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ABCDEFGHIJKLMNOPQRSTUVWXYZAAABAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZBABBBCBDBEBF
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SubtitleBioschemas specification describing a dataset record.UniProt (protein)PDBe (protein)InterPro (protein)PDBe (protein structure)InterPro (entry)InterPro (signature)Sample
BIP - Phenotype (trials/studies)
BIP - Phenotype (cultivars)
BIP - Phenotype (traits/phenotypes)
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DescriptionA Record in a Dataset that can act as a dataset itself (for instance it can has its own distribution). The main difference with a Dataset is that it refers to a particular PhysicalEntity uniquely identified (even if that particular PhysicalEntity turns out to be constitued by multiple PhysicalEntities).
https://bip.earlham.ac.uk/data_tables?model=plant_trials
bip.earlham.ac.ukbip.earlham.ac.uk
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Search for trialSearch for cultivarsSearch for trait
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schema.orgbioschemas
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PropertyExpected TypeDescriptionBSC DescriptionMarginalityCardinality
Controlled Vocabulary
NameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCase
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Extends Dataset
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citationCreativeWork or URLA citation or reference to a creative work, such as a publication, web page, scholarly article, etc.RecommendedMANYpublications"citation": [
{
"@id": "http://www.identifiers.org/pubmed/10194451",
"@type": "ScholarlyArticle",
"name": {
"@language": "en",
"@value": "A novel SH2-containing ..."
},
"sameAs": [
"https://www.ncbi.nlm.nih.gov/pubmed/10194451",
"http://europepmc.org/abstract/MED/10194451",
"http://purl.uniprot.org/citations/10194451"
]
},
...
]
MatchNo MatchNot Match"citation": {
"@id": "http://www.identifiers.org/pubmed:25686603",
"@type": "ScholarlyArticle"
}
Matchliterature"citation": [
{
"@type": "ScholarlyArticle",
"identifier": "https://identifiers.org/pubmed:1279434"
}, ...
]
Matchliterature"citation": {
"@type": "ScholarlyArticle",
"identifier": "https://identifiers.org/pubmed:12169629"
},
Matchplant_trials: data provenance (it has only sometimes this information) Partial MatchNot sureNot Match
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dateCreatedDate or
DateTime
The date on which the CreativeWork/BiologicalEntity was created or the item was added to a DataFeed/Dataset/DataRepository.OptionalONEentry history (integrated into UniProtKB)"dateCreated": "1986-07-21"MatchNo Matchdate created"dateCreated": "1986-07-21"Match
"dateCreated": "2014-08-28",
Matchdate createdPartial Matchdate createdPartial Matchplant_trials: created at3/6/2016 08:36:13Matchplant_variety : year registered1905-06-20 00:00:00MatchPlant scoring unit: created at2016-06-06 16:07:54Match
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dateModifiedDate or
DateTime
The date on which the CreativeWork/BiologicalEntity was most recently modified or when the item's entry was modified within a DataFeed/Dataset/DataRepository.OptionalONElast modified"dateModified": "2017-03-15"MatchNo Matchdate modified"dateModified": "2017-03-15"Match
"datePublished": "2015-02-11",
Matchdate modifiedPartial Matchdate modifiedPartial Matchplant_lines : updated at14/06/2016 16:22:59Matchplant variety: updated at2016-06-14 16:22:59MatchPlant scoring unit: updated at2016-06-14 16:19:59Match
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datePublishedDateDate of first broadcast/publication.OptionalONENo MatchNo Matchpublication date"datePublished": "1986-07-21"Match"dateModified": "2015-03-18",Matchpublication datePartial Matchpublication datePartial MatchNot MatchNot MatchNot Match
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hasPartThingIndicates a Thing that is (in some sense) a part of this Thing.
Inverse property: isPartOf.
OptionalMANYfeaturesNo MatchNo Matchmatches"hasPart": [
{
"@type": "BiologicalEntity",
"biologicalType": ["protein annotation", "domain"]
},...
]
Match"hasPart": {
"@type": "BiologicalEntity",
"@id": "http://identifiers.org/interpro:IPR001245",
"biologicalType": "Domain",
"identifier": "IPR001245",
...
}
MatchTrait ? PlantLine?Not Match
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isBasedOnCreativeWork or
URL or BiologicalEntity
A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.OptionalMANYNo MatchNo MatchNot Match"isBasedOn":
{
"@type": "BiologicalEntity",
"biologicalType": "Protein",
...
}
Matchsignatures"isBasedOn": [
{
"@type": ["BiologicalEntity", "DatasetEntry"],
"isMentionedIn": "https://www.ebi.ac.uk/interpro/member-database/Pfam",
"name": "SH3_9",
"identifier": "https://identifiers.org/pfam:PF14604",
"biologicalType": ["protein annotation", "domain"]
},...
]
MatchNot MatchNot MatchGermplasm/PlantAccession?Not Match
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isPartOfThingIndicates a Thing that this Thing is (in some sense) part of.
Inverse property: hasPart.
OptionalMANYgene"isPartOf": {
"@type": "BiologicalEntity",
"biologicalType": "gene",
"name": {
"@language": "en",
"@value": "ABL1"
}
}
MatchNo MatchNot Matchmatches"isPartOf": [
{
"@type": ["BiologicalEntity", "DatasetEntry"],
"biologicalType": "protein",
"name": "Mitogen-activated protein kinase kinase kinase mlk-1",
"identifier": "https://identifiers.org/uniprot:A0A0K3AV08"
},...
]
Matchmatches"isPartOf": [
{
"@type": ["BiologicalEntity", "DatasetEntry"],
"biologicalType": "protein",
"name": "Mitogen-activated protein kinase kinase kinase mlk-1",
"identifier": "https://identifiers.org/uniprot:A0A0K3AV08"
},...
]
MatchProject / Investigation ?Partial MatchNot MatchPlant Trial associatedhttps://bip.earlham.ac.uk/data_tables?model=plant_trials&query[id]=47Match
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alternateNameTextAn alias for the item.RecommendedMANYalternative names"alternateName": [
{
"@language": "en",
"@value": "ABL1_HUMAN"
},
...
]
MatchNo Matchother names"alternateName": [
"ABL1_HUMAN",
...
]
MatchNo Matchother namesMatchother namesMatchNot Match(canonical_name, to be studied)Partial MatchNot Match
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descriptionTextA description of the item.RecommendedONEfunction"description": {
"@language": "en",
"@value": "Non-receptor tyrosine-protein kinase that plays a role..."
}
MatchNo Matchdescription"description": "Non-receptor tyrosine-protein kinase that plays a role..."MatchNo Matchdescription"description": "SH3 (src Homology-3) domains are …"
Matchdescription"description": "SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase P12931. The structure is a partly opened beta barrel.",
MatchTrial description387 Brassica napus accessions used in the RIPR project for which mRNAseq data were submitted to SRA under PRJNA309367MatchPlant varieties : commentsBrassica napus var. oleifera annua; Spring oilseed rape; erucic acid <1 ; glucosinolates <30 ;MatchNot Match
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identifierPropertyValue or
Text or
URL
The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details. Recommendation: identifiers.org whenever possibleMinimumONEaccession"identifier": "http://www.identifiers.org/uniprot/P00519"Match4-letter PDBe code"identifier": "P00519"Matchaccession"identifier": "http://www.identifiers.org/uniprot/P00519"Match4-letter PDBe code"identifier": "4wa9"Matchaccession"identifier": "https://identifiers.org/interpro:IPR001452"Matchaccession"identifier": "https://identifiers.org/pfam:PF00018"MatchPlant trials : plant_trial_name (or pubmed_id if it's in use)prt7_1996_gr_01MatchPlant variety: plant_variety_name46A74MatchPlant scoring unit urlhttps://bip.earlham.ac.uk/data_tables?model=trait_scores&query[plant_scoring_units.id]=89583Match
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imageImageObject or
URL
An image of the item. This can be a URL or a fully described ImageObject.OptionalMANYfeature viewer"image": "http://www.identifiers.org/uniprot/P00519#showFeaturesViewer"MatchFront view image of the protein in the assembly"image": "http://www.ebi.ac.uk/pdbe/static/entry/4wa9_entity_1_front_image-800x800.png"MatchNot MatchNot MatchNot MatchPlant trials : layout_file_name (field not used yet)MatchNot MatchNot Match
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nameTextThe name of the item.RecommendedONErecommended name"name": "Tyrosine-protein kinase ABL1"MatchName of protein"name": "Tyrosine-protein kinase ABL1"Matchname"name": "Tyrosine-protein kinase ABL1"MatchStructure name"name": "The crystal structure of human abl1 wild type kinase domain in complex with axitinib"Matchname"name": "SH3 domain"Matchname"name": "SH3_1"MatchTrial nameBna_RIPR_batch1MatchPlant variety: plant_variety_name46A74MatchScoring unit namea-0000001Match
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sameAsURLURL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.OptionalMANY"sameAs": "http://purl.uniprot.org/uniprot/P00519"MatchNo Matchsource"sameAs": "http://www.uniprot.org/uniprot/P00519"MatchMatchsourceMatchPlant trials : data_provenance
It sometimes has this information
http://www.brassica.bbsrc.ac.uk/IMSORB/Partial MatchNot MatchNot Match
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urlURLURL of the item.OptionalONE"url": "http://www.uniprot.org/uniprot/P00519"Match"url": "http://www.ebi.ac.uk/pdbe/entry/pdb/4wa9/protein/1"Match"url": "https://www.ebi.ac.uk/protein/P00519"Match"url": "http://pdbe.org/4wa9"MatchMatchMatchURLhttps://bip.earlham.ac.uk/data_tables?model=plant_trials&query[id][]=47MatchNot MatchPlant scoring unit urlhttps://bip.earlham.ac.uk/data_tables?model=trait_scores&query[plant_scoring_units.id]=89583Match
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distributionDataDownloadA downloadable form of this entity, at a specific location, in a specific formatOptionalMANYformat"distribution": {
"@type": "DataDownload",
"url": "http://www.uniprot.org/uniprot/P00519.fasta"
}
Matcharchive mmCIF"distribution": "http://www.ebi.ac.uk/pdbe/entry/pdb/4wa9/fasta?entity=1"Matchsequence"distribution": {
"@type": "DataDownload",
"url": "http://www.uniprot.org/uniprot/P00519.fasta"
}
Matcharchive mmCIF"distribution": "http://www.ebi.ac.uk/pdbe/entry-files/download/4wa9.cif",MatchNot Matchalignment/HMM"distribution": [
{
"type": "DataDownload",
"url": "http://pfam.xfam.org/family/PF00018/alignment/seed/format?format=fasta",
"fileFormat": "chemical/x-fasta",
"description": "FASTA seed alignment"
},...
]
MatchNot MatchNot MatchTrait scoring download linkhttps://bip.earlham.ac.uk/trial_scorings/47.zipMatch
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New properties
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additionalPropertyStructuredValueAny addional property required by this record that is not covered by any other explicit property. The property additionalType from Thing should be used to point to an ontological term describing the nature of this property. OptionalMANYFor instance, involvement in disease, disease association"additionalProperty": {
"@type": "StructuredValue",
"identifier": "http://www.omim.org/entry/608232",
"name": "Leukemia, chronic myeloid (CML)",
"additionalType": "http://semanticscience.org/resource/SIO_000983",
"sameAs": "http://www.uniprot.org/diseases/DI-03735"
}
MatchNo MatchNot MatchNo MatchNot MatchNot Match<TODO>Not MatchNot MatchNot Match
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crossReferenceStructuredValueA pointer to another, somehow related entity.
Usage: Whenever isBasedOn/isBasisFor, isPartOf/hasPart, citation or any other more specific does not work. The property AdditionalProperty from Thing should be used to point to an ontological term describing the nature of the relation/reference. For instance, skos:narrower or skos:related or rdfs:seeAlso
OptionalMANYcross-references"crossReference": [
{
"@type": "BiologicalEntity",
"@id": "www.identifiers.org/pdb/1AB2"
},
...
]
MatchGene name(s) associated with protein"crossReference": {
"@type": "PropertyValue",
"name": "Gene",
"value": ["JTK7", "ABL1", "ABL"]
},
Matchcross-reference"crossReference": [
{
"@type": "BiologicalEntity",
"@id": "www.identifiers.org/pdb/1AB2"
},
...
]
Matchcross-reference"crossReference": [
{
"@type": "BiologicalEntity",
"@id": "www.identifiers.org/pdb/1AB2"
},
...
]
Matchcross-reference"crossReference": [
{
"@type": "BiologicalEntity",
"@id": "www.identifiers.org/pdb/1AB2"
},
...
]
MatchPlant lines/cultivars associated : plant_line_name / plant_variety_nameGBR006_HRIGRU_02865MatchAssociated Plant trials (fields of special interest for this use case: number of them, trial_location_site_name, trial_year)hzau_2003_Weinan_01, hzau_2003_Wuhan_02MatchNot Match
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isBasisForThing or URLA resource for which this resource has been used for the creation of the former.

Inverse property: isBasedOn
OptionalMANYNo MatchNo MatchNot MatchNot Matchintegration"isBasisFor": {
"@type": "BiologicalEntity",
"inDataset": "InterPro",
"name": "SH3 domain",
"identifier": "https://identifiers.org/interpro:IPR001452"
}
MatchNot Matchto be studiedNot Match
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Schema.org mapping
Bioschemas fields