[Obo-phenotype-commits] [phenotype-ontologies] r226 committed - fix

[<phe...@go...>]

Revision: 226
Author:   cmungall
Date:     Wed May 22 22:03:39 2013
Log:      fix
http://code.google.com/p/phenotype-ontologies/source/detail?r=226

Modified:
  /trunk/src/ontology/Makefile

=======================================
--- /trunk/src/ontology/Makefile	Wed May 22 21:16:59 2013
+++ /trunk/src/ontology/Makefile	Wed May 22 22:03:39 2013
@@ -16,6 +16,8 @@
  MP_URL = ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology
  WP_URL =  
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi

+CATALOG = catalog-v001.xml
+
  # ----------------------------------------
  # TOP LEVEL TARGETS
  # ----------------------------------------
@@ -109,9 +111,6 @@
  %-subq.obo: %.obo
  	../tools/make-subq-model-from-obo.pl $< > $@

-# HACKS
-HACKED-catalog-v001.xml: catalog-v001.xml
-	perl -npe 's@uri="@uri="file:@' $< > $@

  # temp hack:
  fixed-behavior_xp.obo: external/behavior-ontology/behavior_xp.obo
@@ -122,7 +121,7 @@
  # ----------------------------------------

  %-ubr.obo: %.obo uberon-simple-vertebrate-bridge.obo
-	owltools $< uberon-simple-vertebrate-bridge.obo  
--add-imports-from-supports --merge-equivalent-classes -f FMA -f MA -f ZFA   
-t UBERON  --merge-equivalent-classes -f FMA -t CL -o -f obo --no-check $@
+	owltools $< uberon-simple-vertebrate-bridge.obo  
--add-imports-from-supports --merge-equivalent-classes -f FMA -f MA -f ZFA   
-t UBERON  --merge-equivalent-classes -f FMA -t CL -o -f obo --no-check  
$@.tmp && grep -v ^import $@.tmp > $@

  # mapping to uberon
  # TODO: don't hardcode idspace
@@ -152,8 +151,11 @@
  merged-mp:
  	ontology-release-runner --allow-overwrite --outdir mp  
--repair-cardinality --no-subsets --no-reasoner --asserted --re-mireot  
mp.obo -b mp/mp-equivalence-axioms.obo $(CORE) $(OBO)/ma.owl  
$(OBO)/uberon/bridge/uberon-bridge-to-ma.owl

+build-mp: mp/mp-equivalence-axioms-subq-ubr.owl mp.owl
+	ontology-release-runner --catalog-xml $(CATALOG)  --ignoreLock  
--skip-release-folder --outdir main --simple --allow-overwrite --reasoner  
elk mp.owl -b $<  $(OBO)/nbo.owl $(OBO)/pato.owl $(OBO)/go.owl  
$(OBO)/uberon.owl $(OBO)/chebi.owl
+
  merged-vt:
-	ontology-release-runner --catalog-xml catalog-v001.xml --allow-overwrite  
--outdir vt/build  --no-subsets --reasoner elk --simple --asserted  
--re-mireot vt/vt.obo -b vt/vt-equivalence-axioms.obo $(CORE)
+	ontology-release-runner --catalog-xml $(CATALOG) --allow-overwrite  
--outdir vt/build  --no-subsets --reasoner elk --simple --asserted  
--re-mireot vt/vt.obo -b vt/vt-equivalence-axioms.obo $(CORE)


  # ----------------------------------------