Resource sb-phenopackets

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.0.0)

Attributes

Type: object
Description: Description of an external resource used for referencing an object. For example the resource may be an ontology such as the HPO or SNOMED. FHIR mapping: CodeSystem (http://www.hl7.org/fhir/codesystem.html)

Properties

Property Type
id string
iriPrefix string
name string
namespacePrefix string
url string
version string

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 ontologies (e.g. SNOMED), use the prefix in identifiers.org

id Value Example
"pato"

iriPrefix

Full IRI prefix which can be used with the namespacePrefix 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. e.g. Using the HPO term encoding the concept of ‘Severe’ OntologyClass: id: ‘HP:0012828’ label: ‘Severe’ Resource: namespacePrefix: ‘HP’ iriPrefix: ‘http://purl.obolibrary.org/obo/HP_’ the term can be resolved to http://purl.obolibrary.org/obo/HP_0012828

iriPrefix Value Example
"http://purl.obolibrary.org/obo/HP_"

name

for OBO Ontologies, the value of this string SHOULD be the same as the title field on http://obofoundry.org however, this field is purely for information purposes and software should not encode any assumptions

name Value Example
"The Human Phenotype Ontology"

namespacePrefix

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 he iriPrefix to form a fully-resolvable IRI

namespacePrefix Value Example
"HP"

url

For OBO ontologies, this should always be the PURL

url Value Examples
"http://purl.obolibrary.org/obo/hp.owl"
"http://purl.obolibrary.org/obo/hp.obo"

version

for OBO ontologies, this should be the versionIRI

version Value Example
"2.97"

Resource Value Examples

{
   "id" : "pato",
   "name" : "PhenotypicFeature And Trait Ontology",
   "namespacePrefix" : "PATO",
   "url" : "http://purl.obolibrary.org/obo/pato.owl",
   "version" : "2018-03-28"
}
{
   "id" : "efo",
   "name" : "Experimental Factor Ontology",
   "namespacePrefix" : "EFO",
   "url" : "http://purl.obolibrary.org/obo/pato.owl",
   "version" : "2.97"
}
{
   "id" : "ncbitaxon",
   "name" : "NCBI organismal classification",
   "namespacePrefix" : "NCBITaxon",
   "url" : "http://purl.obolibrary.org/obo/ncbitaxon.owl",
   "version" : "2018-03-02"
}
{
   "id" : "hp",
   "iriPrefix" : "http://purl.obolibrary.org/obo/HP_",
   "name" : "human phenotype ontology",
   "namespacePrefix" : "HP",
   "url" : "http://purl.obolibrary.org/obo/hp.owl",
   "version" : "2018-03-08"
}