Resource¶

The Resource element is a description of an external resource used for referencing an object. For example the resource may be an ontology such as the HPO or SNOMED or another data resource such as the HGNC or ClinVar.

A Resource is used to contain data used to expand CURIE identifiers when used in an id field. This is known as Identifier resolution.

The MetaData element uses one resource element to describe each resource that is referenced in the Phenopacket.

Data model¶

Field	Type	Multiplicity	Description
id	string	1..1	Resource identifier. e.g. hp. REQUIRED.
name	string	1..1	Formal name of the resource or ontology e.g. human phenotype ontology. REQUIRED.
namespace_prefix	1..1	required	Namespace prefix of the resource e.g HP. REQUIRED.
url	string	1..1	Uniform Resource Locator of the resource. REQUIRED.
version	string	1..1	The version string for the ontology or resource 2018-03-08. REQUIRED.
iri_prefix	string	1..1	Internationalized Resource Identifier such as `http://purl.obolibrary.org/obo/HP_`. REQUIRED.

Example¶

For an ontology, the url SHALL point to the obo or owl file, e.g. This information can also be found at the EBI Ontology Lookup Service

resource:
  id: "hp"
  name: "Human Phenotype Ontology"
  url: "http://www.human-phenotype-ontology.org"
  version: "2018-03-08"
  namespacePrefix: "HP"
  iriPrefix: "http://purl.obolibrary.org/obo/HP_"

Non-ontology resources which use CURIEs as their native identifiers should be treated in a similarly resolvable manner.

resource:
  id: "hgnc"
  name: "HUGO Gene Nomenclature Committee"
  url: "https://www.genenames.org"
  version: "2019-08-08"
  namespacePrefix: "HGNC"
  iriPrefix: "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"

Using this Resource definition it is possible for software to resolve the identifier HGNC:12805 to https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/12805

Non-ontology resources which do not use CURIEs as their native identifiers MUST use the namespace from identifiers.org, when present. For example the UniProt Knowledgebase (https://registry.identifiers.org/registry/uniprot)

resource:
  id: "uniprot"
  name: "UniProt Knowledgebase"
  url: "https://www.uniprot.org"
  version: "2019_07"
  namespacePrefix: "uniprot"
  iriPrefix: "https://purl.uniprot.org/uniprot/"

Using this Resource definition it is possible for software to resolve the identifier uniprot:Q8H0D3 to https://purl.uniprot.org/uniprot/Q8H0D3

Explanations¶

id¶

For OBO ontologies, the value of this string MUST always be the official OBO ID, which is always equivalent to the ID prefix in lower case. Examples: hp, go, mp, mondo Consult http://obofoundry.org for a complete list.

For other resources which do not use native CURIE identifiers (e.g. SNOMED, UniProt, ClinVar), use the prefix in identifiers.org.

name¶

The name of the ontology referred to by the id element, for example, The Human Phenotype Ontology. For OBO Ontologies, the value of this string SHOULD be the same as the title field on http://obofoundry.org

Other resources should use the official title for that resource. Note that this field is purely for information purposes and software should not encode any assumptions.

url¶

For OBO ontologies, this MUST be the PURL, e.g. http://purl.obolibrary.org/obo/hp.owl or http://purl.obolibrary.org/obo/hp.obo

Other resources should link to the official or top-level url e.g. https://www.uniprot.org or https://www.genenames.org

version¶

The version of the resource or ontology used to make the annotation. For OBO ontologies, this SHALL be the versionIRI. For other resources this should be the native version of the resource, e.g UniProt - “2019_08”, DbSNP - “153” for resources without release versions, this field should be left blank.

namespace_prefix¶

The prefix used in the CURIE of an OntologyClass e.g. HP, MP, ECO for example an HPO term will have a CURIE like this - HP:0012828 which should be used in combination with the iri_prefix to form a fully-resolvable IRI.

iri_prefix¶

The full IRI prefix which can be used with the namespace_prefix and the OntologyClass::id to resolve to an IRI for a term. Tools such as the curie-util (https://github.com/prefixcommons/curie-util) can utilise this to produce fully-resolvable IRIs for an OntologyClass.

CURIE¶

The CURIE is defined by the W3C as a means of encoding a “Compact URI”. It is a simple string taking the form of colon (:) separated prefix and reference elements - prefix:reference e.g. HP:0012828 or HGNC:12805.

It is RECOMMENDED to use CURIE identifiers where possible.

Not all resources use CURIEs as identifiers (e.g. SNOMED, UniProt, ClinVar, PubMed). In these cases it is often possible to create a CURIE form of an identifier by using the prefix for that resource from identifiers.org.

Where no CURIE prefix is present in identifiers.org it is possible for a Resource to define a locally-scoped namespace, although if a Phenopacket is being shared publicly this is NOT recommended if the resource is not publicly resolvable.

When using a CURIE identifier a corresponding Resource SHALL also be included in the MetaData section.

Identifier resolution¶

A CURIE identifier can be resolved to an external resource using the Resource element by looking-up the CURIE prefix against the Resource::namespacePrefix and then appending the CURIE reference to the Resource::iriPrefix.

For example, software can use the HPO Resource shown above to resolve the following HPO term encoding the concept of Severe:

ontologyClass:
  id: "HP:0012828"
  label: "Severe"

The id HP:0012828 can be split into the prefix - ‘HP’ and reference - ‘0012828’. The ‘HP’ prefix matches the Resource::namespacePrefix so we can append the reference ‘0012828’ to the Resource::iriPrefix: which produces the URI

http://purl.obolibrary.org/obo/HP_0012828

the term can be resolved to http://purl.obolibrary.org/obo/HP_0012828