Merge branch 'master' into markerset_classification

# Conflicts:
#	bdso-allen.owl
#	bdso-base-ext.json
#	bdso-base-ext.obo
#	bdso-base-ext.owl
#	bdso-base.json
#	bdso-base.obo
#	bdso-base.owl
#	bdso-full.json
#	bdso-full.obo
#	bdso-full.owl
#	bdso-simple-non-classified.json
#	bdso-simple-non-classified.obo
#	bdso-simple-non-classified.owl
#	bdso-simple.json
#	bdso-simple.obo
#	bdso-simple.owl
#	bdso.json
#	bdso.obo
#	bdso.owl

Author: hkir-dev

src/ontology/bdso.Makefile

@@ -102,7 +102,7 @@ $(PATTERNDIR)/data/default/Protein2GeneExpression.txt: $(PATTERNDIR)/data/defaul
 $(PATTERNDIR)/data/default/%_class.tsv: $(PATTERNDIR)/data/default/%_class_base.tsv $(PATTERNDIR)/data/default/%_class_curation.tsv
 	python ../scripts/template_runner.py modifier --merge -i=$< -i2=$(word 2, $^) -o=$@
 
-all_imports: $(IMPORT_FILES)
+all_imports: $(IMPORT_FILES) imports/merged_import.owl
 
 # hard wiring for now.  Work on patsubst later
 mirror/ensmusg.owl: ../templates/ensmusg.tsv .FORCE

src/ontology/catalog-v001.xml

@@ -14,7 +14,7 @@
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/bdscratch/imports/simple_human_import.owl" uri="imports/simple_human_import.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/bdscratch/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/bdscratch/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
-<!--  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/imports/merged_import.owl" uri="imports/merged_import.owl"/>-->
+  <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/pcl/imports/merged_import.owl" uri="imports/merged_import.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/helper.owl" uri="helper.owl"/>
   <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/bdscratch/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
   <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>

src/scripts/pcl_legacy_mapping.py

@@ -2,7 +2,7 @@
 import pandas as pd
 from rdflib import Graph
 
-BDSO_ONT = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../../pcl-full.owl")
+BDSO_ONT = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../../bdso-full.owl")
 PCL_ONT = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../resources/pCL_4.1.0.owl")
 PCL_MAPPING_OUTPUT = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../templates/pCL_mapping.tsv")