BiologicalEntity mapping
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ABCDEFGHIJKLMNOPQRSTUVWXYZAAABAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZBABBBCBDBEBF
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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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https://bip.earlham.ac.uk/data_tables?model=plant_trials
bip.earlham.ac.ukbip.earlham.ac.uk
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schema.orgbioschemasSearch for trialSearch for cultivarsSearch for trait
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PropertyExpected TypeDescriptionSubPropertiesMinimum FieldsCardinality
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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New properties for BiologicalEntity
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associatedDiseaseMedicalCondition OR URLDisease associated to this protein featureOptionalMANYInvolvement in disease, disease association"associatedDisease": {
"@type": "MedicalCondition",
"@id": "http://www.omim.org/entry/608232",
"name": "Leukemia, chronic myeloid (CML)",
"code": {
"@type": "MedicalCode",
"code": "608232",
"codingSystem": "OMIM"
},
"sameAs": "http://www.uniprot.org/diseases/DI-03735"
}
MatchNo MatchNot MatchNo MatchNot MatchNot Match<TODO>Not MatchNot MatchNot Match
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biocoordinatesQuantitativeValueCoordinates in a 1 or 2D space, for instance length/coordinates in a sequence.

Usage (example): Use a QuantitativeValue with properties minValue and maxValue for a region or value for a site in a Protein. Use it only with value for a protein length.
OptionalMANYprotein length "biocoordinates": {
"@type": "QuantitativeValue",
"value": "1130"
}
Match "biocoordinates": [{
"@type": "PropertyValue",
"minValue": 246,
"maxValue": 512
}],
Matchlocation/fragment"biocoordinates": [{
"@type": "PropertyValue",
"minValue": 61,
"maxValue": 147
}, …]
MatchNo Matchlocation/fragment"biocoordinates": [{
"@type": "PropertyValue",
"minValue": 61,
"maxValue": 147
}, …]
Matchlocation/fragment"biocoordinates": [{
"@type": "PropertyValue",
"minValue": 61,
"maxValue": 147
}, …]
MatchNot MatchNot MatchNot Match
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biologicalTypeTextList with types preferably supported by BioSchemas-> enumeration list of values maintained on a wikipage (cf accessibilityAPI in schema.org for implementation). If the value is not on the list then the data will still be parsed but only generic properties will be validated.
{population,individual,tissue,cell,molecule,protein,nucleic acid}
MinimumMANY"biologicalType": "protein"Match"biologicalType": "protein"Matchtype"biologicalType": "protein"Match"biologicalType": "ProteinStructure"Matchtype["protein annotation", "domain"]Matchtype["protein annotation", "domain"]Matchfixed term"biologicalType": "Phenotype", "variety", "plant line"Partial Matchtaxonomic terms / Infraspecific_name (MIAPPE)"biologicalType": "individual"Partial Matchfixed term"biologicalType": "Phenotype"Partial Match
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crossReferenceThingA pointer to another, somehow related entity.
Usage: Whenever isBasedOn/isBasisFor, isPartOf/hasPart, citation or any other more specific does not work.
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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isBasisForCreativeWork or
URL or BiologicalEntity
A 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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phenotypeText, Url, PropertyValueTo associate a biological entity to phenotypic information , whether the entity presents the phenotype or causes it.OptionalMANYNo MatchNo MatchNot MatchNo MatchNot MatchNot Matchname (trait_descriptor.name); method (trait_descriptor.scoring_method); scale (trait_descriptor.units_of_measurements); ontology_id (traits.label)name: Leaf Caesium concentration; method: 3-5 leaves per plant were pooled and freeze-dried. These were then ground and digested in nitric acid in a microwave digester prior to analysis by inductively coupled plasma-mass spectrometry; scale: mg/kgMatchname (trait_descriptor.name); method (trait_descriptor.scoring_method); scale (trait_descriptor.units_of_measurements); ontology_id (traits.label)name: Leaf Caesium concentration; method: 3-5 leaves per plant were pooled and freeze-dried. These were then ground and digested in nitric acid in a microwave digester prior to analysis by inductively coupled plasma-mass spectrometry; scale: mg/kgMatchname (trait_descriptor.name); method (trait_descriptor.scoring_method); scale (trait_descriptor.units_of_measurements); ontology_id (traits.label)name: Leaf Caesium concentration; method: 3-5 leaves per plant were pooled and freeze-dried. These were then ground and digested in nitric acid in a microwave digester prior to analysis by inductively coupled plasma-mass spectrometry; scale: mg/kgMatch
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representationText or URL or PropertyValueRepresentation of this entity. For instance, chemical structure or sequenceOptionalMANYsequenceNo Matchsequence"representation": "GSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGK"Matchsequence"representation": "MLEICLKLVGCKSKKGLSSS..."MatchNo MatchNot Matchalignment/HMMPartial MatchNot MatchNot MatchNot Match
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sampleBiologicalEntity or URL
Clarify usage...
OptionalMANYNo MatchNo MatchNot MatchNo MatchNot MatchNot MatchNot MatchNot MatchSample to be better definedNot Match
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taxonURL
A url pointing to NCBI Taxonomy or a taxonomic resource
OptionalMANYYesorganism"taxon": "http://www.uniprot.org/taxonomy/9606"Matchsource organism"taxon": "http://identifiers.org/taxonomy:9606",Matchspecies"taxon": "http://www.uniprot.org/taxonomy/9606"Matchsource organism"taxon": "http://www.uniprot.org/taxonomy/9606"MatchspeciesPartial MatchspeciesPartial MatchPlant Line : Species (to be adapted from current GR ontology)https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3708&lvl=3&lin=f&keep=1&srchmode=1&unlockPartial MatchPlant Line : Species (to be adapted from current GR ontology)https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3708&lvl=3&lin=f&keep=1&srchmode=1&unlockPartial MatchNot Match
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Reused properties from BiologicalEntity
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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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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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hasPartBiologicalEntityIndicates a BiologicalEntity that is (in some sense) a part of this BiologicalEntity.
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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isPartOfBiologicalEntityIndicates a BiologicalEntity that this BiologicalEntity 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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locationPlacePosition where this entity is located or originates from (e.g. an entity from Polynesia islands or an Anatomical location. If multiple locations with multiple purposes (collection, storage) should be modelled, please use the additionalProperty from Place to specify this. OptionalMANYNo MatchNo MatchNot MatchNot MatchNot MatchPlant trials: trial location site name/ experimental site name (MIAPPE). It can be included as free text in 'Place:address' field.Wharf GroundMatchNot MatchPlant scoring unit: data owned byUniversity NottinghamPartial Match
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measurementTechniqueText, url, PropertyValue
To describe the process used to obtain a biological entity or which is associated with that entity (i.e procedure to obtain it or measure/characterise it)
OptionalMANYNo Matchmethod (Solution NMR, X-ray diffraction, Electron Microscopy, Small Angle Scattering or a combination)"measurementTechnique": "X-ray diffraction",MatchNot Matchmethod (Solution NMR, X-ray diffraction, Electron Microscopy, Small Angle Scattering or a combination)"measurementTechnique": "X-ray diffraction",MatchNot Matchalignment/HMM"measurementTechnique": "HMM"
MatchTrial descriptionLeaf mineral concentration data of compost - grown lines of the RIPR panel generated by ICP-MS analysis.MatchNot MatchPlant scoring unit : scoring methodThe scoring system was developed to take into account the host plant response and the growth of the pathogen as measured by the amount and type of sporulation. The combination of these characters gave six interaction phenotype classes of host/pathogen inMatch
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New properties for Thing
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isMentionedInThingCretiveWork, Dataset, collection mentioning this entity

Inverse of:mentions
RecommendedONEdataset"isMentionedIn": {
"@type": "Dataset",
"@id": "http://www.uniprot.org/news/2017/03/15/release"
}
MatchNo Matchsource"isMentionedIn": {
"@type": "Dataset",
"@id": "http://www.uniprot.org/news/2017/03/15/release"
}
MatchNo MatchNot Matchmember database"isMentionedIn": "https://www.ebi.ac.uk/interpro/member-database/Pfam"MatchNot MatchNot MatchNot Match
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Reused properties from Thing
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additionalPropertyPropertyValueA property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org.OptionalMANYNo Matchresolution
boundMolecule
expressionSystem
biochemicalFunction
biological process
"additionalProperty": [
{
"@type": "PropertyValue",
"name": "resolution",
"value": "2.2Å"
},{
"@type": "PropertyValue",
"name": "boundMolecule",
"value": "http://identifiers.org/pdb.ligand:AXI"
},{
"@type": "PropertyValue",
"name": "expressionSystem",
"value": "http://identifiers.org/taxonomy:7108",
"description": "Spodoptera frugiperda"
},{
"@type": "PropertyValue",
"name": "biochemicalFunction",
"value": "http://identifiers.org/GO:0005524",
"description": "ATP binding"
},{
"@type": "PropertyValue",
"name": "biologicalProcess",
"value": "http://identifiers.org/GO:0007169",
"description": "transmembrane receptor protein tyrosine kinase signaling pathway"
},{
"@type": "PropertyValue",
"name": "assemblyComposition",
"value": "hetero trimer"
},{
"@type": "PropertyValue",
"name": "preferredAssembly",
"value": "1"
}
]
MatchNot Matchresolution
boundMolecule
expressionSystem
biochemicalFunction
biological process
"additionalProperty": [
{
"@type": "PropertyValue",
"name": "resolution",
"value": "2.2Å"
},{
"@type": "PropertyValue",
"name": "boundMolecule",
"value": "http://identifiers.org/pdb.ligand:AXI"
},{
"@type": "PropertyValue",
"name": "expressionSystem",
"value": "http://identifiers.org/taxonomy:7108",
"description": "Spodoptera frugiperda"
},{
"@type": "PropertyValue",
"name": "biochemicalFunction",
"value": "http://identifiers.org/GO:0005524",
"description": "ATP binding"
},{
"@type": "PropertyValue",
"name": "biologicalProcess",
"value": "http://identifiers.org/GO:0007169",
"description": "transmembrane receptor protein tyrosine kinase signaling pathway"
},{
"@type": "PropertyValue",
"name": "assemblyComposition",
"value": "hetero trimer"
},{
"@type": "PropertyValue",
"name": "preferredAssembly",
"value": "1"
}
]
MatchNot MatchNot MatchPlant trial: trial location site nameexperimentalSiteName: unspecified glasshouse in Wellesbourne; geographicLocationStudy: UKMatch
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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
35
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
36
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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Schema.org mapping
Bioschemas fields