Protein Mapping
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ABCDEFGHIJKLMNOPQRSTUVZAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZ
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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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additionalTypeURLAn 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.Bioschemas usage.

Any ontology term describing the protein concept.
RecommendedMANYSIO, PR, SO, othersformat"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 MatchTrait scoring download linkhttps://bip.earlham.ac.uk/trial_scorings/47.zipMatch
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alternateNameTextAn alias for the item.RecommendedMANYalternative 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.Bioschemas usage.

Protein 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 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.MinimumONEaccession"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"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 MatchPlant trials : layout_file_name (field not used yet)MatchNot MatchNot Match
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mainEntityOfPageCreativeWork 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
Bioschemas usage.

Link via Record or URL to the main Record representing this entity in a dataset
OptionalONE
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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"MatchTrial nameBna_RIPR_batch1MatchPlant variety: plant_variety_name46A74MatchScoring unit namea-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.Bioschemas usage.

Link to the official webpage associated to this entity.
RecommendedONE
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New properties
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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.

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.
Bioschemas usage.

Additional to the use of name and description to describe this property in a human-readable way, additionalType should be used to specify the nature of the property/relation. For instance, if the property refers to a gene/protein disease association, you could use http://semanticscience.org/resource/SIO_000983 as additionalType for the additionalProperty.

Controlled vocabularies should be used whenever possible.
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 Match<TODO>Not MatchNot MatchNot Match
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bioschemas:associatedDisease
MedicalContidion or URL
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.
Protein profile usage.

* additionalType for additionalProperty should be set to SIO:000983 (gene-disease association)
* name for additionalProperty should be set to "associated disease"
* value for additionalProperty:
** should have @type "StructuredValue",
** should have additionalType ["MedicalCondition", "SIO:010299"]
** whenever possible, use the MedicalCode to refer to an ontology term such as those in OMIM
RecommendedMANYSIO:000983, SIO:010299, OMIM, any other well-known ontology describing diseases
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bioschemas:transcribedFrom
BioChemEntity, bioschemas:Gene or URL
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.
Protein profile usage.

* additionalType for additionalProperty should be set to SIO:010081 (is transcribed from)
* name for additionalProperty should be set to "gene"
* value for additionalProperty:
** should have @type "BioChemEntity",
** should have additionalType SIO:010035 (gene)
RecommendedMANYSIO:010081, SIO:010035
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isContainedIn
BioChemEntity or URL
Indicates a BioChemEntity that this BioChemEntity is (in some sense) part of.
RecommendedMANY
NCBI Taxon, UniProt taxonomy
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contains
BioChemEntity or URL
Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.
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.

Bioschemas usage.

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).

Bioschemas usage.

This property could be used, for instance, to register a sequence protein as it is a representation of the protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty.
OptionalMANY
Yes, as it better suits to describe the nature of the representation
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Schema.org mapping
Bioschemas fields