Gene DRAFT Profile

Version: 0.6-DRAFT-2020_04_02 (02 April 2020)

Bioschemas profile describing a Gene in Life Sciences

If you spot any errors or omissions with this type, please file an issue in our GitHub.

Description Contributors Links

Contributors

The following people have been involved in the creation of this specification document. They are all members of the Genes group.

Group Leader(s)

Leyla Garcia

Denise Carvalho-Silva

Other team members

Schema.org hierarchy

This Profile fits into the schema.org hierarchy as follows:

Thing > BioChemEntity > Gene

Description

This Gene profile specification presents the markup for describing a Gene.

Summary of Changes

Changes introduced on Gene profile 0.6-DRAFT-2020_04_02 in response to issue 353

encodes property updated to encodesBioChemEntity, still recommended
additionalProperty removed
associatedDisease range updated
examples using DefinedTerm now include link to external vocabularies via property inDefinedTermSet (hasMolecularFunction, isInvolvedInBiologicalProcess, taxonomicRange). Note: isTranscribedInto and isVariantOf do not exist on the Gene type so they were removed, isVariantOf was replaced on Gene type by alternativeOf)
hasCategoryCode property removed

Additional changes after looking at BioChemEntity and Gene types:

hasRepresentation moved to optional. There is another property
hasBioPolymerSequence for the sequence text. hasRepresentation can be used to link to a page containing the corresponding sequence so both are now optional and people can decide which one suits better to them
properties directly from Gene type not previously included on the Gene profile were added as optional (expressedIn and hasStatus)

Latest profiles

Latest release: 0.7-RELEASE

Previous profiles

Previous version: 0.5-DRAFT-2019_06_14

Group	Use Cases	Cross Walk	Task & Issues	Examples	Live Deploys
Genes

You can read the release version of this specification here.

Key to specification table

Schema.org properties where the Expected Types have been changed, or new (i.e., Bioschemas created) properties/types are green.

Schema.org properties/types are red.

Pending Schema.org properties/types are blue.

External (i.e., from 3rd party ontology) properties/types are black.

CD = Cardinality

View all examples

//Property: alternateName
{
    "@type": "Gene",
    "alternateName": "AD1"
}


//Property: description
{
    "@type": "Gene",
    "description": "amyloid beta precursor"
}


//Property: encodesBioChemEntity
{
  "@type": "Gene",
  "encodesBioChemEntity": { 
    "@type": "Protein",
    "identifier": "uniprotkb:P05067",
    "url": "https://www.uniprot.org/uniprot/P05067"
  }
}


//Property: hasBioChemEntityPart
//Contains a variant
{
  "@type": "Gene",
  "hasBioChemEntityPart": { 
    "@type": "BioChemEntity",
    "identifier": "rs577882423",
    },
    "url": "https://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000142192;r=21:25880550-26171128;vf=110312838"
  }
}



//Property: hasMolecularFunction
//Gene enabling a GO molecular function
{
  "@type": "Gene",
  "hasMolecularFunction": {
    "@type": "DefinedTerm",
    "url": "http://purl.obolibrary.org/obo/GO_0000166",
    "termCode": "GO:0000166",
    "name": "nucleotide binding",
    "inDefinedTermSet": {
      "@type": "DefinedTermSet",
      "name": "Gene Ontology",
      "url": "https://bioportal.bioontology.org/ontologies/GO"
    } 
  }
}


//Property: hasRepresentation
{
  "@type": "Gene",
  "hasRepresentation": "https://www.ncbi.nlm.nih.gov/nuccore/NC_000021.9?report=fasta&from=25880550&to=26171128&strand=true"
}


//Property: identifier
//Using a text, remember you still need @id in any case
{
    "@type": "Gene",
    "identifier": "ENSG00000142192"
}
//Using a URL directly (looks like a text), remember you need @id in any case
{
    "@type": "Gene",
    "identifier": "http://identifiers.org/ensembl:ENSG00000142192"
}
//Using a URL modeled as schema:URL (equivalent to the previous one but more verbose), remember you need @id in any case
{
    "@type": "Gene",
    "identifier": {
      "@type": "URL",
      "url": "http://identifiers.org/ensembl:ENSG00000142192"
    }
}


//Property: image
//Using a URL directly (looks like a text)
{
  "@type": "Gene",
  "image": "https://en.wikipedia.org/wiki/Amyloid_precursor_protein#/media/File:Ideogram_human_chromosome_21.svg"
}


//Property: isInvolvedInBiologicalProcess
//Gene involved in a GO biological process
{
  "@type": "Gene",
  "isInvolvedInBiologicalProcess": {
    "@type": "DefefinedTerm",
    "url": "http://purl.obolibrary.org/obo/GO_0000278",
    "termCode": "GO:0000278",
    "name": "mitotic cell cycle",
    "inDefinedTermSet": {
      "@type": "DefinedTermSet",
      "name": "Gene Ontology",
      "url": "https://bioportal.bioontology.org/ontologies/GO"
    } 
  }
}


//Property: isPartOfBioChemEntity
//Is contained in a chromosome in positions X to Y
{
  "@type": "Gene",
  "isPartOfBioChemEntity": {
    "@type": "BioChemEntity",
    "name": "Chromosome 21",
  }
}



//Property: mainEntityOfPage
//From DataRecord
{

  "@type": "DataRecord",
  "@id": "http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000142192",
  "mainEntity": {
    "@type": "Gene",
    "name": "Name and any other property for this Gene entity"
  }
}

//Also possible from Gene
{
  "@type": "Gene",
  "mainEntityOfPage": { "@id": "http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000142192" }
}


//Property: name
{
  "@type": "Gene",
  "name": "APP"
}


//Property: sameAs
{
  "@type": "Gene",
  "sameAs": "https://www.wikidata.org/wiki/Q14865870"
}


//Property: taxonomicRange
{
  "@type": "Gene",
  "taxonomicRange": {
    "@type": "DefinedTerm",
    "termCode": "9606",
    "url": "http://purl.bioontology.org/ontology/NCBITAXON/9606",
    "sameAs": "http://purl.uniprot.org/taxonomy/9606",
    "inDefinedTermSet": {
      "@type": "DefinedTermSet",
      "name": "NCBI taxon",
      "url": "https://bioportal.bioontology.org/ontologies/NCBITAXON"
    } 
  }
}


//Property: url
{
  "@type": "Gene",
  "url": "https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000142192;r=21:25880550-26171128"
}

Property	Expected Type	Description	CD	Controlled Vocabulary	Example
Marginality: Minimum.
identifier	PropertyValue Text URL	Schema: 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.	ONE		View ≪identifier≫ example Property ≪identifier≫ example //Using a text, remember you still need @id in any case { "@type": "Gene", "identifier": "ENSG00000142192" } //Using a URL directly (looks like a text), remember you need @id in any case { "@type": "Gene", "identifier": "http://identifiers.org/ensembl:ENSG00000142192" } //Using a URL modeled as schema:URL (equivalent to the previous one but more verbose), remember you need @id in any case { "@type": "Gene", "identifier": { "@type": "URL", "url": "http://identifiers.org/ensembl:ENSG00000142192" } }
name	Text	Schema: The name of the item.	ONE		View ≪name≫ example Property ≪name≫ example `{ "@type": "Gene", "name": "APP" }`
Marginality: Recommended.
description	Text	Schema: A description of the item.	ONE		View ≪description≫ example Property ≪description≫ example `{ "@type": "Gene", "description": "amyloid beta precursor" }`
encodesBioChemEntity	BioChemEntity	Schema: This property is used to link to gene products encoded (even indirectly) from this gene such as RNA or proteins. Bioschemas: For genes, this property is used to express in a generic way gene products encoded by this gene, for instance RNA or Protein	MANY		View ≪encodesBioChemEntity≫ example Property ≪encodesBioChemEntity≫ example `{ "@type": "Gene", "encodesBioChemEntity": { "@type": "Protein", "identifier": "uniprotkb:P05067", "url": "https://www.uniprot.org/uniprot/P05067" } }`
isPartOfBioChemEntity	BioChemEntity	Schema: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntity Bioschemas: For genes, it is recommended to at least specify the DNA/chromosome containing this gene	MANY		View ≪isPartOfBioChemEntity≫ example Property ≪isPartOfBioChemEntity≫ example `//Is contained in a chromosome in positions X to Y { "@type": "Gene", "isPartOfBioChemEntity": { "@type": "BioChemEntity", "name": "Chromosome 21", } }`
url	URL	Schema: URL of the item. Bioschemas: Link to the official webpage associated to this entity.	ONE		View ≪url≫ example Property ≪url≫ example `{ "@type": "Gene", "url": "https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000142192;r=21:25880550-26171128" }`
Marginality: Optional.
alternateName	Text	Schema: An alias for the item.	MANY		View ≪alternateName≫ example Property ≪alternateName≫ example `{ "@type": "Gene", "alternateName": "AD1" }`
alternativeOf	Gene	Bioschemas: Is variant of. Use this property to express when a gene is a variant of any other gene.	MANY
associatedDisease	MedicalCondition PropertyValue URL	Schema: Disease associated to this BioChemEntity
expressedIn	AnatomicalStructure AnatomicalSystem BioChemEntity DefinedTerm	Schema: Tissue, organ, biological sample, etc in which activity of this gene has been observed experimentally. For example brain, digestive system.	MANY
hasBioChemEntityPart	BioChemEntity	Schema: Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity Bioschemas: For genes, it can be used to link to gene sequence annotations such as variants or so.	MANY		View ≪hasBioChemEntityPart≫ example Property ≪hasBioChemEntityPart≫ example `//Contains a variant { "@type": "Gene", "hasBioChemEntityPart": { "@type": "BioChemEntity", "identifier": "rs577882423", }, "url": "https://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000142192;r=21:25880550-26171128;vf=110312838" } }`
hasBioPolymerSequence	Text	Schema: A symbolic representation of a BioChemEnity. For example, a nucleotide sequence of a Gene or an amino acid sequence of a Protein.	ONE
hasMolecularFunction	DefinedTerm PropertyValue URL	Bioschemas: GO molecular function enabled by the gene/protein.	MANY	Only the molecular function branch of Gene Ontology (GO)	View ≪hasMolecularFunction≫ example Property ≪hasMolecularFunction≫ example `//Gene enabling a GO molecular function { "@type": "Gene", "hasMolecularFunction": { "@type": "DefinedTerm", "url": "http://purl.obolibrary.org/obo/GO_0000166", "termCode": "GO:0000166", "name": "nucleotide binding", "inDefinedTermSet": { "@type": "DefinedTermSet", "name": "Gene Ontology", "url": "https://bioportal.bioontology.org/ontologies/GO" } } }`
hasRepresentation	PropertyValue Text URL	Schema: A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image. Bioschemas: For genes it can be used to link to a page with the corresponding sequence. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty or a third-party ontology predicate.	MANY		View ≪hasRepresentation≫ example Property ≪hasRepresentation≫ example `{ "@type": "Gene", "hasRepresentation": "https://www.ncbi.nlm.nih.gov/nuccore/NC_000021.9?report=fasta&from=25880550&to=26171128&strand=true" }`
hasStatus	Text	Schema: One of pseudogene, dead, killed, live, predicted, suppressed.	ONE
image	ImageObject URL	Schema: An image of the item. This can be a URL or a fully described ImageObject.	ONE		View ≪image≫ example Property ≪image≫ example `//Using a URL directly (looks like a text) { "@type": "Gene", "image": "https://en.wikipedia.org/wiki/Amyloid_precursor_protein#/media/File:Ideogram_human_chromosome_21.svg" }`
isInvolvedInBiologicalProcess	DefinedTerm PropertyValue URL	Bioschemas: GO biological process this gene/protein is involved in.	MANY	Only the biological process branch of Gene Ontology (GO)	View ≪isInvolvedInBiologicalProcess≫ example Property ≪isInvolvedInBiologicalProcess≫ example `//Gene involved in a GO biological process { "@type": "Gene", "isInvolvedInBiologicalProcess": { "@type": "DefefinedTerm", "url": "http://purl.obolibrary.org/obo/GO_0000278", "termCode": "GO:0000278", "name": "mitotic cell cycle", "inDefinedTermSet": { "@type": "DefinedTermSet", "name": "Gene Ontology", "url": "https://bioportal.bioontology.org/ontologies/GO" } } }`
isLocatedInSubcellularLocation	DefinedTerm PropertyValue URL	Bioschemas: GO subcellular location this gene/protein is located in.	MANY	Only the subcellular location branch of Gene Ontology (GO)
mainEntityOfPage	CreativeWork URL	Schema: 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: 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.	ONE		View ≪mainEntityOfPage≫ example Property ≪mainEntityOfPage≫ example `//From DataRecord { "@type": "DataRecord", "@id": "http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000142192", "mainEntity": { "@type": "Gene", "name": "Name and any other property for this Gene entity" } } //Also possible from Gene { "@type": "Gene", "mainEntityOfPage": { "@id": "http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000142192" } }`
sameAs	URL	Schema: 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.	MANY		View ≪sameAs≫ example Property ≪sameAs≫ example `{ "@type": "Gene", "sameAs": "https://www.wikidata.org/wiki/Q14865870" }`
taxonomicRange	DefinedTerm Taxon Text URL	Schema: The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.			View ≪taxonomicRange≫ example Property ≪taxonomicRange≫ example `{ "@type": "Gene", "taxonomicRange": { "@type": "DefinedTerm", "termCode": "9606", "url": "http://purl.bioontology.org/ontology/NCBITAXON/9606", "sameAs": "http://purl.uniprot.org/taxonomy/9606", "inDefinedTermSet": { "@type": "DefinedTermSet", "name": "NCBI taxon", "url": "https://bioportal.bioontology.org/ontologies/NCBITAXON" } } }`