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.
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)
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
- 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 |
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You can read the release version of this specification here.
Key to specification table
- Green properties/types are proposed by Bioschemas, or indicate proposed changes by Bioschemas to Schema.org
- Red properties/types exist in the core of Schema.org
- Blue properties/types exist in the pending area of Schema.org
- Black properties/types are reused from external vocabularies/ontologies
CD = Cardinality
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 |
|
|
name |
Text |
Schema: The name of the item. |
ONE |
|
|
Marginality: Recommended. | |||||
description |
Text |
Schema: A description of the item. |
ONE |
|
|
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 |
|
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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 |
|
|
url |
URL |
Schema: URL of the item. Bioschemas: Link to the official webpage associated to this entity. |
ONE |
|
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Marginality: Optional. | |||||
alternateName |
Text |
Schema: An alias for the item. |
MANY |
|
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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 |
|
|
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) |
|
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 |
|
|
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 |
|
|
isInvolvedInBiologicalProcess |
DefinedTerm PropertyValue URL |
Bioschemas: GO biological process this gene/protein is involved in. |
MANY | Only the biological process branch of Gene Ontology (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 |
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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 |
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taxonomicRange |
DefinedTerm Taxon Text URL |
Schema: The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity. |
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