From: Chris M. <cmu...@us...> - 2007-08-12 03:07:04
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Update of /cvsroot/obo/obo/ontology/phenotype/phenotype_xp In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv19408 Modified Files: Makefile Log Message: Index: Makefile =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/phenotype_xp/Makefile,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** Makefile 3 Aug 2007 19:31:23 -0000 1.11 --- Makefile 12 Aug 2007 03:07:06 -0000 1.12 *************** *** 1,3 **** ! OBOL=obol -r relationship -r spatial -r pato -r relationship -r ro_proposed -table_pred user:process/3 -table_pred user:process5/3 -table_pred user:bearer/3 -table_pred user:quality/3 -table_pred user:gross_anatomical/3 -table_pred user:gross_anatomical5/3 -table_pred user:cell5/3 -table_pred user:cell/3 -table_pred user:cellular_component/3 -table_pred user:cellular_component5/3 -table_pred classdef_parser:any_kind_of/3 -table_pred ontol_db:subclassT/2 obol-parse -u ontol_manifest_synonym_from_plural $(OBOL_ARGS) BP_SRC=mammalian_phenotype_xp plant_trait_xp worm_phenotype_xp --- 1,3 ---- ! OBOL=obol -r relationship -r spatial -r pato -r relationship -r ro_proposed -table_pred user:process/3 -table_pred user:process5/3 -table_pred user:bearer/3 -table_pred user:quality/3 -table_pred user:gross_anatomical/3 -table_pred user:gross_anatomical5/3 -table_pred user:cell5/3 -table_pred user:cell/3 -table_pred user:cellular_component/3 -table_pred user:cellular_component5/3 -table_pred user:phenotype/3 -table_pred classdef_parser:any_kind_of/3 -table_pred ontol_db:subclassT/2 obol-parse -u ontol_manifest_synonym_from_plural $(OBOL_ARGS) BP_SRC=mammalian_phenotype_xp plant_trait_xp worm_phenotype_xp *************** *** 31,39 **** # just use the MP templates with worm for now... worm_phenotype_xp-obol.obo: $(PATO_OBO) ! $(OBOL) -u obol_worm_phenotype_xp -table_pred user:phenotype/3 -r go -r worm_anatomy -r worm_development -r cell -r xchebi -r worm_phenotype obol-parse -parse_rule phenotype -xp_policy newonly "belongs(ID,'C_elegans_phenotype_ontology')" >& $@.tmp && mv $@.tmp $@ disease_xp-obol.obo: $(PATO_OBO) ! $(OBOL) -u obol_disease_xp -u ontol_manifest_exact_from_related_synonym -table_pred user:phenotype/3 -table_pred user:bearer/3 -r go -r fma_downcase -i taxon_virus.obo -i taxon_bacteria.obo -r cell -r xchebi -r disease -parse_rule disease -xp_policy newonly "belongs(ID,'disease_ontology')" >& $@.tmp && mv $@.tmp $@ # seed using alignments --- 31,40 ---- # just use the MP templates with worm for now... + # try promoting related syns worm_phenotype_xp-obol.obo: $(PATO_OBO) ! $(OBOL) -u ontol_manifest_exact_from_related_synonym -u obol_worm_phenotype_xp -r go -r worm_anatomy -r worm_development -r cell -r xchebi -r worm_phenotype obol-parse -parse_rule phenotype -xp_policy newonly "belongs(ID,'C_elegans_phenotype_ontology')" >& $@.tmp && mv $@.tmp $@ disease_xp-obol.obo: $(PATO_OBO) ! $(OBOL) -u obol_disease_xp -u ontol_manifest_exact_from_related_synonym -r go -r fma_downcase -i taxon_virus.obo -i taxon_bacteria.obo -r cell -r xchebi -r disease -parse_rule disease -xp_policy newonly "belongs(ID,'disease_ontology')" >& $@.tmp && mv $@.tmp $@ # seed using alignments *************** *** 41,44 **** --- 42,50 ---- $(OBOL) -xp_policy newonly -u obol_mammalian_phenotype_xp -r fma_downcase -r cell -r xchebi -r fma obol-parse -parse_rule phenotype -xp_policy newonly -i omim_ontol_pheno-downcase.obo -i $< "(substr(_,XID,ID,_,_,_,_),belongs(ID,omim))" >& $@.tmp && mv $@.tmp $@ + # only do a subset + mammalian_phenotype_xp-above-%.obo: $(MP_OBO) $(PATO_OBO) ../mammalian_phenotype_xp.obo + $(OBOL) -u ontol_manifest_synonym_from_plural -u obol_mammalian_phenotype_xp -r go -r mouse_anatomy -r cell -r xchebi -i $< -i pheno_synonyms.obo -i ../mammalian_phenotype_xp.obo obol-parse -parse_rule phenotype -xp_policy newonly "(belongs(ID,'MPheno.ontology'),ID @> '$*')" >& $@.tmp && mv $@.tmp $@ + + # =================== # taxons |