diff --git a/server/Makefile b/server/Makefile index 5100de1..4e7d8bd 100644 --- a/server/Makefile +++ b/server/Makefile @@ -4,36 +4,37 @@ CATALOG = catalog-v001.xml DATA = ../data MIRROR= mirror -MM = $(DATA)/Mus_musculus +#MM = $(DATA)/Mus_musculus ##MM_G2P = $(MM)/Mm-gene-to-phenotype-BF.txt -MM_G2P = $(MM)/Mm_gene_phenotype.txt -MM_G2L = $(MM)/Mm_gene_labels.txt +#MM_G2P = $(MM)/Mm_gene_phenotype.txt +#MM_G2L = $(MM)/Mm_gene_labels.txt -DR = $(DATA)/Danio_rerio +#DR = $(DATA)/Danio_rerio ##DR_G2P = $(DR)/Dr-gene-to-phenotype-BF.txt -DR_G2P = $(DR)/Dr_gene_phenotype.txt -DR_G2L = $(DR)/Dr_gene_labels.txt +#DR_G2P = $(DR)/Dr_gene_phenotype.txt +#DR_G2L = $(DR)/Dr_gene_labels.txt # TODO: genes -DM = $(DATA)/Drosophila_melanogaster -DM_G2P = $(DM)/Dm_gene_phenotype.txt -DM_G2L = $(DM)/Dm_gene_labels.txt +#DM = $(DATA)/Drosophila_melanogaster +#DM_G2P = $(DM)/Dm_gene_phenotype.txt +#DM_G2L = $(DM)/Dm_gene_labels.txt -CE = $(DATA)/Caenorhabditis_elegans -CE_G2P = $(CE)/Ce_gene_phenotype.txt -CE_G2L = $(CE)/Ce_gene_labels.txt +#CE = $(DATA)/Caenorhabditis_elegans +#CE_G2P = $(CE)/Ce_gene_phenotype.txt +#CE_G2L = $(CE)/Ce_gene_labels.txt HS = $(DATA)/Homo_sapiens HS_D2P = $(HS)/Hs_disease_phenotype.txt HS_D2L = $(HS)/Hs_disease_labels.txt -CASE = $(DATA)/Cases -CASE_C2P = $(CASE)/UDP_case_phenotype.txt -CASE_C2L = $(CASE)/UDP_case_labels.txt +#CASE = $(DATA)/Cases +#CASE_C2P = $(CASE)/UDP_case_phenotype.txt +#CASE_C2L = $(CASE)/UDP_case_labels.txt #ROOT = $(UPHENO)/metazoa.owl #ROOT = $(UPHENO)/vertebrate.owl -ROOT = $(UPHENO)/monarch.owl +#ROOT = $(UPHENO)/monarch.owl +ROOT = http://purl.obolibrary.org/obo/hp.owl USECAT = --catalog-xml $(ONT)/catalog-v001.xml @@ -52,7 +53,7 @@ $(CATALOG): # TODO: trigger rebuild all.owl: additional-associations.txt additional-labels.txt $(DR_G2P) $(MM_G2P) $(HS_D2P) $(DM_D2P) $(CE_G2P) - $(OWLTOOLS) $(ROOT) --merge-imports-closure --load-instances additional-associations.txt --load-labels additional-labels.txt --load-instances $(MM_G2P) --load-labels $(MM_G2L) --load-instances $(DR_G2P) --load-instances $(CASE_C2P) --load-labels $(CASE_C2L) --load-labels $(DR_G2L) --load-instances $(HS_D2P) --load-labels $(HS_D2L) --load-instances $(DM_G2P) --load-labels $(DM_G2L) --load-instances $(CE_G2P) --load-labels $(CE_G2L) --merge-support-ontologies --remove-axioms -t ObjectPropertyDomain --remove-axioms -t ObjectPropertyRange --remove-axioms -t DisjointClasses -o $@ + $(OWLTOOLS) $(ROOT) --merge-imports-closure --load-instances additional-associations.txt --load-labels additional-labels.txt --load-instances $(HS_D2P) --load-labels $(HS_D2L) --merge-support-ontologies --remove-axioms -t ObjectPropertyDomain --remove-axioms -t ObjectPropertyRange --remove-axioms -t DisjointClasses -o $@ owlsim.cache: all.owl