Protein Mapping 0.5
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SubtitleBioschemas specification describing a Protein (BioChemEntity profile) in Life SciencesUniProt (protein)PDBe (protein)InterPro (protein)PDBe (protein structure)Sample
BIP - Phenotype (trials/studies)
BIP - Phenotype (cultivars)
BIP - Phenotype (traits/phenotypes)
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DescriptionThis Protein profile specification presents the BioChemEntity usage when describing a Protein.
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
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 Thing
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additionalTypeURL
An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.
Any ontology term describing the protein concept. This is in addition to the official type to describe a protein

Official proposed term for the profile describing a protein: http://purl.obolibrary.org/obo/PR_000000001
OptionalMANYAny suitable ontologyformat
"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 MatchNot Match
Trait scoring download link
https://bip.earlham.ac.uk/trial_scorings/47.zip
Match
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alternateNameTextAn alias for the item._OptionalMANY
alternative names
"alternateName": [
{
"@language": "en",
"@value": "ABL1_HUMAN"
},
...
]
MatchNo Matchother names
"alternateName": [
"ABL1_HUMAN",
...
]
MatchNo MatchNot Match
(canonical_name, to be studied)
Partial MatchNot Match
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descriptionTextA description of the item.
Protein function. We recommend to start the description with "Function: [...]"
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 MatchTrial description
387 Brassica napus accessions used in the RIPR project for which mRNAseq data were submitted to SRA under PRJNA309367
Match
Plant varieties : comments
Brassica napus var. oleifera annua; Spring oilseed rape; erucic acid <1 ; glucosinolates <30 ;
MatchNot Match
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identifier
PropertyValue 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.
_MinimumONEaccession
"identifier": "http://www.identifiers.org/uniprot/P00519"
Match
4-letter PDBe code
"identifier": "P00519"Matchaccession
"identifier": "http://www.identifiers.org/uniprot/P00519"
Match
4-letter PDBe code
"identifier": "4wa9"
Match
Plant trials : plant_trial_name (or pubmed_id if it's in use)
prt7_1996_gr_01Match
Plant variety: plant_variety_name
46A74Match
Plant scoring unit url
https://bip.earlham.ac.uk/data_tables?model=trait_scores&query[plant_scoring_units.id]=89583
Match
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image
ImageObject 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
Front 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 Match
Plant trials : layout_file_name (field not used yet)
MatchNot MatchNot Match
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mainEntityOfPage
CreativeWork or URL
Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.
Inverse property: mainEntity
Link via DataRecord to the main DataRecord representing this entity in a dataset. It is usually preferred to use mainEntity from a DataRecord to point to its corresponding entity.
OptionalONE
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nameTextThe name of the item._MinimumONE
recommended name
"name": "Tyrosine-protein kinase ABL1"
Match
Name of protein
"name": "Tyrosine-protein kinase ABL1"Matchname
"name": "Tyrosine-protein kinase ABL1"
Match
Structure name
"name": "The crystal structure of human abl1 wild type kinase domain in complex with axitinib"
MatchTrial nameBna_RIPR_batch1Match
Plant variety: plant_variety_name
46A74Match
Scoring unit name
a-0000001Match
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sameAsURL
URL 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.

Bioschemas usage.

Link to any resource other than the Record and the official Webpage, for instance a Wikipedia page.
_OptionalMANY
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urlURLURL of the item.
Link to the official webpage associated to this entity.
RecommendedONE
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New properties
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additionalPropertyPropertyValue
A 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.

Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, ...) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.
Whenever possible, please use a property coined in a third-party well-know vocabulary. For instance, you can directly use http://purl.obolibrary.org/obo/RO_0002327 as a property to express how a protein or gene enables some GO molecular function. If you still want or need to use additionalProperty, please use (i) property name to specify the name of the property, (ii) additionalType (if possible) to better specify the nature of the property, and (iii) value to link to the object/range of this property.
OptionalMANY
For 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 Match<TODO>Not MatchNot MatchNot Match
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http://purl.obolibrary.org/obo/so#associated_with
MedicalContidion or URL
Disease associated to this protein, if any.RecommendedMANY
SIO:000983, SIO:010299, OMIM, any other well-known ontology describing diseases
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http://semanticscience.org/resource/SIO_010083
BioChemEntity, bioschemas:Gene
Gene(s) from which this protein was translated from. In addtion to the schema:BioChemEntity type, this property also expects a bioschemas:Gene profile.
RecommendedMANY
SIO:010081, SIO:010035
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isContainedInBioChemEntity
Indicates a BioChemEntity that this BioChemEntity is (in some sense) part of.
For proteins, it is recommended to at least specify the taxon/organism associated to the described protein. For taxon/organism, it is a good practice to use categoryCode to point to a controlled vacabulary such as NCBI taxon or UniProt Taxonomy. Including as well the GO cellular locations is optional; for cellular locations it is a good practice to use categorryCode to point to a GO Cellular Location term
RecommendedMANY
NCBI Taxon, UniProt taxonomy
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containsBioChemEntity
Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.
For proteins, it can be used to link to protein sequence annotations such as domains, sites, regions, etc.

OptionalMANY
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location
Place, PostalAddress, PropertyValue, Text or URL
The location of for example where the event is happening, an organization is located, or where an action takes place.
In Bioschemas location can be refer to a position in a chromosome or sequence or to a physical place where, for instance, a sample is stored. Using additionalType is advised to make the distinction. For instance, FALDO can be used for sequence coordinates.
OptionalMANY
Yes, as it better suits to describe the location.
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hasRepresentation
PropertyValue, Text or URL
A representation for this entity other than, for instance, an image (used image property for that) or the main web page/record (use mainEntityOfPage for that, and see background notes, http://schema.org/docs/datamodel.html#mainEntityBackground, for sameAs and url).
For proteins, this property could be used, for instance, to register a protein sequence as a representation of the protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty or a third-party ontology predicate
OptionalMANY
Yes, as it better suits to describe the nature of the representation
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http://purl.obolibrary.org/obo/RO_0002327
Text, URL, BioChemEntity, bioschemas:ProteinAnnotation
GO molecular function enabled by the proteinOptionalMANY
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http://purl.obolibrary.org/obo/RO_0002331
Text, URL, BioChemEntity, bioschemas:ProteinAnnotation
GO biological process this protein is involved inOptionalMANY
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categoryCodeCategoryCode
A controlled vocabulary term equivalent to this entity. For instance, an organism coined in NCBI taxonomy can be represented as a
BioChemEntity. As it also exists as a term in an ontology, it would be
nice to capture that information via categoryCode.
_OptionalMANY
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