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Change ontology term identifier #694

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Change ontology term identifier #694

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bb38274
Change ontology term identifier
david4096 Aug 22, 2016
347b058
post Vancouver changes
mcourtot Oct 21, 2016
db068f8
fixed termId
mbaudis Oct 21, 2016
c886594
doc
mbaudis Oct 21, 2016
122f70e
Fix casing
david4096 Jan 10, 2017
e83c882
Update process schemas
david4096 Feb 2, 2017
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98 changes: 27 additions & 71 deletions doc/source/appendix/ontologies.rst
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Expand Up @@ -38,15 +38,11 @@ What is the minimum attribute requirement for OntologyTerm in GA4GH?

Conceptually (and consistent with the metadata branch)

:ontologyId:
required and implemented as URI
we assume this resolves to a meaningful document, e.g. http://purl.obolibrary.org/obo/SO_0000147
:termId:
required and implemented as CURIE
we assume this resolves to a meaningful document, e.g. http://purl.obolibrary.org/obo/SO_0000147, using a prefix mapper, e.g. SO: <=> http://purl.obolibrary.org/obo/SO_
:term:
preferred but not required (e.g. ‘exon’); corresponds to class label
:sourceName:
not required since should be resolved from prefix etc., but supporting/fall-back in case of non-standard/deprecated/entropic annotations; possible use for CURIEs in compact sequence ontology implementations (e.g. SO:0000147)
:sourceVersion:
not required but good practice; if no explicit versioning, ISO8601 formatted data of retrieval should be used


Ontology Selection and Overlap
Expand Down Expand Up @@ -84,122 +80,82 @@ Examples
Genotypic sex
=============

:ontologyId:
"http://purl.obolibrary.org/obo/PATO_0020001",
:termId:
"PATO:0020001",
:term:
"male genotypic sex" ,
:sourceName:
"PATO Phenotypic quality",



Sequence Ontology
=================

:ontologyId:
"http://purl.obolibrary.org/obo/SO_0001583",
:termId:
"SO:0001583",
:term:
"missense_variant",
:sourceName:
"Sequence Ontology",
:sourceVersion:
"release_2.5.3"



Human Phenotype ontology
========================

:ontologyId:
"http://purl.obolibrary.org/obo/HP_0000819",
:termId:
"HP:0000819",
:term:
"Diabetes mellitus",
:sourceName:
"human_phenotype Ontology",
:sourceVersion:
"release_Jan2016*"


----

:ontologyId:
"http://www.ebi.ac.uk/efo/HP_0012059",
:termId:
"HP:0012059",
:term:
"Lentigo maligna melanoma",
:sourceName:
"human_phenotype_ontology",
:sourceVersion:
"2016-01-14”



Body part (Uberon)
==================

:ontologyId:
"http://www.ebi.ac.uk/efo/UBERON_0003403",
:termId:
"UBERON:0003403",
:term:
"skin of forearm",
:sourceName:
"uberon",
:sourceVersion:
"2015-11-23”


Human disease ontology
======================

:ontologyId:
"http://purl.obolibrary.org/obo/DOID_9351",
:termId:
"DOID:9351",
:term:
"diabetes mellitus",
:sourceName:
"disease_ontology",
:sourceVersion:
"2016-01-25"


Experimental factor ontology
============================

:ontologyId:
"http://purl.obolibrary.org/obo/EFO_0000400",
:termId:
"EFO:0000400",
:term:
"diabetes mellitus",
:sourceName:
"experimental_factor_ontology",
:sourceVersion:
"V2.68”


----

:ontologyId:
"http://www.ebi.ac.uk/efo/EFO_0004422",
:termId:
"EFO:0004422",
:term:
"exome",
:sourceName:
"Experimental Factor Ontology",
:sourceVersion:
"release_2.68"


SNOMEDCT representation of ICD-O 3 Cancer Histology
===================================================

:ontologyId:
"http://purl.bioontology.org/ontology/SNMI/M-94703“
:term:
"Medulloblastoma, NOS”
:sourceName:
"SNOMED CT model component”
:sourceVersion:
"2016-01-28"


Unit Ontology
=============

:ontologyId:
"http://purl.obolibrary.org/obo/UO_0000016",
:termId:
"UO:0000016",
:term:
"millimetre",
:sourceName:
"Unit Ontology",
:sourceVersion:
"2015-12-17"

32 changes: 9 additions & 23 deletions python/ga4gh/schemas/ga4gh/metadata_pb2.py
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18 changes: 4 additions & 14 deletions src/main/proto/ga4gh/metadata.proto
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Expand Up @@ -7,25 +7,15 @@ import "google/protobuf/struct.proto";
// An ontology term describing an attribute. (e.g. the phenotype attribute
// 'polydactyly' from HPO)
message OntologyTerm {
// Ontology source identifier - the identifier, a CURIE (preferred) or PURL
// for an ontology source e.g. http://purl.obolibrary.org/obo/hp.obo It
// Ontology term identifier - the CURIE for an ontology term. It
// differs from the standard GA4GH schema's :ref:`id <apidesign_object_ids>`
// in that it is a URI pointing to an information resource outside of the
// in that it is a CURIE pointing to an information resource outside of the
// scope of the schema or its resource implementation.
string id = 1;
string term_id = 1;

// Ontology term - the representation the id is pointing to.
// Ontology term - the label of the ontology term the termId is pointing to.
string term = 2;

// Ontology source name - the name of ontology from which the term is obtained
// e.g. 'Human Phenotype Ontology'
string source_name = 3;

// Ontology source version - the version of the ontology from which the
// OntologyTerm is obtained; e.g. 2.6.1. There is no standard for ontology
// versioning and some frequently released ontologies may use a datestamp, or
// build number.
string source_version = 4;
}

// A Dataset is a collection of related data of multiple types.
Expand Down