Change ontology term identifier (#694)

* Change ontology term identifier
Ontology terms had an ambigious 'id' field and description. This PR renames the field to term_id to remove the confusion over the role of the field, as well as improves the comment for its proper use. A field 'term_uri' has been added that allows one to specify the full URI for a term if it is available.
Change ontologies appendix documentation to reflect change
Slight formatting and wording adjustments of appendix doc
Change CURIE to URI
Fix casing

* post Vancouver changes

modified after Vancouver meeting to use CURIE throughout, remove
termURI and remove sourceName and source version.

* fixed termId

* doc

* Fix casing

* Update process schemas

doc/source/appendix/ontologies.rst

@@ -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
@@ -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"
+

src/main/proto/ga4gh/metadata.proto

@@ -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.