Protein Mapping
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SubtitleBioschemas specification describing the usage of BiologicalEntity for the “Protein” biological type. UniProt (protein)PDBe (protein)InterPro (protein)
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DescriptionThis protein specification presents the usage of the generic type BiologicalEntity by the biological type “protein”. Please be aware “protein” is NOT a schema.org type but a BiologicalEntity profile.
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schema.orgbioschemas
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PropertyExpected TypeDescriptionBSC DescriptionMarginalityCardinality
Controlled Vocabulary
NameContent ExampleUseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCase
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Extends CreativeWork
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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"
]
},
...
]
Match
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dateCreatedDate or
DateTime
The date on which the BiologicalEntity was created or the item was added to a DataFeed.OptionalONEentry history (integrated into UniProtKB)"dateCreated": "1986-07-21"Match
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dateModifiedDate or
DateTime
The date on which the BiologicalEntity was most recently modified or when the item's entry was modified within a DataFeed.OptionalONElast modified"dateModified": "2017-03-15"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"
}
Match
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hasPartBiologicalEntityIndicates a BiologicalEntity that is (in some sense) a part of this BiologicalEntity.
Inverse property: isPartOf.
OptionalMANYfeaturesNo 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"
}
}
Match
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New properties
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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"
}
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.
RecommendedONEprotein length "biocoordinates": {
"@type": "QuantitativeValue",
"value": "1130"
}
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
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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"
},
...
]
Match
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representationText or URL or PropertyValueRepresentation of this entity. For instance, chemical structure or sequenceOptionalMANYsequenceNo Match
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taxonURL
A url pointing to NCBI Taxonomy or a taxonomic resource
OptionalMANYYesorganism"taxon": "http://www.uniprot.org/taxonomy/9606"Match
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isMentionedInThingCreativeWork, Dataset, collection mentioning this entity

Inverse of:mentions
RecommendedONEdataset"isMentionedIn": {
"@type": "Dataset",
"@id": "http://www.uniprot.org/news/2017/03/15/release"
}
Match
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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.

Avoid it if possible, otherwise use it carefully. Please keep in mind that Bioschemas does not pretend to model every single possible field but mainly those useful for discoverability, summarization and accessibility.
OptionalMANYNo Match
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alternateNameTextAn alias for the item.RecommendedMANYalternative names"alternateName": [
{
"@language": "en",
"@value": "ABL1_HUMAN"
},
...
]
Match
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descriptionTextA description of the item.RecommendedONEfunction"description": {
"@language": "en",
"@value": "Non-receptor tyrosine-protein kinase that plays a role..."
}
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"Match
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imageImageObject or
URL
An image of the item. This can be a URL or a fully described ImageObject.RecommendedMANYfeature viewer"image": "http://www.identifiers.org/uniprot/P00519#showFeaturesViewer"Match
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nameTextThe name of the item.RecommendedONErecommended name"name": "Tyrosine-protein kinase ABL1"Match
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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.RecommendedMANY"sameAs": "http://purl.uniprot.org/uniprot/P00519"Match
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urlURLURL of the item.RecommendedONE"url": "http://www.uniprot.org/uniprot/P00519"Match
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Schema.org mapping
Bioschemas fields