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[Obo-phenotype-commits] obo/ontology/phenotype/phenotype_xp galen-pato-aln.tbl, NONE, 1.1 Makefile, 1.14, 1.15
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From: Chris M. <cmu...@us...> - 2008-01-18 02:41:57
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Update of /cvsroot/obo/obo/ontology/phenotype/phenotype_xp In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv6274 Modified Files: Makefile Added Files: galen-pato-aln.tbl Log Message: Index: Makefile =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/phenotype_xp/Makefile,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** Makefile 15 Oct 2007 21:27:29 -0000 1.14 --- Makefile 18 Jan 2008 02:41:55 -0000 1.15 *************** *** 27,30 **** --- 27,37 ---- $(OBOL) -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')" >& $@.tmp && mv $@.tmp $@ + # only ones that cannot otherwise be caught + mammalian_phenotype_xp_fma-obol.obo: $(MP_OBO) $(PATO_OBO) ../mammalian_phenotype_xp.obo + $(OBOL) -u obol_mammalian_phenotype_xp -r go -r fma_downcase -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')" >& $@.tmp && mv $@.tmp $@ + + mammalian_phenotype_xp_fma-above-%.obo: $(MP_OBO) $(PATO_OBO) ../mammalian_phenotype_xp.obo ../mammalian_phenotype_xp_fma.obo + $(OBOL) -u obol_mammalian_phenotype_xp -r go -r fma_downcase -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 $@ + plant_trait_xp-obol.obo: $(TO_OBO) $(PATO_OBO) $(TO_DIR)/plant_trait_xp.obo $(OBOL) -u obol_plant_trait_xp -ro go -r plant_anatomy -r plant_environment -r cell -r xchebi -i $< -i $(TO_DIR)/plant_trait_xp.obo obol-parse -parse_rule trait -xp_policy newonly "belongs(ID,plant_trait_ontology)" >& $@.tmp && mv $@.tmp $@ *************** *** 45,49 **** $(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 $@ --- 52,69 ---- $(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 $@ ! omim_subset.txt: ! ./getomimids.sh > $@ ! ! omim_subset.pro: omim_subset.txt ! tbl2p -p omim $< > $@ ! ! omim_pheno_xp_fma_subset-obol.obo: omim_pheno_subset.obo ! $(OBOL) -xp_policy newonly -r fma_downcase -r cell -r xchebi -r fma obol-parse -parse_rule phenotype -xp_policy newonly -i $< "belongs(ID,omim)" >& $@.tmp && mv $@.tmp $@ ! ! omim_pheno_subset.obo: omim_subset.pro ! blip ontol-subset -i $< -i omim_ontol-downcase.obo -query "(omim(OMIM),restriction(OMIM,_,ID))" -to obo > $@.tmp && mv $@.tmp $@ ! .PRECIOUS: omim_pheno_subset.obo ! ! # only do those above a number 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 $@ *************** *** 114,120 **** .PRECIOUS: wp-pato-aln.tbl yp-obo-aln.tbl: obol ontol-align -stem -shownames -r yeast_phenotype -r go -r pato -r fungal_anatomy yeast_phenotype_ontology > $@.tmp && mv $@.tmp $@ ! .PRECIOUS: wp-pato-aln.tbl pato-omim-aln.tbl: --- 134,147 ---- .PRECIOUS: wp-pato-aln.tbl + galen-pato-aln.tbl: + obol ontol-align -stem -shownames -r galen -i $(PATO_OBO) galen quality > $@.tmp && mv $@.tmp $@ + .PRECIOUS: galen-pato-aln.tbl + yp-obo-aln.tbl: obol ontol-align -stem -shownames -r yeast_phenotype -r go -r pato -r fungal_anatomy yeast_phenotype_ontology > $@.tmp && mv $@.tmp $@ ! ! yp-pato-aln.tbl: ! obol ontol-align -stem -shownames -r yeast_phenotype -r pato yeast_phenotype_ontology > $@.tmp && mv $@.tmp $@ ! .PRECIOUS: yp-pato-aln.tbl pato-omim-aln.tbl: --- NEW FILE: galen-pato-aln.tbl --- substr exact-exact galen:Absorption PATO:0001293 galen quality absorption absorption quality eq exact-exact galen:Acceleration PATO:0001028 galen quality acceleration acceleration substr exact-exact galen:Acceleration PATO:0001753 galen quality acceleration accelerated growth eq exact-exact galen:Acid PATO:0001429 galen quality acid acidic eq exact-exact galen:Acid PATO:0001842 galen quality acid acidity eq exact-exact galen:Acidity PATO:0001429 galen quality acidity acidic eq exact-exact galen:Acidity PATO:0001842 galen quality acidity acidity substr exact-exact galen:Action PATO:0001463 galen quality action action potential eq exact-exact galen:Activity PATO:0001707 galen quality activity active substr exact-exact galen:Activity PATO:0001740 galen quality activity activity (of a radionuclide) eq exact-exact galen:Adolescence PATO:0001189 galen quality adolescence adolescent eq exact-exact galen:Adolescent PATO:0001189 galen quality adolescent adolescent substr exact-exact galen:Advancing PATO:0000500 galen quality advancing advanced phase eq exact-exact galen:Age PATO:0000011 galen quality age age eq exact-exact galen:Aggregating PATO:0001629 galen quality aggregating aggregated substr exact-exact galen:Aligator PATO:0001652 galen quality aligator alignment substr exact-exact galen:Aligator PATO:0001653 galen quality aligator aligned with substr exact-related galen:Aligator PATO:0001653 galen quality aligator aligned with eq exact-exact galen:Aligning PATO:0001652 galen quality aligning alignment [...3750 lines suppressed...] substr exact-exact PATO:0001900 galen:FrontalLobeSubduralSpace quality galen front frontal lobe subdural space substr exact-exact PATO:0001900 galen:FrontalNerve quality galen front frontal nerve substr exact-exact PATO:0001900 galen:FrontalProcessOfMaxilla quality galen front frontal process of maxilla substr exact-exact PATO:0001900 galen:FrontalProcessOfZygomaticBone quality galen front frontal process of zygomatic bone substr exact-exact PATO:0001900 galen:FrontalSinus quality galen front frontal sinus substr exact-exact PATO:0001900 galen:FrontalSinusExamination quality galen front frontal sinus examination substr exact-exact PATO:0001900 galen:FrontalSinusitis quality galen front frontal sinusitis substr exact-exact PATO:0001900 galen:FrontalSuture quality galen front frontal suture substr exact-exact PATO:0001900 galen:Frontalis quality galen front frontalis substr exact-exact PATO:0001900 galen:FrontoEthmoidalSuture quality galen front fronto ethmoidal suture substr exact-exact PATO:0001900 galen:FrontoLacrimalSuture quality galen front fronto lacrimal suture substr exact-exact PATO:0001900 galen:FrontoMaxillarySuture quality galen front fronto maxillary suture substr exact-exact PATO:0001900 galen:FrontoNasalSuture quality galen front fronto nasal suture substr exact-exact PATO:0001900 galen:FrontoZygomaticSuture quality galen front fronto zygomatic suture eq exact-exact PATO:0001901 galen:Back quality galen back back substr exact-exact PATO:0001901 galen:BackExamination quality galen back back examination substr exact-exact PATO:0001901 galen:BackPain quality galen back back pain substr exact-exact PATO:0001901 galen:BackPainSymptom quality galen back back pain symptom substr exact-exact PATO:0001901 galen:BackgroundRetinopathy quality galen back background retinopathy substr exact-exact PATO:0001901 galen:BackwardFlow quality galen back backward flow |