ABCDEFGHIJKLMNOPQRSTUVWXYZAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZBABBBCBDBEBF
1
SubtitleBioschemas specification describing the usage of BiologicalEntity for the “Protein” biological type. UniProt (protein)PDBe (protein)InterPro (protein)
2
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.
3
4
schema.orgbioschemas
5
PropertyExpected TypeDescriptionBSC DescriptionMarginalityCardinalityControlled VocabularyNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseName
Content Example
UseCaseNameContent ExampleUseCaseName
Content Example
UseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseName
Content Example
UseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCaseNameContent ExampleUseCase
6
Extends CreativeWork
7
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
8
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
9
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
10
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
11
hasPartBiologicalEntityIndicates a BiologicalEntity that is (in some sense) a part of this BiologicalEntity.
Inverse property: isPartOf.		OptionalMANYfeaturesNo Match
12
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
13
New properties
14
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
15
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
16
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
17
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
18
representationText or URL or PropertyValueRepresentation of this entity. For instance, chemical structure or sequenceOptionalMANYsequenceNo Match
19
taxonURL
A url pointing to NCBI Taxonomy or a taxonomic resource
OptionalMANYYesorganism"taxon": "http://www.uniprot.org/taxonomy/9606"Match
20
isMentionedInThingCreativeWork, Dataset, collection mentioning this entity

Inverse of:mentions		RecommendedONEdataset"isMentionedIn": {
"@type": "Dataset",
"@id": "http://www.uniprot.org/news/2017/03/15/release"
}		Match
21
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
22
alternateNameTextAn alias for the item.RecommendedMANYalternative names"alternateName": [
{
"@language": "en",
"@value": "ABL1_HUMAN"
},
...
]
Match
23
descriptionTextA description of the item.RecommendedONEfunction"description": {
"@language": "en",
"@value": "Non-receptor tyrosine-protein kinase that plays a role..."
}		Match
24
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
25
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
26
nameTextThe name of the item.RecommendedONErecommended name"name": "Tyrosine-protein kinase ABL1"Match
27
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
28
urlURLURL of the item.RecommendedONE"url": "http://www.uniprot.org/uniprot/P00519"Match
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100