OBOL_NOGO=obol -r obol_av -r go_synonyms -r ubo -r relationship -r spatial -table_pred user:process5/3 -table_pred user:process/3 -table_pred classdef_parser:any_kind_of/3 -table_pred user:continuant/3 -table_pred ontol_db:subclassT/2 -table_pred user:cell/3 -table_pred user:cell5/3 -table_pred user:cellular_component/3 -table_pred user:cellular_component5/3 -table_pred user:chemical/3 -table_pred user:quality_in_bearer/3 -table_pred user:quality/3 obol-parse -xp_policy newonly -i ro_test.obo OBOL=$(OBOL_NOGO) -r go ANAT= -r fly_anatomy -r plant_anatomy -r zebrafish_anatomy -r mouse_anatomy -r xenopus_anatomy -r caro BP_XP=biological_process_xp-obol.obo BP_XP_AN=biological_process_xp_anatomy-obol.obo BP_XP_CL=biological_process_xp_cell-obol.obo BP_XP_CC=biological_process_xp_cellular_component-obol.obo BP_XP_MF=biological_process_xp_molecular_function-obol.obo BP_XP_BP=biological_process_xp_self-obol.obo BP_XP_MOP=biological_process_xp_multi_organism_process-obol.obo BP_XP_CC_MOP=biological_process_xp_cellular_component_multispecies-obol.obo BP_XP_R=biological_process_xp_regulation-obol.obo BP_XP_RoP=biological_process_xp_regulation_of_process-obol.obo BP_XP_RoF=biological_process_xp_regulation_of_function-obol.obo BP_XP_Q=biological_process_xp_quality-obol.obo BP_XP_SQ=biological_process_xp_sequence-obol.obo BP_XP_CH=biological_process_xp_chebi-obol.obo BP_XP_PRO=biological_process_xp_protein-obol.obo BP_XP_SIG=biological_process_xp_signaling-obol.obo BP_XP_ANU=biological_process_xp_uber_anatomy-obol.obo BP_XP_QANU=biological_process_xp_quality-uber_anatomy-obol.obo BP_XP_ANF=biological_process_xp_fly_anatomy-obol.obo BP_XP_ANFU=biological_process_xp_fungal_anatomy-obol.obo BP_XP_ANX=biological_process_xp_xenopus-obol.obo BP_XP_ANDD=biological_process_xp_dicty_anatomy-obol.obo BP_XP_ANZ=biological_process_xp_zebrafish_anatomy-obol.obo BP_XP_ANM=biological_process_xp_mouse_anatomy-obol.obo BP_XP_ANP=biological_process_xp_plant_anatomy-obol.obo BP_XP_ANH=biological_process_xp_human_anatomy-obol.obo BP_XP_Dev=biological_process_xp_development-obol.obo BP_XP_STIM=biological_process_xp_stimulus-obol.obo MF_XP_CH=molecular_function_xp_chebi-obol.obo MF_XP_CH_PRO=molecular_function_xp_chebi_pro-obol.obo MFCat_XP_CH=catalysis_xp_chebi-obol.obo # MF_XP_BP? MF_XP_GO=molecular_function_xp_go-obol.obo MF_XP_MF=molecular_function_xp_self-obol.obo MF_XP_ANU=molecular_function_xp_uberon-obol.obo MF_XP_PRO=molecular_function_xp_protein-obol.obo CC_XP_CC=cellular_component_xp_self-obol.obo CC_XP_GO=cellular_component_xp_go-obol.obo CC_XP_CL=cellular_component_xp_cell-obol.obo CC_XP_PRO=cellular_component_xp_protein-obol.obo CC_XP_PRO_GREP=cellular_component_xp_protein-grep-obol.obo CC_XP_GENE=cellular_component_xp_gene-obol.obo CC_XP_FAO=cellular_component_xp_fungal_anatomy-obol.obo MF_XP_MF_EDIT=../xps/molecular_function_xp_regulators.obo MF_XP_PRO_EDIT=../xps/molecular_function_xp_protein.obo #MF_XP_GO_EDIT=../xps/molecular_function_xp_go.obo MF_XP_CC_EDIT=../xps/molecular_function_xp_cellular_component.obo MF_XP_CH_EDIT=../xps/molecular_function_xp_chebi.obo MF_XP_CH_PRO_EDIT=../xps/molecular_function_xp_chebi_protein.obo BP_XP_BP_EDIT=../xps/biological_process_xp_self.obo BP_XP_CC_EDIT=../xps/biological_process_xp_cellular_component.obo BP_XP_MF_EDIT=../xps/biological_process_xp_molecular_function.obo BP_XP_CL_EDIT=../xps/biological_process_xp_cell.obo BP_XP_CH_EDIT=../xps/biological_process_xp_chebi.obo BP_XP_PRO_EDIT=../xps/biological_process_xp_protein.obo BP_XP_MOP_EDIT=../xps/biological_process_xp_multi_organism_process.obo CC_XP_CC_EDIT=../xps/cellular_component_xp_self.obo CC_XP_CC_UNVETTED=../xps/cellular_component_xp_self-unvetted.obo CC_XP_GO_EDIT=../xps/cellular_component_xp_go.obo CC_XP_CL_EDIT=../xps/cellular_component_xp_cell.obo CC_XP_CH_EDIT=../xps/biological_process_xp_chebi.obo BP_XP_ANU_EDIT=../xps/biological_process_xp_uber_anatomy.obo BP_XP_ANF_EDIT=../xps/biological_process_xp_fly_anatomy.obo BP_XP_ANFU_EDIT=../xps/biological_process_xp_fungal_anatomy.obo BP_XP_ANDD_EDIT=../xps/biological_process_xp_dicty_anatomy.obo BP_XP_ANZ_EDIT=../xps/biological_process_xp_zebrafish_anatomy.obo BP_XP_ANM_EDIT=../xps/biological_process_xp_mouse_anatomy.obo BP_XP_ANP_EDIT=../xps/biological_process_xp_plant_anatomy.obo BP_XP_ANH_EDIT=../xps/biological_process_xp_human_anatomy.obo BP_SRC= $(BP_XP_CL) $(BP_XP_BP) $(BP_XP_Q) $(BP_XP_ANU) $(BP_XP_ANP) $(BP_XP_ANDD) BP_OBOL=$(patsubst %,%-obol.obo,$(BP_SRC)) BP_SRC_INPUT=$(patsubst %,-i %,$(BP_OBOL)) CC_SRC= $(CC_XP_CC) $(CC_XP_GO) $(CC_XP_CL) $(CC_XP_CH) MF_SRC= $(MF_XP_MF) $(MF_XP_CC) $(MF_XP_CH) $(MF_XP_CH_PRO) ALL_SRC=$(BP_SRC) $(CC_SRC) $(MF_SRC) ALL_IMPLIED=$(patsubst %-obol.obo,%-implied.obo,$(ALL_SRC)) INC_BP_Main= -i $(BP_XP_CL_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_BP_EDIT) -i $(BP_XP_R) -i $(BP_XP_Q) -i $(BP_XP_CH_EDIT) -i $(BP_XP_ANU_EDIT) -i $(BP_XP_ANZ_EDIT) -i $(BP_XP_ANP_EDIT) -i $(BP_XP_ANF_EDIT) -i $(BP_XP_ANFU_EDIT) -i $(BP_XP_PRO_EDIT) GO=../../ontology/editors/gene_ontology_write.obo #REGLIVE=../regulates_xp_live/go_reglive_withPosNeg_withPF.obo REGLIVE=../regulates_xp_live/go_reglive_withPosNeg_withPF-bpgenus.obo TAXDIR=../../quality_control/annotation_checks/taxon_checks/ GO2TAX=$(TAXDIR)/taxon_go_triggers.obo TAXSLIM=$(TAXDIR)/ncbi_taxon_slim.obo INC_TAX= -i $(GO2TAX) -i $(TAXSLIM) -table_pred ontol_db:bf_parentRT/2 all: $(ALL_SRC) all_implied: $(ALL_IMPLIED) TABLE_ANATOMY=-table_pred user:gross_anatomical/3 -table_pred user:gross_anatomical5/3 # =================== # biological process # =================== # BP all $(BP_XP): $(BP_OBOL) $(GO) $(OBOL) -u obol_go_xp_all -r cell -r xchebi -r pato -parse_rule process $(BP_SRC_INPUT) "belongs(ID,biological_process)" >& $@.tmp && mv $@.tmp $@ # BP regulation terms # this is generated regularly as a separate process in the above directory # note: changed to RoBP+MF #$(BP_XP_RoP): ../gene_ontology_xp.obo $(BP_XP_R): $(REGLIVE) obo-grep.pl -r intersection_of $< | obo-filter-tags.pl -t id -t intersection_of - > $@.tmp && mv $@.tmp $@ $(BP_XP_RoP): $(BP_XP_R) # TODO # multi-organism process # biological_role included in MOP_EDIT $(BP_XP_MOP): $(BP_XP_R) $(BP_XP_CC_EDIT) $(BP_XP_MOP_EDIT) $(GO) $(OBOL) -i $< -i $(BP_XP_CC_EDIT) -i $(BP_XP_MOP_EDIT) -u obol_biological_process_xp_self -parse_rule process "parentT(ID,'GO:0051704')" >& $@.tmp && mv $@.tmp $@ # one-off #PAMGO = PAMGO-Sep3.obo PAMGO_EDIT = ../xps/biological_process_xp_pamgo_new.obo pamgo-obol.obo: $(BP_XP_R) $(BP_XP_CC_EDIT) $(BP_XP_MOP_EDIT) $(PAMGO_EDIT) $(OBOL) -i $< -i $(BP_XP_CC_EDIT) -i $(BP_XP_MOP_EDIT) -i $(PAMGO_EDIT) -u obol_biological_process_xp_self -parse_rule process "(class(ID),sub_atom(ID,_,_,_,'GO:0075'))" >& $@.tmp && mv $@.tmp $@ pamgo-reasoned.obo: obo2obo $(BP_XP_CC_MOP): $(BP_XP_R) $(BP_XP_CC_EDIT) $(BP_XP_MOP_EDIT) $(GO) $(OBOL) -i $< -i $(BP_XP_CC_EDIT) -i $(BP_XP_MOP_EDIT) -u obol_biological_process_xp_anatomy_multispecies -parse_rule process "subclassT(ID,'GO:0051704')" >& $@.tmp && mv $@.tmp $@ # BP x BP # extends MOP and regulation xps $(BP_XP_BP): $(BP_XP_R) $(BP_XP_CC_EDIT) $(BP_XP_MOP_EDIT) $(GO) $(OBOL) -i $< -i $(BP_XP_CC_EDIT) -i $(BP_XP_MOP_EDIT) -i $(BP_XP_BP_EDIT) -u obol_biological_process_xp_self -parse_rule process "(belongs(ID,biological_process),\+genus(ID,_))" >& $@.tmp && mv $@.tmp $@ plus-$(BP_XP_BP): $(BP_XP_R) $(BP_XP_CC_EDIT) $(BP_XP_MOP_EDIT) $(GO) obol obol-suggest -i $< -i $(BP_XP_CL_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) -i $(BP_XP_BP_EDIT) -i $(BP_XP_MOP_EDIT) -r go "belongs(ID,biological_process)" >& $@.tmp && mv $@.tmp $@ involved_in-$(BP_XP_BP): blip-findall -u ontol_writer_obo -r go -u metadata_nlp "term_split_over_strict(E,A,B,'involved in'),id_idspace(A,'GO'),id_idspace(B,'GO'),write_cdef(obo,E,cdef(A,[part_of=B])),fail" > $@ # BP x PATO (regulation) # Example: regulation of size # Note: this will make more sense when we have a shared anatomy ontology, so we can have regulation of BLOOD pressure # We include CL so we can have "establishment and/or maintenance of neuroblast polarity" $(BP_X_Q): $(GO) $(OBOL) -u obol_biological_process_xp_quality -u obol_biological_process_xp_cell -r pato -r cell -r xchebi -parse_rule process -i $(BP_XP_BP) -i $(BP_XP_RoP) -i $(BP_XP_RoF) -i $(BP_XP_CC) -i $(BP_XP_CL) -i $(BP_XP_CH) -xp_ontology quality "belongs(ID,'biological_process')" >& $@.tmp && mv $@.tmp $@ #### $(OBOL) -u obol_biological_process_xp_quality -u obol_biological_process_xp_cell -r pato -r cell -r xchebi -parse_rule process -i $(BP_XP_BP) -i $(BP_XP_RoP) -i $(BP_XP_CC) -i $(BP_XP_CL) -i $(BP_XP_CH) "(belongs(ID,'biological_process'),subclassT(ID,Root),class(Root,'regulation of biological quality'))" >& $@.tmp && mv $@.tmp $@ # BP x MF (regulation) # todo: other BP-MF links? $(BP_XP_RoF): $(BP_XP_CL) $(BP_XP_BP) $(GO) $(OBOL) -u obol_biological_process_xp_function -parse_rule process -i $(BP_XP_BP) "(belongs(ID,biological_process),subclassRT(ID,Root),class(Root,'regulation of a molecular function'))" >& $@.tmp && mv $@.tmp $@ # BP x CC - any biological_process that refers to a cellular_component # eg U12-dependent spliceosome disassembly $(BP_XP_CC): $(BP_XP_CC_EDIT) $(GO) $(OBOL) -u obol_biological_process_xp_cellular_component -parse_rule process -i $< -i $(BP_XP_BP_EDIT) -i $(BP_XP_CL_EDIT) -i $(BP_XP_R) -i $< -xp_ontology cellular_component "(belongs(ID,biological_process))" >& $@.tmp && mv $@.tmp $@ #$(BP_XP_CC): bp-cc-aln.tbl $(BP_XP_CC_EDIT) # $(OBOL) -u obol_biological_process_xp_cellular_component -parse_rule process -i $< -i $(BP_XP_BP_EDIT) -i $(BP_XP_CL_EDIT) -i $(BP_XP_RoP) -i $< -i $(BP_XP_CC_EDIT) -xp_ontology cellular_component "(substr(_,XID,ID,_,_,_,_),belongs(ID,biological_process))" >& $@.tmp && mv $@.tmp $@ #organization-$(BP_XP_CC): $(BP_XP_CC_EDIT) $(GO) # $(OBOL) -u obol_biological_process_xp_cellular_component -parse_rule process -i $< -i $(BP_XP_BP_EDIT) -i $(BP_XP_CL_EDIT) -i $(BP_XP_R) -i $< -xp_ontology cellular_component "(belongs(ID,biological_process),entity_label_scope(ID,N,_),(sub_atom(N,_,_,0,organization);sub_atom(N,_,_,0,biogenesis)))" >& $@.tmp && mv $@.tmp $@ organization-$(BP_XP_CC): $(BP_XP_CC_EDIT) $(GO) $(OBOL) -u obol_biological_process_xp_cellular_component -parse_rule process -i $< -i $(BP_XP_BP_EDIT) -i $(BP_XP_CL_EDIT) -i $(BP_XP_R) -i $< -xp_ontology cellular_component "(subclassRT(ID,'GO:0016043'))" >& $@.tmp && mv $@.tmp $@ endmatch-%-$(BP_XP_CC): $(BP_XP_CC_EDIT) $(GO) $(OBOL) -u obol_biological_process_xp_cellular_component -parse_rule process -i $< -i $(BP_XP_BP_EDIT) -i $(BP_XP_CL_EDIT) -i $(BP_XP_R) -i $< -xp_ontology cellular_component "(belongs(ID,biological_process),entity_label_scope(ID,N,_),sub_atom(N,_,_,0,'$*'))" >& $@.tmp && mv $@.tmp $@ $(BP_XP_MF): $(BP_XP_MF_EDIT) $(GO) $(OBOL) -u obol_biological_process_xp_function -parse_rule process -i $< -i $(BP_XP_MF_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CL_EDIT) -i $(BP_XP_CH_EDIT) -i $(BP_XP_R) -i $< -xp_ontology molecular_function "(subclassT(ID,'GO:0008152'))" >& $@.tmp && mv $@.tmp $@ # BP x CL $(BP_XP_CL): $(BP_XP_CL_EDIT) $(GO) $(OBOL) -u obol_biological_process_xp_cell -u obol_biological_process_xp_cellular_component -r cell -r hemo_CL -parse_rule process -i $(BP_XP_RoP) -i $(BP_XP_CL_EDIT) -i $(BP_XP_CH_EDIT) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) "belongs(ID,biological_process)" >& $@.tmp && mv $@.tmp $@ ## NEW new-CL.txt: obol qobol-newterms -ontology GO -r cell -tag bp -tag generic -tag cell -subclass GO:0009987 -taxon NCBITaxon:33208 > $@ # (obol qobol-newterms -ontology GO -xont CL -subclass GO:0009987 -tag bp -tag generic -tag cell -undefined_only true -export obo > $@) 2> $@.err new-CL-cd.txt: obol qobol-newterms -ontology GO -r CL -tag generic -subclass GO:0030154 > $@ new-RoBQ.txt: obol qobol-newterms -ontology GO -tag bp -tag regulation -tag quality -subclass GO:0065008 > $@ new-INVOLVED.txt: obol qobol-newterms -ontology GO -tag bp -tag involved > $@ x-bq-obol.obo: obol qobol -ontology GO -i bbq.obo -subclass GO:0065008 -tag quality -tag regulation -undefined_only true -export obo -scope all > $@ bbq-obol.obo: obol qobol -ontology BBQ -tag trait -tag bbq -undefined_only true -export obo -scope all > $@ new-UBERON.txt: obol qobol-newterms -ontology GO -r uberonp -r goxp/biological_process_xp_uber_anatomy -r goxp/biological_process_xp_fly_anatomy -r goxp/biological_process_xp_fungal_anatomy -tag bp -tag generic -tag anatomy -subclass GO:0032502 -not_subclass GO:0048468 -taxon NCBITaxon:33208 > $@ new-GOCHE.txt: obol qobol-newterms -ontology GO -tag bp -tag generic -tag chemical -subclass GO:0008152 > $@ new-PR.txt: obol qobol-newterms -ontology GO -r protein -r goxp/molecular_function_xp_protein -tag binding -subclass GO:0005515 -not_subclass GO:0032403 -not_subclass GO:0019904 > $@ new-CC-assembly.txt: obol qobol-newterms -ontology GO -r go_xp -tag generic -subclass GO:0022607 > $@ ESTAB_LOC = GO:0051234 MAINT_LOC = GO:0051235 bp_xp_generic-obol.obo: (obol qobol -ontology GO -r chebi -r ions -r go_transport -tag generic -tag bp -undefined_only true -export obo > $@) >& $@.err bp_xp_transport-obol.obo: (obol qobol -ontology GO -r go_xp -r chebi -r ions -r go_transport -subclass $(ESTAB_LOC) -tag transport -undefined_only true -export obo > $@) >& $@.err bp_xp_transport-obol-allsyns.obo: obol qobol -ontology GO -r go_xp -r chebi -r ions -r go_transport -subclass $(ESTAB_LOC) -tag transport -undefined_only true -export obo -scope all > $@ porter.obo: ./hack-porter.pl ../../ontology/editors/gene_ontology_write.obo > $@ mf_xp_transport-obol.obo: (obol qobol -ontology GO -r chebi -r ions -i porter.obo -subclass GO:0005215 -tag transport -undefined_only true -export obo > $@) >& $@.err mf_xp_transport-obol-allsyns.obo: obol qobol -ontology GO -r chebi -r ions -i porter.obo -subclass GO:0005215 -tag transport -undefined_only true -export obo -scope all > $@ # DEP go-t.obo: blip-findall -r go ontol-query -query "parentRT(ID,part_of,'GO:0051179')" -to obo > go-t.obo go-p.obo: owltools http://purl.obolibrary.org/obo/go.owl --make-subset-by-properties part_of // -o -f obo $@ go-xp-t-all.obo: go-p.obo ( obol qobol -debug foo -idspace GO -scope all -i $< -r go_xp_chebi -r chebi -r ions -r go_transport -oneof transport -oneof generic -undefined_only true -export obo -union GO:0051179 -union GO:0051234 -union GO:0051235 > $@ ) >& $@.err bp_xp_uberon-obol.obo: obol qobol -ontology GO -xont UBERON -tag bp -tag anatomy -undefined_only true -export obo > $@ bp_xp_cl-obol.obo: (obol qobol -debug qobol -ontology GO -xont CL -subclass GO:0009987 -tag bp -tag generic -tag cell -undefined_only true -export obo > $@) 2> $@.err bp_xp_involved-obol.obo: obol qobol -ontology GO -tag bp -tag involved -undefined_only true -export obo > $@ #bp_xp_involved-obol.obo: # obol qobol -ontology GO -tag bp -tag involved -undefined_only true -export obo > $@ bp_xp_po-obol.obo: obol qobol -ontology GO -xont PO -tag bp -tag generic -tag anatomy -undefined_only true -export obo > $@ bp_xp_po_cl-obol.obo: obol qobol -ontology GO -xont PO -tag bp -tag cell -tag generic -undefined_only true -subclass GO:0009987 -export obo > $@ mf_xp_pro-obol.obo: obol qobol -ontology GO -xont PR -subclass GO:0005515 -tag binding -undefined_only true -export obo > $@ mf_xp_pro-RA-obol.obo: obol qobol -ontology GO -xont PR -subclass GO:0004872 -tag receptor_activity -undefined_only true -export obo > $@ bp_xp_fao-obol.obo: obol qobol -debug qobol -ontology GO -r FAO -r goxp/biological_process_xp_fungal_anatomy -r goxp/biological_process_xp_uber_anatomy -tag bp -tag generic -tag anatomy -undefined_only true -export obo > $@ bp_xp_zfa-obol.obo: obol qobol -ontology GO -r zebrafish_anatomy -r goxp/biological_process_xp_zebrafish_anatomy -tag bp -tag generic -tag anatomy -undefined_only true -export obo > $@ bp_xp_xao-obol.obo: obol qobol -ontology GO -r xenopus_anatomy -r goxp/biological_process_xp_uber_anatomy -tag bp -tag generic -tag anatomy -undefined_only true -export obo > $@ bp_xp_wbbt-obol.obo: obol qobol -debug qobol -ontology GO -r worm_anatomy -subclass GO:0032502 -r goxp/biological_process_xp_worm_anatomy -r goxp/biological_process_xp_uber_anatomy -tag bp -tag generic -tag anatomy -undefined_only true -export obo > $@ bp_xp_chebi-obol.obo: obol qobol -ontology GO -xont CHEBI -tag bp -tag generic -tag chemical -undefined_only true -export obo > $@ bp_xp_allchebi-obol.obo: obol -i chebi_lite.obo qobol -ontology GO -xont CHEBI -tag bp -tag generic -tag chemical -undefined_only true -export obo > $@ bp_xp_cc-occurs_in-obol.obo: obol qobol -ontology GO -tag bp -tag cc -tag in -undefined_only true -export obo > $@ ## # we seed this with an alignment between BP and CL # also include chebi xps to avoid false +ves (eg spermine transport) # we DON'T include curated go_xp_cell for now, as the goal is to redo this differentiation-$(BP_XP_CL): $(BP_XP_CL_EDIT) $(GO) $(OBOL) -u obol_biological_process_xp_cell -u obol_biological_process_xp_cellular_component -r cell -parse_rule process -i $(BP_XP_RoP) -i $(BP_XP_CL_EDIT) -i $(BP_XP_CH_EDIT) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) "(subclassT(ID,'GO:0030154'))" >& $@.tmp && mv $@.tmp $@ # BP x CHEBI # we seed this with an alignment between BP and CHEBI # we exclude anything part of curated go-xp-chebi links $(BP_XP_CH): $(GO) $(OBOL) -u obol_biological_process_xp_chemical -r xchebi -parse_rule process -i $(BP_XP_R) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) "belongs(ID,biological_process)" >& $@.tmp && mv $@.tmp $@ #$(BP_XP_CH): bp-chebi-aln.tbl # $(OBOL) -u obol_biological_process_xp_chemical -r xchebi -parse_rule process -i $(BP_XP_RoP) -i $(BP_XP_RoF) -i $(BP_XP_Q) -i $(BP_XP_BP) -i $(BP_XP_CC) -i $(BP_XP_CH_EDIT) -i bp-chebi-aln.tbl "(substr(_,XID,ID,_,_,_,_),belongs(ID,biological_process))" >& $@.tmp && mv $@.tmp $@ transport-$(BP_XP_CH): $(GO) $(OBOL) -u obol_biological_process_xp_chemical -r xchebi -parse_rule process -i $(BP_XP_RoP) -i $(BP_XP_RoF) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) "(subclassT(ID,'GO:0006810'))" >& $@.tmp && mv $@.tmp $@ metabolic-$(BP_XP_CH): $(GO) $(OBOL) -u obol_biological_process_xp_chemical -r xchebi -parse_rule process -i $(BP_XP_R) -i $(BP_XP_RoF) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) "(subclassT(ID,'GO:0008152'))" >& $@.tmp && mv $@.tmp $@ fixed-pro.obo: pro.obo ./remove-protein.pl $< > $@ no-pro-go.obo: gene_ontology_write.obo ./remove-protein.pl $< > $@ # BP x PRO $(BP_XP_PRO): $(GO) $(OBOL) -i fixed-pro.obo -i no-pro-go.obo -parse_rule process $(INC_BP_Main) "(belongs(ID,biological_process))" >& $@.tmp && mv $@.tmp $@ force-$(BP_XP_PRO): $(GO) $(OBOL) -debug protein -u obol_biological_process_xp_protein_with_force -r protein -parse_rule process -i $(BP_XP_R) -i $(BP_XP_Q) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) -i $(BP_XP_PRO_EDIT) "(belongs(X,biological_process),differentium(X,_,P),id_idspace(P,'PRO'),debug(protein,'P:~w',[X]),subclassRT(ID,X))" >& $@.tmp && mv $@.tmp $@ # BP x MF - signaling (relies on PRO / BF x MF) $(BP_XP_SIG): $(GO) $(OBOL) -u obol_biological_process_xp_signaling -r protein -parse_rule process -i $(BP_XP_R) -i $(BP_XP_Q) -i $(BP_XP_BP_EDIT) -i $(BP_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) -i $(MF_XP_PRO_EDIT) -i $(BP_XP_PRO_EDIT) "(belongs(ID,biological_process),class(ID,N),sub_atom(N,_,_,0,'signaling pathway'))" >& $@.tmp && mv $@.tmp $@ # BP x anatomy - development EXPERIMENTAL # use the _with_force version to force materialization of anatomical continuant anonymous classes # at this stage this will mostly generate anon terms, as we are lacking CARO+ # todo: first rerun sc anatomy xps, exclude uberon. manually edit so that it's species centric $(BP_XP_Dev): $(GO) $(OBOL) -r uberon $(BP_ANAT_PARAMS) -u obol_biological_process_xp_anatomy_with_force -u obol_biological_process_xp_self -r caro -r cell -parse_rule process $(INC_BP_Main) "(belongs(ID,biological_process),parentT(ID,Root),class(Root,'developmental process'))" >& $@.tmp && mv $@.tmp $@ $(BP_XP_STIM): $(GO) stimulus.obo $(OBOL) -u obol_biological_process_xp_stimulus_force -parse_rule process $(INC_BP_Main) "(belongs(ID,biological_process),subclassT(ID,Root),class(Root,'response to stimulus'))" >& $@.tmp && mv $@.tmp $@ stimulus.obo: $(BP_XP_STIM) $(GO) blip-ddb -r go -i $< -u ontol_db io-convert -to obo -u ontol_manifest_abduced_links -include ontology//stimulus -midgoal manifest -o $@ # BP x anatomy - using ssAOs # examples: wing disc pattern formation; central nervous system neuron axonogenesis # we overpredict: treat related synonyms as exact (TODO: only for anatomies); this is because many AOs don't use synonym scopes yet # we also overstate defs, making them more specific than is the case, as we are limited by ssAOs # - this can result in unusual xps, like optic placode formation = formation of fly:primordium zf:optic # we also throw in PATO: eg e.g. regulation of blood pressure $(BP_XP_AN): bp-anat-aln.tbl $(GO) $(OBOL) -u ontol_manifest_exact_from_related_synonym -u obol_biological_process_xp_anatomy_with_force -u obol_biological_process_xp_self -u obol_biological_process_xp_quality -u obol_biological_process_xp_cell -r cell -r pato $(ANAT) $(TABLE_ANATOMY) -parse_rule process $(INC_BP_Main) -i $< "(class(Root,'developmental process'),belongs(ID,biological_process),(subclassT(ID,Root) ; substr(_,XID,ID,_,_,_,_),\+belongs(XID,biological_process)))" >& $@.tmp && mv $@.tmp $@ BP_ANAT_PARAMS= -u obol_biological_process_xp_anatomy -u obol_biological_process_xp_self -u obol_biological_process_xp_quality -u obol_biological_process_xp_cell -parse_rule process $(INC_BP_Main) -r cell -r pato -newonly # uberon $(BP_XP_ANU): $(GO) $(OBOL) -r uberon $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -u obol_biological_process_xp_quality -i $< $(INC_BP_Main) "belongs(ID,biological_process),\+genus(ID,_),subclassT(ID,'GO:0032502')" >& $@.tmp && mv $@.tmp $@ # $(OBOL) -u metadata_nlp -r uberon $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -u obol_biological_process_xp_quality -i $< $(INC_BP_Main) -index "metadata_db:entity_label/2" -goal "index_labels(false)" "belongs(ID,biological_process),\+genus(ID,_),entity_pair_nlp_subset_of(U,ID,1),id_idspace(U,'UBERON')" >& $@.tmp && mv $@.tmp $@ # $(OBOL) -r uberon $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -u obol_biological_process_xp_quality -i $< $(INC_BP_Main) "belongs(ID,biological_process)" >& $@.tmp && mv $@.tmp $@ under-$(PARENT)-$(BP_XP_ANU): $(GO) $(OBOL) -table_pred ontol_db:bf_parentRT/2 -r uberon -r cell $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -u obol_biological_process_xp_quality -i $< $(INC_BP_Main) "belongs(ID,biological_process),bf_parentRT(ID,'GO:$(PARENT)')" >& $@.tmp && mv $@.tmp $@ # uberon+pato : e.g. regulation of blood vessel diameter $(BP_XP_QANU): $(GO) $(OBOL) -r uberon $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -u obol_biological_process_xp_quality -r pato -i $< "belongs(ID,biological_process),subclassRT(ID,'GO:0065008')" >& $@.tmp && mv $@.tmp $@ development-$(BP_XP_ANU): $(GO) $(OBOL) -r uberon $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -u obol_biological_process_xp_quality -r pato -i $< "(belongs(ID,biological_process),subclassT(ID,'GO:0032502'))" >& $@.tmp && mv $@.tmp $@ $(BP_XP_ANM): bp-mouse_anat-aln.tbl $(GO) $(OBOL) -r mouse_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -i $< "(substr(_,XID,ID,_,_,_,_),belongs(ID,biological_process),belongs(XID,'adult_mouse_anatomy.gxd'),\+class(XID,cell),\+genus(ID,_))" >& $@.tmp && mv $@.tmp $@ #$(BP_XP_ANP): bp-plant_anat-aln.tbl $(GO) # $(OBOL) -r plant_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -i $< "(substr(_,XID,ID,_,_,_,_),belongs(ID,biological_process),belongs(XID,'plant_structure'),\+class(XID,cell),\+genus(ID,_))" >& $@.tmp && mv $@.tmp $@ $(BP_XP_ANP): $(GO) $(OBOL) -u ontol_manifest_exact_from_related_synonym -r plant_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "bf_parentRT(ID,'GO:0032502')" >& $@.tmp && mv $@.tmp $@ ## $(OBOL) -u ontol_manifest_exact_from_related_synonym -r plant_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "class(X,'Viridiplantae'),belongs(ID,biological_process),bf_parentRT(ID,X)" >& $@.tmp && mv $@.tmp $@ # fly anatomy # only BP terms unique to fly # use related synonyms? only for fly? $(BP_XP_ANF): $(GO) $(OBOL) -u ontol_manifest_exact_from_related_synonym -r fly_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "class(X,'Arthropoda'),belongs(ID,biological_process),bf_parentRT(ID,X)" >& $@.tmp && mv $@.tmp $@ $(BP_XP_ANFU): $(GO) $(OBOL) -u ontol_manifest_exact_from_related_synonym -r fungal_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "bf_parentRT(ID,'GO:0048856')" >& $@.tmp && mv $@.tmp $@ ## $(OBOL) -u ontol_manifest_exact_from_related_synonym -r fungal_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "class(X,'Fungi'),belongs(ID,biological_process),bf_parentRT(ID,X)" >& $@.tmp && mv $@.tmp $@ $(BP_XP_ANZ): $(GO) $(OBOL) -u ontol_manifest_exact_from_related_synonym -r zebrafish_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "class(X,'Teleosti'),belongs(ID,biological_process),bf_parentRT(ID,X)" >& $@.tmp && mv $@.tmp $@ # DEPRECATED: # fma alignment has lots of true negatives; also include everything in the developmental branch, or reg of BQ $(BP_XP_ANH): bp-fma_anat-aln.tbl $(GO) $(OBOL) -r fma_downcase $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) -i $< "(((substr(_,XID,ID,_,_,_,_),belongs(XID,'fma'),\+class(XID,cell)) ; (class(Root,'anatomical structure development'),parentT(ID,Root)) ; (class(Root,'regulation of biological quality'),parentT(ID,Root))),belongs(ID,biological_process),\+genus(ID,_))" >& $@.tmp && mv $@.tmp $@ $(BP_XP_ANDD): $(GO) $(OBOL) -u ontol_manifest_exact_from_related_synonym -r zebrafish_anatomy $(TABLE_ANATOMY) $(BP_ANAT_PARAMS) $(INC_TAX) "class(X,'Amoebozoa'),belongs(ID,biological_process),bf_parentRT(ID,X)" >& $@.tmp && mv $@.tmp $@ # BP x SO -- experimental # only use children of LSF $(BP_XP_SQ): bp-sequence-aln.tbl $(GO) $(OBOL) -u obol_biological_process_xp_sequence -r sequence -r xchebi -i $(BP_XP_CC_EDIT) -parse_rule process -i $(BP_XP_RoP) -i bp-sequence-aln.tbl "(substr(_,XID,ID,_,_,_,_),belongs(ID,biological_process),class(XRootID,'sequence_feature'),subclassT(XID,XRootID))" >& $@.tmp && mv $@.tmp $@ # generic # do NOT us related synonyms biological_process_xp_%_anatomy-obol.obo: $(GO) $(OBOL) -r $*_anatomy $(BP_ANAT_PARAMS) $(INC_BP_Main) -i $< -i ../xps/biological_process_xp_$*_anatomy.obo "parentT(ID,'GO:0048856')" >& $@.tmp && mv $@.tmp $@ # =================== # molecular function # =================== MF_ARGS = -u ontol_manifest_synonym_from_molecular_function -table_pred metadata_db:entity_synonym/2 -table_pred metadata_db:entity_synonym_scope/3 # MF x CHEBI $(MF_XP_CH): $(GO) $(OBOL) -i $(MF_XP_CH_EDIT) -i $(MF_XP_MF_EDIT) -i $(MF_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) -u obol_molecular_function_xp_chemical -r xchebi -parse_rule molecular_function "belongs(ID,molecular_function)" >& $@.tmp && mv $@.tmp $@ # MF x (CHEBI u PRO) $(MF_XP_CH_PRO): $(GO) $(OBOL) -i $(MF_XP_CH_EDIT) -i $(MF_XP_CH_PRO_EDIT) -i $(MF_XP_MF_EDIT) -i $(MF_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) -u obol_molecular_function_xp_chemical -r xchebi -r protein -parse_rule molecular_function "belongs(ID,molecular_function)" >& $@.tmp && mv $@.tmp $@ # deprec? $(MFCat_XP_CH): $(GO) $(OBOL) -i $(MF_XP_MF_EDIT) -i $(MF_XP_CC_EDIT) -i $(MF_XP_CH_EDIT) -u obol_molecular_function_xp_chemical -r xchebi -parse_rule def "subclassT(ID,'GO:0003824')" >& $@.tmp && mv $@.tmp $@ # this this is the best way... catalysis-chebi.txt: (blip-findall -debug chebi -r xchebi -r go -u query_go function_participants/4 -label > $@ ) >& $@.err # MF x Uberon: mostly structural constituents $(MF_XP_ANU): $(GO) $(OBOL) -i $(MF_XP_CC_EDIT) -i $(MF_XP_MF_EDIT) -u obol_molecular_function_xp_cellular_component -r uberon -parse_rule molecular_function "belongs(ID,molecular_function)" >& $@.tmp && mv $@.tmp $@ # MF x PRO $(MF_XP_PRO): $(GO) $(OBOL) -i $(MF_XP_CH_EDIT) -i $(MF_XP_PRO_EDIT) -i $(MF_XP_MF_EDIT) -i $(MF_XP_CC_EDIT) -u obol_molecular_function_xp_chemical -i fixed-pro.obo -i no-pro-go.obo -r xchebi -parse_rule molecular_function "belongs(ID,molecular_function)" >& $@.tmp && mv $@.tmp $@ binding-$(MF_XP_PRO): $(GO) $(OBOL) -i $(MF_XP_CH_EDIT) -i $(MF_XP_PRO_EDIT) -i $(MF_XP_MF_EDIT) -i $(MF_XP_CC_EDIT) -u obol_molecular_function_xp_binding -r protein -r xchebi -parse_rule molecular_function "belongs(ID,molecular_function),class(ID,N),sub_atom(N,_,_,0,binding)" >& $@.tmp && mv $@.tmp $@ # MF x GO # eg structural constituent of cell wall; lamelin-1 binding [in chemical grammar] $(MF_XP_GO): $(GO) $(OBOL) -i $(MF_XP_MF_EDIT) -i $(MF_XP_CC_EDIT) -i $(BP_XP_CH_EDIT) -u obol_molecular_function_xp_cellular_component -u obol_molecular_function_xp_chemical -parse_rule molecular_function "belongs(ID,molecular_function)" >& $@.tmp && mv $@.tmp $@ # MF regulator activity $(MF_XP_MF): $(GO).noactivity.obo $(OBOL_NOGO) -i $< -i $(MF_XP_MF_EDIT) $(MF_ARGS) -u obol_molecular_function_xp_self -parse_rule molecular_function "belongs(ID,molecular_function)" >& $@.tmp && mv $@.tmp $@ # =================== # cellular component # =================== # CC x CC # self/intra-cc $(CC_XP_CC): $(CC_XP_CC_EDIT) $(GO) $(OBOL_NOGO) -i $< -i $(CC_XP_CC_UNVETTED) -r obo/cellular_component -u ontol_manifest_synonym_from_molecular_function -u obol_cellular_component_xp -parse_rule cellular_component "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ plus-$(CC_XP_CC): $(CC_XP_CC_EDIT) $(GO) obol obol-suggest -i $< -i $(CC_XP_CL_EDIT) -i $(CC_XP_GO_EDIT) -r obo/cellular_component "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ # CC x GO # both self-xps and xps to function # redundant with CC x CC # examples: # Golgi apparatus membrane (CC x CC) # virion transport vesicle (CC x CC) # DNA helicase complex $(CC_XP_GO): $(CC_XP_CC_EDIT) $(CC_XP_CL_EDIT) $(GO) $(OBOL) -u ontol_manifest_synonym_from_molecular_function -u obol_cellular_component_xp -u obol_cellular_component_xp_function -u obol_cellular_component_xp_biological_process -i $(CC_XP_CC_EDIT) -i $(CC_XP_CL_EDIT) -i $(CC_XP_GO_EDIT) -parse_rule cellular_component "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ # CC x CL # examples: B cell receptor complex # exclude cc_xp_go $(CC_XP_CL): $(CC_XP_GO) $(CC_XP_CC_EDIT) $(GO) $(OBOL) -u obol_cellular_component_xp_cell -parse_rule cellular_component -r cell -i $(CC_XP_GO) -i $(CC_XP_CC_EDIT) -i $(CC_XP_CL_EDIT) -i $< "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ $(CC_XP_PRO): $(CC_XP_CC_EDIT) $(GO) $(OBOL) -u obol_cellular_component_xp_protein -parse_rule cellular_component -r protein -i $(CC_XP_CC_EDIT) -i $(CC_XP_CL_EDIT) -i $< "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ $(CC_XP_PRO_GREP): $(CC_XP_CC_EDIT) $(GO) obol -u onto_grep onto-grep -r protein -r go -query "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ $(CC_XP_GENE): $(CC_XP_CC_EDIT) $(GO) obol -u onto_grep onto-grep -r gene/10090 -r go -query "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ # e.g.: sexual spore wall $(CC_XP_FAO): $(CC_XP_GO_EDIT) $(CC_XP_CC_EDIT) $(CC_XP_CL_EDIT) $(GO) $(OBOL) -u obol_cellular_component_xp_cell -parse_rule cellular_component -r fungal_anatomy -i $(CC_XP_GO) -i $(CC_XP_CC_EDIT) -i $< "belongs(ID,cellular_component)" >& $@.tmp && mv $@.tmp $@ NIF-Subcellular-entity.obo: NIF-Subcellular.obo blip -i $< ontol-query -query "subclassRT(ID,'NIF_Subcellular:nlx_subcell_100315')" -to obo > $@ cc.obo: blip -r go ontol-query -query "subclassRT(ID,'GO:0005575')" -to obo > $@ cellular_component-align-NIF.obo: NIF-Subcellular-entity.obo blip -i NIF-Subcellular.obo -i cc.obo -u onto_grep onto-exact-align -exclude_xref -exclude_xref_strict -disp 'format(obo)' > $@.tmp && obo-simple-merge.pl $@.tmp > $@ # obol -debug obol -i $< -r obo/cellular_component ontol-align -stem -shownames > $@.tmp && mv $@.tmp $@ # obol -debug obol -u onto_grep -i $< -r obo/cellular_component onto-exact-align -ont birnlex_anatomy -ont2 cellular_component -exclude_xref_strict -exclude_xref -disp 'format(obo)' > $@.tmp && mv $@.tmp $@ # from NIF: cellular_component_links_cell.obo: blip-findall -r go -i nif_subcellular_xp.obo -i nif_subcellular.obo -i nif_cell.obo -r cell -u query_go "part_of_from_xref('GO','CL',A,B)" | cut -f4,5 | tbl2obolinks.pl --rel part_of - signaling-obol.obo: blip -r go ontol-query -u obol_signaling -n '%signaling pathway' -to obo | obo-grep.pl -r intersection_of - | obo-filter-tags.pl -t id -t def -t intersection_of > $@ # =================== # comparison # =================== go_xp_cell.diff: $(GO) obol -i ro_test.obo -r relationship -r cell -r go -i ../go_xp_cell.obo -i $(BP_XP_CL) ontol-diff-cdef > $@.tmp && mv $@.tmp $@ timing-bp-cell.txt: $(GO) blip -r implied/go -r implied/cell -i biological_process_xp_cell-obol.obo -u query_go_xp findall formation2/7 > $@.tmp && mv $@.tmp $@ timing-bp-%.txt: $(GO) blip -r implied/go -r implied/$*_anatomy -i biological_process_xp_$*_anatomy-obol.obo -u query_go_xp findall formation2/7 > $@.tmp && mv $@.tmp $@ go_xp_regulation_new.obo: $(REGLIVE) obol obol-generate-xps -idspace GO: -id_offset 9000000 -debug obol -u xp_reg_go -i $< > $@.tmp && mv $@.tmp $@ .PRECIOUS: go_xp_regulation_new.obo %.noactivity.obo: % ./fix-mf.pl $< > $@ %_wn1.obo: %.obo obol -i $< -r pato -r go -u obol_biological_process_xp_regulation obol-generate-names -write_synonyms > $@.tmp && mv $@.tmp $@ .PRECIOUS: %_wn1.obo %_wn.obo: %_wn1.obo obo2obo -o $@ $< $*.obo %_plusgo.obo: %_wn.obo $(REGLIVE) obo2obo -o -saveimpliedlinks $@ $< $(REGLIVE) # =================== # chebi-hacking # =================== CHEBI=$(HOME)/cvs/obo/ontology/chemical/chebi.obo xchebi.obo: $(CHEBI) (./go-transform-chebi.pl $< > $@.tmp) >& $@.log && mv $@.tmp $@ # remove xrefs as these don't parse correctly in CHEBI chebi_lite.obo: $(CHEBI) perl -ne 'print unless /^relationship: (\S+)/ && $$1 !~ /conjug/ && $$1 !~ /parent_hydride/' $< | grep -v ^xref > $@ # grep -v ^relationship: $< > $@ chebi_lite2.obo: $(CHEBI) grep -v ^relationship: $< > $@ chebi_ultralite.obo: $(CHEBI) grep -v ^relationship: $< | grep -v ^is_a > $@ chebi_minilite.obo: chebi_lite.obo blip-findall -i goche.obo "class(X)" -select "goche_id(X)" -write_prolog > goche_id.pro && blip -i $< -i goche_id.pro ontol-query -table_pred subclassT/2 -query "goche_id(X),subclassRT(X,ID)" -to obo > $@ chebi_with_formula.obo: blip -r chebi -u ontol_manifest_cdef_from_chebi_formula io-convert -to obo -o $@.tmp && mv $@.tmp $@ .PRECIOUS: chebi_with_formula.obo chebi_formula.obo: chebi_with_formula.obo obo-grep.pl -r 'id: FORMULA' $< > $@ chebi_isa_formula.obo: chebi_with_formula.obo obo-filter-tags.pl -t namespace -i id: $< | grep -v 'is_a: CHEBI' | obo-grep.pl -r 'id: CHEBI' - | obo-grep.pl -r 'is_a: FORMULA' - > $@ # inverse entailment chebi_inv-ontol_db.pro: # blip-findall -r goxp/biological_process_xp_chebi -r go -u query_chebi "inverse_entail(A,B)" -select "subclass(A,B)" -write_prolog > $@ blip-findall -table_pred user:inverse_entail/2 -r goxp/biological_process_xp_chebi -r implied/go -u query_chebi "inverse_entail_nr(A,B)" -select "subclass(A,B)" -write_prolog > $@ .PRECIOUS: chebi_inv-ontol_db.pro # chego is now goche #chego.obo: chebi_inv-ontol_db.pro # blip -i chebi_ultralite.obo -i $< ontol-query -query "subclass(ID,_);subclass(_,ID)" -to obo > $@ #.PRECIOUS: chego.obo # no MF for now... go_xp_goche-newlinks.txt: goche.obo blip-reasoner -explain genus_differentia -explain genus -r go -i goche.obo -i ../xps/biological_process_xp_chebi.obo > $@.tmp go_xp_goche-implied.obo: goche.obo obo2obo -o -saveimpliedlinks $@ ../../ontology/editors/gene_ontology_write.obo goche.obo ../xps/biological_process_xp_chebi.obo go_xp_goche-merged.obo: goche.obo obo2obo -o $@ ../../ontology/editors/gene_ontology_write.obo goche.obo ../xps/biological_process_xp_chebi.obo go_xp_goche-mireot.obo: go_xp_goche-merged.obo blip -i $< -table_pred "ontol_db:bf_parentRT/2" ontol-query -query "differentium(X,_,Y),(bf_parentRT(X,ID);bf_parentRT(Y,ID))" -to obo > $@ %-abduced.txt: %.obo blip-findall -r implied/$< -u query_chebi "inverse_entail_nr(A,B),\+subclass(A,B)" -select "subclass(A,B)" -label > $@ #chebi_inv-nr.obo: chebi_inv.obo # obo2obo -o -saveimpliedlinks -filterredundantlinks $@ $< cvs_update: cvs update ; cd ../../ontology/ && cvs update ; echo updated goche_all: goche-uniq-subclass.txt goche-uniq-subclass-filtered.txt goche-uniq-subclass-summary.txt goche-diff-labels.txt goche_all_cycle: cvs_update goche_all goche-diff.txt: goche.obo chebi_lite.obo blip-findall -i $< -i chebi_lite.obo -table_pred src_subclassT/3 -u ontol_diff "diff_subclass/8" > $@.tmp && sort -u $@.tmp > $@ goche-uniq-subclass.txt: goche.obo $(GO) chebi_lite.obo blip-findall -u ontol_diff -r implied/goche.obo -r implied/chebi_lite.obo uniq_subclass/3 -label | sort -u > $@ goche-uniq-subclass2.txt: goche.obo $(GO) chebi_lite.obo blip-findall -u ontol_diff -r implied/goche.obo -r implied/chebi_lite.obo uniq_subclass/5 -label | sort -u > $@ goche-uniq-subclass-filtered.txt: goche-uniq-subclass.txt blip-findall -ff tbl^goche-uniq-subclass.txt -ff tbl^goche-chebi-mixed-rel.txt "uniq_subclass(A,B,S),\+r(A,_,B)" -select "uniq_subclass(A,B,S)" > goche-uniq-subclass-filtered.txt goche-uniq-subclass-partitioned.txt: goche.obo $(GO) blip-findall -i goche_chooser.pro -u ontol_diff -r implied/goche.obo -r implied/chebi_lite.obo "uniq_subclass(X,Y,S),goche_set(Y,C)" -select "uniq_subclass(C,X,Y,S)" -label | sort -u > $@ goche-uniq-subclass-with-defs.txt: goche.obo $(GO) blip-findall -u ontol_diff -r implied/goche.obo -r implied/chebi_lite.obo uniq_subclass_with_defs/5 -label | sort -u > $@ goche-uniq-subclass-summary.txt: goche-uniq-subclass.txt cut -f4,5 $< | count-occ.pl > $@ #? goche-uniq-subclass-defs.txt: goche.obo $(GO) blip-findall -u ontol_diff -i goche.obo -i chebi_lite.obo "uniq_subclass(A,B,S),(X=A;X=B),G=def(X,D),fact_clausesource(G,S)" -select "def(X,D,S)" -label | sort -u > $@ goche-diff-labels.txt: goche.obo $(GO) blip-findall -u ontol_diff -i goche.obo -i chebi_lite.obo diff_label/5 > $@ goche-switched-labels.txt: goche.obo $(GO) blip-findall -u ontol_diff -i goche.obo -i chebi_lite.obo "fact_clausesource(entity_label(X1,N1),S1),fact_clausesource(entity_label(X1,N2),S2),N1\=N2,fact_clausesource(entity_label(X2,N2),S1),X1\=X2,fact_clausesource(entity_label(X2,N1),S2)" -select "switch(X1,N1,X2,N2,S1,S2)" > $@ goche-diff-defs.txt: goche.obo $(GO) blip-findall -u ontol_diff -i goche.obo -i chebi_lite.obo "diff_def(X,D1,D2,S1,S2),D1\='x.',D2\='x.'" -select "diff_def(X,D1,D2,S1,S2)" -label > $@ goche-orphan.txt: goche.obo blip-findall -i $< "class(X),\+subclass(X,_)" -select X -label > $@ goche-partition.txt: goche.obo blip-findall -i $< "class(X),subclassT(X,Y),\+subclass(Y,_)" -select "partition(X,Y)" -label > $@ goche-cycles.txt: goche.obo blip-findall -i $< "subclass_cycle(X,Y)" -select X-Y -label > $@ goche-chebi-cycles.txt: goche.obo blip-findall -i chebi_lite.obo -i $< "subclass_cycle(X,Y)" -select X-Y -label > $@ CHREL= -rel has_functional_parent -rel is_conjugate_base_of -rel is_conjugate_acid_of -rel subclass goche-n-%.png: blip ontol-subset $(CHREL) -i goche.obo -r chebi -u ontol_config_goche -n "$*" -to png > "$@" goche-id-%.png: blip ontol-subset -i goche.obo -r chebi -u ontol_config_goche -id "CHEBI:$*" -to png > $@ go-abduce-propagation-rel-from-chebi.txt: blip-findall -r go -r chebi -r goxp/biological_process_xp_chebi -u query_chebi "abduce_inference_over/6" -label -use_tabs > $@ go-abduce-non-propagation-rel-from-chebi.txt: blip-findall -r go -r chebi -r goxp/biological_process_xp_chebi -u query_chebi "neg_abduce_inference_over/6" -label -use_tabs > $@ goche-chebi-mixed-rel.txt: goche.obo blip-findall -u ontol_diff -i goche.obo -r chebi "src_subclass(goche,A,B),restriction(A,R,Z),src_subclassRT(chebi,Z,B),\+src_subclassT(chebi,A,B)" -select "r(A,R,B)" -label > $@.tmp && sort -u $@.tmp > $@ goche-chebi-mixed-neg-rel.txt: goche.obo blip-findall -u ontol_diff -i goche.obo -r chebi "class_in(A,goche),restriction(A,R,Z),src_subclassRT(chebi,Z,B),class_in(B,goche),\+src_subclass(goche,A,B),\+src_subclassT(chebi,A,B)" -select "r(A,R,B)" -label > $@.tmp && sort -u $@.tmp > $@ goche-defs.txt: goche.obo blip-findall -i goche.obo -r go -u query_chebi chebi_def_from_go/0 > $@ go_goche_split.tbl: goche.obo blip-findall -i $< -i go_chebi_genus_label.pro -u metadata_nlp -r go "genus_label(Tail),term_ends_with(E,S,SN,Tail,S1,S2),\+id_idspace(S,'GO')" -select "term_ends_with(E,S,SN,Tail,S1,S2)" -label > $@ .PRECIOUS: go_goche_split.tbl go_goche_split-summarize.txt: go_goche_split.tbl blip-findall -i $< "setof(E-F,term_ends_with(A,B,C,D,E,F),EFs)" -select "term_ends_with(A,B,C,D,EFs)" > $@ go_goche_split-non-exact.txt: go_goche_split.tbl blip-findall -u query_chebi -i $< "setof(E-F,term_ends_with_inexact(A,B,C,D,E,F),EFs)" -select "term_ends_with(A,B,C,D,EFs)" > $@ go_oxoacid_ref.txt: blip-findall -i go_chebi_genus_label.pro -table_pred ontol_db:subclassT/2 -u query_chebi -r go -r chebi "go_oxoacid_ref/4" -label > $@.tmp && sort -u $@.tmp > $@ goche_labels.obo: goche.obo grep -v ^is_a: $< > $@ go_justify_by_chebi.txt: goche_labels.obo blip-findall -i go_chebi_genus_label.pro -r implied/biological_process_xp_chebi-minimir.obo -i $< -r go -u query_chebi justify_subclass/5 -label > $@.tmp && sort -u $@.tmp > $@ go_no_justify_by_chebi.txt: goche_labels.obo blip-findall -i go_chebi_genus_label.pro -r implied/biological_process_xp_chebi-minimir.obo -i $< -r go -u query_chebi no_justify_subclass/4 -label > $@.tmp && sort -u $@.tmp > $@ .PRECIOUS: go_no_justify_by_chebi.txt go_no_justify_by_chebi-filtered.txt: go_no_justify_by_chebi.txt grep -v GOCHE $< | cut -f4,5 | grep CHEBI | sort -u > $@ go_new_by_chebi.txt: goche_labels.obo blip-findall -i go_chebi_genus_label.pro -r implied/biological_process_xp_chebi-minimir.obo -i $< -r go -u query_chebi new_subclass/5 -label > $@.tmp && sort -u $@.tmp > $@ not_in_xp.txt: blip-findall -i go_chebi_genus_label.pro -r implied/biological_process_xp_chebi-minimir.obo -r go -u query_chebi "genus_label(GN),atom_concat(' ',GN,Z),class(X,XN),atom_concat(CN,Z,XN),\+quick_def(X,_,_),\+genus(X,_)" -select "noxp(GN,CN,X,XN)" # =================== # plain links # =================== cellular_component_links_to_molecular_function.obo: cellular_component_xp_go-obol.obo obo-xp-to-link.pl --idspace GO -a -r has_function $< > $@.tmp && mv $@.tmp $@ # =================== # generic # =================== .PRECIOUS: %-obol.obo %-implied.obo: %-imports.obo %-obol.obo obo2obo -o -allowdangling -saveimpliedlinks $@ $< %-newlinks.txt: %.obo blip-reasoner -i $< -import_all -explain genus_differentia -explain genus > $@.tmp && filterreasoner.pl $@.tmp > $@ #%-newlinks.txt: %-imports.obo %-obol.obo # blip-reasoner -i $< -import_all -explain genus_differentia -explain genus > $@.tmp && mv $@.tmp $@ %-slurp.obo: %-imports.obo %-obol.obo obo2obo -o $@ $< %-stats: % grep -c ^id: $< %-non-go: % obo-grep.pl --neg -r 'id: GO' $< bp-chebi-aln.tbl: $(GO) obol ontol-align -stem -shownames -r biological_process -r xchebi biological_process chebi_ontology > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-chebi-aln.tbl cc-chebi-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/cellular_component -r xchebi cellular_component chebi_ontology > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-chebi-aln.tbl bp-protein-aln.tbl: $(GO) obol -debug blip -debug ontol ontol-align -stem -shownames -r go -r protein biological_process pro > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-protein-aln.tbl bp-cell-aln.tbl: $(GO) obol ontol-align -stem -shownames -r go -r cell biological_process cell > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-cell-aln.tbl bp-sequence-aln.tbl: $(GO) obol ontol-align -stem -shownames -r go -r sequence biological_process sequence > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-sequence-aln.tbl bp-cc-aln.tbl: $(GO) obol ontol-align -stem -shownames -r go biological_process cellular_component > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-cc-aln.tbl mf-cc-aln.tbl: $(GO) obol ontol-align -stem -shownames -r go molecular_function cellular_component > $@.tmp && mv $@.tmp $@ .PRECIOUS: mf-cc-aln.tbl mf-bp-aln.tbl: $(GO) obol ontol-align -stem -shownames -r go molecular_function biological_process > $@.tmp && mv $@.tmp $@ .PRECIOUS: mf-bp-aln.tbl bp-anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r go $(ANAT) > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-anat-aln.tbl bp-fly_anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r fly_anatomy biological_process fly_anatomy.ontology > $@.tmp && mv $@.tmp $@ bp-uberon-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r uberon biological_process uberon > $@.tmp && mv $@.tmp $@ bp-mouse_anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r mouse_anatomy biological_process adult_mouse_anatomy.gxd > $@.tmp && mv $@.tmp $@ bp-plant_anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r plant_anatomy biological_process plant_structure > $@.tmp && mv $@.tmp $@ bp-fma_anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r fma biological_process fma > $@.tmp && mv $@.tmp $@ bp-dicty_anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r dicty_anatomy biological_process Dictyostelium_discoideum_anatomy > $@.tmp && mv $@.tmp $@ bp-%_anat-aln.tbl: $(GO) obol ontol-align -stem -shownames -r obo/biological_process -r $*_anatomy biological_process $*_anatomy > $@.tmp && mv $@.tmp $@ .PRECIOUS: bp-%_anat-aln.tbl # =================== # reporting # =================== list-defined-ids: obo-grep.pl -r intersection_of: *.obo | grep ^id: | perl -ne 'print "$$1\n" if /id: (GO:\d+)/' | sort -u df-undefined.txt: blip-findall -debug foo -r go -r goxp/biological_process_xp_uber_anatomy -r goxp/biological_process_xp_cell "parentRT(ID,'GO:0032502'),debug(foo,'check: ~w',[ID]),\+genus(ID,_)" -select ID -label > $@