new parent SO:0001260 #246

Author: hkir-dev

src/ontology/bdso-edit.owl

@@ -29,6 +29,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000004>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_P60041>))
 Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000956>))
+Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001260>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002100>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002292>))
@@ -149,6 +150,8 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000004> "Mar
 SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000004> <http://purl.obolibrary.org/obo/PCL_1000002>)
 SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000004> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0070007>))
 
+# Class: <http://purl.obolibrary.org/obo/SO_0001260> (sequence_collection)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/SO_0001260> "sequence_collection")
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000028> "symbol")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015001> "has exemplar data")

src/ontology/helper.owl

@@ -12,8 +12,6 @@ Declaration(Class(:PCL_0010001))
 AnnotationAssertion(rdfs:label :PCL_0010001 "Cluster")
 Declaration(Class(:PCL_0010002))
 AnnotationAssertion(rdfs:label :PCL_0010002 "Taxonomy")
-Declaration(Class(:PCL_0010003))
-AnnotationAssertion(rdfs:label :PCL_0010003 "Gene Set")
 
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))
 

src/patterns/data/default/CCN201912131_marker_set.tsv

@@ -508,7 +508,7 @@ def generate_marker_gene_set_template(taxonomy_file_path, output_filepath):
                     if 'Species_abbv' in taxonomy_config:
                         d['Species_abbv'] = taxonomy_config['Species_abbv'][0]
                     d['Brain_region'] = taxonomy_config['Brain_region'][0]
-                    d['Parent'] = PCL_PREFIX + "0010003"
+                    d['Parent'] = "SO:0001260"  # sequence collection
 
                     for k in class_seed:
                         if not (k in d.keys()):