Merge pull request #13 from BioComputingUP/IDPOv1.0

Push IDPO version (new release)

Author: XimeAixa

.gitignore

@@ -66,4 +66,4 @@ src/patterns/data/**/*.txt
 src/patterns/pattern_owl_seed.txt
 src/patterns/all_pattern_terms.txt
 
-# End of ODK-managed rules
+# End of ODK-managed rules

docs/odk-workflows/RepositoryFileStructure.md

@@ -17,8 +17,8 @@ These are the current imports in IDPO
 | Import | URL | Type |
 | ------ | --- | ---- |
 | ro | http://purl.obolibrary.org/obo/ro.owl | slme |
-| go | http://purl.obolibrary.org/obo/go.owl | slme |
 | omo | http://purl.obolibrary.org/obo/omo.owl | slme |
+| bfo | http://purl.obolibrary.org/obo/bfo.owl | slme |
 ## Components
 Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:
 

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                5e5f3480a3ca9b4a1dcb31ef7f894f3562a8568494dd58195ca1e90b4b0d245b
+CONFIG_HASH=                85e84f816ca42dc77e6261e6ed6f9b757a7fd91496e00b26a9312398d2e403b9
 
 
 # ----------------------------------------
@@ -188,7 +188,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro go omo
+IMPORTS =  ro omo bfo
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -463,14 +463,6 @@ mirror-ro: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl
 
 
-## ONTOLOGY: go
-.PHONY: mirror-go
-.PRECIOUS: $(MIRRORDIR)/go.owl
-mirror-go: | $(TMPDIR)
-	curl -L $(OBOBASE)/go.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl
-
-
 ## ONTOLOGY: omo
 .PHONY: mirror-omo
 .PRECIOUS: $(MIRRORDIR)/omo.owl
@@ -479,6 +471,14 @@ mirror-omo: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl
 
 
+## ONTOLOGY: bfo
+.PHONY: mirror-bfo
+.PRECIOUS: $(MIRRORDIR)/bfo.owl
+mirror-bfo: | $(TMPDIR)
+	curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(TMPDIR)/bfo-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/bfo-download.owl -o $(TMPDIR)/$@.owl
+
+
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

src/ontology/catalog-v001.xml

@@ -1,8 +1,8 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+<?xml version='1.0' encoding='UTF-8'?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
   <group id="odk-managed-catalog" prefer="public">
-    <uri name="http://purl.obolibrary.org/obo/idpo/imports/ro_import.owl" uri="imports/ro_import.owl"/>
-    <uri name="http://purl.obolibrary.org/obo/idpo/imports/go_import.owl" uri="imports/go_import.owl"/>
-    <uri name="http://purl.obolibrary.org/obo/idpo/imports/omo_import.owl" uri="imports/omo_import.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/idpo/imports/ro_import.owl" uri="imports/ro_import.owl" />
+    <uri name="http://purl.obolibrary.org/obo/idpo/imports/omo_import.owl" uri="imports/omo_import.owl" />
+    <uri name="http://purl.obolibrary.org/obo/idpo/imports/bfo_import.owl" uri="imports/bfo_import.owl" />
   </group>
 </catalog>