_C17002"",""NCIT_C17006"",""NCIT_C16312""" United Kingdom "Country in which organization resides, the organization list is maintained at https://github.com/cnr-ibba/IMAGE-InjectTool/blob/devel/django-data/image/image_app/management/commands/organization_list.csv" standard Organization role ontology_id mandatory yes "descendants of ""EFO_0002012""" Submitter "the role of the organization, e.g. biobank, funder" -standard Publication DOI doi optional no """doi://10.1139/o09-005""" "Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication" +standard Publication DOI doi optional no """doi:10.1139/o09-005""" "Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication" standard Gene bank name text mandatory no """CryoWeb""" "The name of the gene bank that the data of this submission belongs to, ideally use the value stored in EUGENA" standard Gene bank country limited value mandatory no """Italy""" "Country in which the gene bank resides, particularly important when different countries use the same database infrastructure, e.g. CryoWeb. The controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary" -standard Data source type limited value mandatory no """CyroWeb"", ""CRB-Anim"",""Template""" """CryoWeb""" the type of the data source the current Inject tool can handle +standard Data source type limited value mandatory no """CryoWeb"", ""CRB-Anim"",""Template""" """CryoWeb""" the type of the data source the current Inject tool can handle standard Data source version text mandatory no """2018-04-27"", ""version 1.5""" "the version of the data source, suggested to be either the dump date or the version number used by the source" standard Species ontology_id mandatory no "descendants of ""NCBITaxon_1""" Sus scrofa the species of the sample record organism conditions: Material:Organism -organism Child of BioSample ID or Alternative animal ID optional max 2 SAMEA4450075 or 11 Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted +organism Child of text optional max 2 SAMEA4450075 or 11 Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted organism Supplied breed text mandatory no Bunte Bentheimer "the breed information contained in the original data source, could be a local language or breed variation" organism EFABIS Breed country text mandatory no Germany "the country where the breed locates, the country name should be in the INSDC list" organism Mapped breed ontology_id recommended no "descendants of ""LBO_0000000""" LBO_0000347 "If possible breed will be mapped to a standardised breed ontology, both supplied and mapped breed will be available to end users" @@ -36,7 +36,7 @@ organism Birth location accuracy limited value mandatory no """missing geographi specimen from organism conditions: Material:Specimen from Organism specimen from organism Derived from text mandatory no SAMEA4450079 The data source id or alternative id of the animal from which the sample was collected specimen from organism Specimen collection protocol uri recommended no ftp://ftp.faang.ebi.ac.uk/ftp/protocols/samples/WUR_SOP_animal_sampling_20160405.pdf A URL link to the protocol used to collect this sample -specimen from organism Collection date date mandatory no "YYYY-MM-DD, YYYY-MM, YYYY" 1992-01-17 Date when the sample was collected +specimen from organism Collection date date mandatory no "YYYY-MM-DD, YYYY-MM, YYYY" 17/01/1992 Date when the sample was collected specimen from organism Collection place latitude number recommended no decimal degrees 47.86591 latitude of the place where the sample was collected specimen from organism Collection place longitude number recommended no decimal degrees 12.19115 longitude of the place where the sample was collected specimen from organism Collection place text mandatory no Germany name of the place where the sample was collected @@ -44,8 +44,8 @@ specimen from organism Collection place accuracy limited value mandatory no """m specimen from organism Organism part ontology_id mandatory no descendants of UBERON_0001062 UBERON_0001968 (semen) Ontology for organism part where the specimen was taken from specimen from organism Developmental stage ontology_id recommended no descendants of EFO_0000399 EFO_0001272 (adult) developmental stage of the animal from which the specimen is collected specimen from organism Physiological stage ontology_id recommended no descendants of PATO_0000261 PATO_0001701 (mature) physiological stage of the animal from which the specimen is collected -specimen from organism Animal age at collection number optional no 3 years Animal age at the point of collection. -specimen from organism Availability uri_value or text recommended no """no longer available"",""mailto:a.valid@email""" mailto:vdc-internal@ebi.ac.uk "Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts." +specimen from organism Animal age at collection number optional no """minutes"",""hours"",""days"",""weeks"",""months"",""years"",""minute"",""hour"",""day"",""week"",""month"",""year""" 3 years Animal age at the point of collection. +specimen from organism Availability text recommended no """no longer available"",""mailto:a.valid@email""" mailto:vdc-internal@ebi.ac.uk "Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:samples@example.ac.uk'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts." specimen from organism Sample storage text recommended no """ambient temperature"",""cut slide"",""frozen, -80 degrees Celsius freezer"",""frozen, -20 degrees Celsius freezer"",""frozen, liquid nitrogen"",""frozen, vapor phase"",""paraffin block"",""RNAlater, frozen -20 degrees Celsius"",""TRIzol, frozen"",""paraffin block at ambient temperatures (+15 to +30 degrees Celsius)"",""freeze dried""" "How the sample was stored. Temperatures are in degree Celsius. 'Frozen, vapor phase' refers to storing samples above liquid nitrogen in the vapor" specimen from organism Sample storage processing text recommended no """cryopreservation in liquid nitrogen (dead tissue)"",""cryopreservation in dry ice (dead tissue)"",""cryopreservation of live cells in liquid nitrogen"",""cryopreservation, other"",""formalin fixed, unbuffered"",""formalin fixed, buffered"",""formalin fixed and paraffin embedded"",""freeze dried (vaiable for reproduction)"",""freeze dried""" How the sample was prepared for storage specimen from organism Sampling to preparation interval number optional no """minutes"",""hours"",""days"",""weeks"",""months"",""years"",""minute"",""hour"",""day"",""week"",""month"",""year""" "How long between the sample being taken and the assay experiment preperations commencing. If sample preperations were then left in intermediate stages after preperation commenced, for example as sheared chromatin, then this should be made clear in your protocols" diff --git a/scripts/generateRulesetInJSON.pl b/scripts/generateRulesetInJSON.pl index 033988b..e01f124 100644 --- a/scripts/generateRulesetInJSON.pl +++ b/scripts/generateRulesetInJSON.pl @@ -148,12 +148,6 @@ print JSON_OUT "$json\n"; close JSON_OUT; -sub trim(){ - my $s = shift; - $s =~ s/^\s+|\s+$//g; - return $s; -} - sub usage(){ print "Usage: perl generateRulesetInJSON.pl \n"; print "This script convert the rulesets in TSV format (compiled in Excel) into a JSON file.\n";