SequenceAnnotation DRAFT Profile

Version: 0.7-DRAFT (05 July 2021)

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

Schema.org hierarchy

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

Thing > BioChemEntity > SequenceAnnotation

Description

Used to provide metadata about Sequence Annotations. The sequence can be an amino acid (protein) or nucleic acid (Gene, DNA, RNA).

Summary of Changes

This version supersedes the ProteinAnnotation 0.6-DRAFT.

Change base type to SequenceAnnotation
location is replaced with sequenceLocation; promoted to minimal
sequenceOrientation added as a minimal property
sequenceValue added as a recommended property
valueReference added as an optional property
sameAs promoted to a recommended property

Latest profiles

Latest release: none

Latest draft: 0.7-DRAFT

Previous profiles

Previous version: 0.6-DRAFT

Contributors

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

Group Leader(s)

Maria Martin

Leyla Jael Castro

Other team members

Gustavo Salazar-Orejuela

Victoria Dominguez Del Angel

Nathan Dunn

Jerven Bolleman

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

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: alternateName
{
"alternateName": [" BRCA2_hlx"]
}

//Property: creationMethod
{
  "creationMethod": {
    "@type": "PropertyValue",
    "value": "imported manually asserted information used in automatic assertion",
    "valueReference": {
      "@type": "CategoryCode",
      "codeValue": "ECO:0000322",
      "inCategorySet": {
        "@type": "CategoryCodeSet",
        "name": "ECO Evidence Code Ontology"
      }
    }
  }
}


//Property: description
{
    "description": "This entry represents a domain found in BRCA2 proteins. This domain adopts a helical..."
}

//Property: image
{
  "image": {
    "@id": "https://www.ebi.ac.uk/interpro/assets/images/ssf_logo.1Jk.avif"
  }
}

//Property: isLocatedInSubcellularLocation
{
  "isLocatedInSubcellularLocation": [
    "http://identifiers.org/GO:0012505",
    "http://identifiers.org/GO:0009707" 
  ]
}

//Property: isPartOfBioChemEntity
//A protein variant is contained in the proteine sequence:
{
  "isPartOfBioChemEntity": {"@id": "http://purl.uniprot.org/uniprot/P05067"}
}

//Property: name
{
  "name": "Breast cancer type 2 susceptibility protein, helical domain"
}

//Property: sameAs
{
  "sameAs": "https://www.ebi.ac.uk/interpro/entry/pfam/PF09169/"
}

//Property: sequenceLocation
{
  "sequenceLocation": {
    "@type":"SequenceRange",
    "rangeStart":20,
    "rangeEnd":73
  }
}

//Property: sequenceOrientation
{
  "sequenceOrientation": 0
}

//Property: sequenceValue
{
  "sequenceValue": "AMSQSLLKTTQEPLARDPVKLP"
}

//Property: url
{
  "url": "https://www.ebi.ac.uk/interpro/entry/IPR015252"
}

Property	Expected Type	Description	CD	Controlled Vocabulary	Example
Marginality: Minimum.
@context	URL	Used to provide the context (namespaces) for the JSON-LD file. Not needed in other serialisations.	ONE		Property ≪@context≫ example `{ "@context": "https://schema.org/" }`
@type	Text	Schema.org/Bioschemas class for the resource declared using JSON-LD syntax. For other serialisations please use the appropriate mechanism. While it is permissible to provide multiple types, it is preferred to use a single type.	MANY	Schema.org, Bioschemas	Property ≪@type≫ example `{ "@type": "SequenceAnnotation" }`
@id	IRI	Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach.	ONE		Property ≪@id≫ example `{ "@id": "http://example.com/entity/A12345" }`
dct:conformsTo	IRI	Used to state the Bioschemas profile that the markup relates to. The versioned URL of the profile must be used. Note that we use a CURIE in the table here but the full URL for Dublin Core terms must be used in the markup (http://purl.org/dc/terms/conformsTo), see example.	ONE	Bioschemas profile versioned URL	Property ≪dct:conformsTo≫ example `{ "http://purl.org/dc/terms/conformsTo": { "@id": "https://bioschemas.org/profiles/SequenceAnnotation/0.7-DRAFT", "@type": "CreativeWork" } }`
sequenceLocation	SequenceRange	Schema: A range/position location where this annotation or BioChemEntity is located reagrding another BioChemEntity, for instance a BioChemStructure in a Protein.	MANY	FALDO may be used	Property ≪sequenceLocation≫ example `{ "sequenceLocation": { "@type":"SequenceRange", "rangeStart":20, "rangeEnd":73 } }`
Marginality: Recommended.
creationMethod	PropertyValue Text URL	Schema: Method used to create or obtain this annotation or BioChemEntity; please use PropertyValue if you want to include any evidence.	ONE		Property ≪creationMethod≫ example `{ "creationMethod": { "@type": "PropertyValue", "value": "imported manually asserted information used in automatic assertion", "valueReference": { "@type": "CategoryCode", "codeValue": "ECO:0000322", "inCategorySet": { "@type": "CategoryCodeSet", "name": "ECO Evidence Code Ontology" } } } }`
description	Text	Schema: A description of the item.	ONE		Property ≪description≫ example `{ "description": "This entry represents a domain found in BRCA2 proteins. This domain adopts a helical..." }`
image	ImageObject URL	Schema: An image of the item. This can be a URL or a fully described ImageObject.	MANY		Property ≪image≫ example `{ "image": { "@id": "https://www.ebi.ac.uk/interpro/assets/images/ssf_logo.1Jk.avif" } }`
name	Text	Schema: The name of the item.	ONE		Property ≪name≫ example `{ "name": "Breast cancer type 2 susceptibility protein, helical domain" }`
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. Bioschemas: Link to any resource other than the Record and the official webpage, for instance a Wikipedia page.	MANY		Property ≪sameAs≫ example `{ "sameAs": "https://www.ebi.ac.uk/interpro/entry/pfam/PF09169/" }`
sequenceOrientation	Integer	Schema: One of 1, 0 or -1.			Property ≪sequenceOrientation≫ example `{ "sequenceOrientation": 0 }`
sequenceValue	Text URL	Schema: -			Property ≪sequenceValue≫ example `{ "sequenceValue": "AMSQSLLKTTQEPLARDPVKLP" }`
url	URL	Schema: URL of the item. Bioschemas: Link to the official webpage associated to this entity	ONE		Property ≪url≫ example `{ "url": "https://www.ebi.ac.uk/interpro/entry/IPR015252" }`
Marginality: Optional.
alternateName	Text	Schema: An alias for the item.	MANY		Property ≪alternateName≫ example `{ "alternateName": [" BRCA2_hlx"] }`
hasBioChemEntityPart	BioChemEntity	Schema: Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity.	MANY
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.	MANY
isLocatedInSubcellularLocation	DefinedTerm PropertyValue URL	Schema: Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.	MANY	Any URL to a GO cellular_component	Property ≪isLocatedInSubcellularLocation≫ example `{ "isLocatedInSubcellularLocation": [ "http://identifiers.org/GO:0012505", "http://identifiers.org/GO:0009707" ] }`
isPartOfBioChemEntity	BioChemEntity URL	Schema: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart.	MANY		Property ≪isPartOfBioChemEntity≫ example `//A protein variant is contained in the proteine sequence: { "isPartOfBioChemEntity": {"@id": "http://purl.uniprot.org/uniprot/P05067"} }`
valueReference	DefinedTerm Enumeration PropertyValue QualitativeValue QuantitativeValue StructuredValue Text URL	Schema: A pointer to a secondary value that provides additional information on the original value, e.g. a reference temperature.