Merge pull request #633 from geneontology/issue-620-change-default-closure

Issue 620 change default closure

Author: kltm

golr/solr/conf/schema.xml

@@ -23,7 +23,7 @@
     <!-- bioentity: Gene of gene product ID. -->
     <!-- annotation: A unique (and internal) combination of bioentity and ontology class. -->
     <!-- general: The mangled internal ID for this entity. -->
-    <!-- model_annotation: A unique (and internal) thing. -->
+    <!-- model_annotation: CURIE form of annoton (molecular function individual) -->
     <!-- noctua_model_meta: The mangled internal ID for this entity. -->
     <!-- family: Family ID. -->
     <!-- bbop_ann_ev_agg: Gene/product ID. -->
@@ -126,6 +126,8 @@
     <field name="topology_graph_json" type="string" required="false" multiValued="false" indexed="false" stored="true"/>
     <!-- ontology: JSON blob form of the local relation transitivity graph. Uses various relations (including regulates, occurs in, capable_of). -->
     <field name="regulates_transitivity_graph_json" type="string" required="false" multiValued="false" indexed="false" stored="true"/>
+    <!-- ontology: JSON blob form of the local relation transitivity graph. -->
+    <field name="isa_partof_transitivity_graph_json" type="string" required="false" multiValued="false" indexed="false" stored="true"/>
     <!-- ontology: JSON blob form of all immediate neighbors of the term. -->
     <field name="neighborhood_graph_json" type="string" required="false" multiValued="false" indexed="false" stored="true"/>
     <!-- ontology: JSON blob form of all immediate neighbors of the term; in the case that there are too many neighbors to transport, the number will be artificially reduced. -->
@@ -201,14 +203,14 @@
     <!-- bioentity_for_browser: Taxonomic group -->
     <!-- annotation: Taxonomic group. -->
     <!-- annotation_for_browser: Taxonomic group. -->
-    <!-- model_annotation: GAF column 13 (taxon). -->
+    <!-- model_annotation: taxon of the entity in enabled_by -->
     <!-- bbop_ann_ev_agg: Column 13: taxon. -->
     <field name="taxon" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!-- bioentity: Taxonomic group -->
     <!-- bioentity_for_browser: Taxonomic group -->
     <!-- annotation: Taxonomic group and ancestral groups. -->
     <!-- annotation_for_browser: Taxonomic group and ancestral groups. -->
-    <!-- model_annotation: Taxon derived from GAF column 13 and ncbi_taxonomy.obo. -->
+    <!-- model_annotation: label for taxon -->
     <!-- bbop_ann_ev_agg: Derived from C13 + ncbi_taxonomy.obo. -->
     <field name="taxon_label" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of taxon_label.-->
@@ -218,14 +220,14 @@
     <!-- bioentity_for_browser: Taxonomic group and ancestral groups. -->
     <!-- annotation: Taxonomic group and ancestral groups. -->
     <!-- annotation_for_browser: Taxonomic group and ancestral groups. -->
-    <!-- model_annotation: Taxon IDs derived from GAF column 13 and ncbi_taxonomy.obo. -->
+    <!-- model_annotation: is_a closure of taxon -->
     <!-- bbop_ann_ev_agg: IDs derived from C13 + ncbi_taxonomy.obo. -->
     <field name="taxon_closure" type="string" required="false" multiValued="true" indexed="true" stored="true"/>
     <!-- bioentity: Taxonomic group and ancestral groups. -->
     <!-- bioentity_for_browser: Taxonomic group and ancestral groups. -->
     <!-- annotation: Taxonomic group and ancestral groups. -->
     <!-- annotation_for_browser: Taxonomic group and ancestral groups. -->
-    <!-- model_annotation: Taxon label closure derived from GAF column 13 and ncbi_taxonomy.obo. -->
+    <!-- model_annotation: labels of is_a closure. -->
     <!-- bbop_ann_ev_agg: Labels derived from C13 + ncbi_taxonomy.obo. -->
     <field name="taxon_closure_label" type="string" required="false" multiValued="true" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of taxon_closure_label.-->
@@ -262,7 +264,7 @@
     <field name="annotation_class_list_map" type="string" required="false" multiValued="false" indexed="false" stored="true"/>
     <!-- bioentity: PANTHER families that are associated with this entity. -->
     <!-- annotation: PANTHER families that are associated with this entity. -->
-    <!-- model_annotation: PANTHER family IDs that are associated with this entity. -->
+    <!-- model_annotation: PANTHER family IDs that are associated with this entity, not yet populated. -->
     <!-- family: PANTHER family IDs that are associated with this entity. -->
     <!-- bbop_ann_ev_agg: Family IDs that are associated with this entity. -->
     <field name="panther_family" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
@@ -413,52 +415,52 @@
     <!--An easily searchable (TextField tokenized) version of general_blob.-->
     <field name="general_blob_searchable" type="text_searchable" required="false" multiValued="false" indexed="true" stored="true"/>
     <copyField source="general_blob" dest="general_blob_searchable"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: Same as id -->
     <!-- noctua_model_meta: The title(s) associated with the model. -->
     <field name="annotation_unit" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: Generally not display but for debug purpose can be concatenation of gene product label, function, process etc -->
     <!-- noctua_model_meta: The title(s) associated with the model. -->
     <field name="annotation_unit_label" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of annotation_unit_label.-->
     <field name="annotation_unit_label_searchable" type="text_searchable" required="false" multiValued="false" indexed="true" stored="true"/>
     <copyField source="annotation_unit_label" dest="annotation_unit_label_searchable"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: The CURIE of the model to which the annoton belongs -->
     <field name="model" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: The dc:title of the model to which the annoton belongs -->
     <field name="model_label" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of model_label.-->
     <field name="model_label_searchable" type="text_searchable" required="false" multiValued="false" indexed="true" stored="true"/>
     <copyField source="model_label" dest="model_label_searchable"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: The URI of the model to which the annoton belongs -->
     <field name="model_url" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: Curation status -->
     <!-- noctua_model_meta: The editorial state of the model. -->
     <field name="model_state" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!-- model_annotation: set of all literal values of all annotation assertions in model -->
     <field name="annotation_value" type="string" required="false" multiValued="true" indexed="true" stored="true"/>
-    <!-- model_annotation: ???. -->
+    <!-- model_annotation: Value of dc:contributor fields for the annoton -->
     <!-- noctua_model_meta: Contributor identity. -->
     <field name="contributor" type="string" required="false" multiValued="true" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of contributor.-->
     <field name="contributor_searchable" type="text_searchable" required="false" multiValued="true" indexed="true" stored="true"/>
     <copyField source="contributor" dest="contributor_searchable"/>
-    <!-- model_annotation: Last modified -->
+    <!-- model_annotation: Value of dc:date field for the annoton -->
     <!-- noctua_model_meta: Model last modification dates. -->
     <field name="model_date" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of model_date.-->
     <field name="model_date_searchable" type="text_searchable" required="false" multiValued="false" indexed="true" stored="true"/>
     <copyField source="model_date" dest="model_date_searchable"/>
-    <!-- model_annotation: ??? -->
+    <!-- model_annotation: The CURIE for the ro:enabled_by.rdf:type value of the annoton/MF individual -->
     <field name="enabled_by" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of enabled_by.-->
     <field name="enabled_by_searchable" type="text_searchable" required="false" multiValued="false" indexed="true" stored="true"/>
     <copyField source="enabled_by" dest="enabled_by_searchable"/>
-    <!-- model_annotation: ??? -->
+    <!-- model_annotation: Searchable label version of the gene product -->
     <field name="enabled_by_label" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!--An easily searchable (TextField tokenized) version of enabled_by_label.-->
     <field name="enabled_by_label_searchable" type="text_searchable" required="false" multiValued="false" indexed="true" stored="true"/>
     <copyField source="enabled_by_label" dest="enabled_by_label_searchable"/>
-    <!-- model_annotation: Function acc/ID. -->
+    <!-- model_annotation: This is the value of rdf:type for the annoton/MF instance -->
     <field name="function_class" type="string" required="false" multiValued="false" indexed="true" stored="true"/>
     <!-- model_annotation: Common function name. -->
     <field name="function_class_label" type="string" required="false" multiValued="false" indexed="true" stored="true"/>

javascript/web/Browse.js

@@ -27,6 +27,11 @@ var jquery_engine = require('bbop-rest-manager').jquery;
 var golr_manager = require('bbop-manager-golr');
 var golr_response = require('bbop-response-golr');
 
+// Default closure relation. Starting setup to deal with future of
+// #620.
+//var default_closure_relation_set = 'regulates';
+var default_closure_relation_set = 'isa_partof';
+
 // // Graphs.
 // var model = require('bbop-graph');
 
@@ -40,33 +45,33 @@ var golr_response = require('bbop-response-golr');
 
 // Manager creation wrapper (we use it a couple of times).
 function _create_manager(personality){
-    
+
     // Create manager.
     var engine = new jquery_engine(golr_response);
     engine.method('GET');
     engine.use_jsonp(true);
     var manager = new golr_manager(gserv, gconf, engine, 'async');
-    
+
     // Manager settings.
     var confc = gconf.get_class(personality);
     manager.set_personality(personality);
     manager.add_query_filter('document_category',
 			     confc.document_category(), ['*']);
-    
-    return manager;	
+
+    return manager;
 }
 
 ///
 ///
 ///
 
 function BrowseInit(){
-    
+
     ///
     /// General setup--resource locations.
     /// Solr server, GOlr config, etc.
     ///
-    
+
     ///
     /// The info shield.
     ///
@@ -103,7 +108,7 @@ function BrowseInit(){
 	    uid,
 	    {
 		'transitivity_graph_field':
-		'regulates_transitivity_graph_json',
+		default_closure_relation_set + '_transitivity_graph_json',
 		'base_icon_url': sd.image_base,
 		'info_icon': 'info',
 		'current_icon': 'current_term',