OBO=        http://purl.obolibrary.org/obo

all: mf-merged.owl

#########################################
#
# Downloads
#
tsv: rhea-tsv.tar.gz
	tar -zxvf $<


rhea-tsv.tar.gz:
	wget ftp://ftp.ebi.ac.uk/pub/databases/rhea/tsv/rhea-tsv.tar.gz

# rhea 'basic' - just names subsets and xrefs, some isas
rhea.obo: tsv/rhea2xrefs.tsv
	./util/tsv2obo.pl $< > $@

rhea-biopax_lite.owl: rhea-biopax_lite.owl.gz
	gzip -dc $< > $@

rhea-biopax_lite.owl.gz:
	wget ftp://ftp.ebi.ac.uk/pub/databases/rhea/biopax/$@
.PRECIOUS: rhea-biopax_lite.owl.gz

#########################################
#
# Basic Reports
#

reports:  go-rhea-align-via-xref.rpt go-rhea-align-via-xref.rpt go-rhea-xref-cardinality-all.rpt go-rhea-xref-summary-2.rpt go-rhea-xref-summary.rpt

go-rhea-align-via-xref.rpt: rhea.obo
	blip-findall -r go  -consult util/check_go.pro -i $< xref_check/4 -label -no_pred -use_tabs > $@

go-rhea-xref-cardinality.rpt:  rhea.obo
	blip-findall -r go  -consult util/card_report.pro card/3 -no_pred -label -use_tabs > $@.tmp && cut -f1,3-8 $@.tmp | mysort -k2 > $@

go-rhea-xref-cardinality-all.rpt: rhea-pathway_db.pro  rhea.obo
	blip-findall -r go -i $<  -consult util/card_report.pro card/3 -no_pred -label -use_tabs > $@.tmp && cut -f1,3-8 $@.tmp | mysort -k2 > $@

go-rhea-xref-summary.rpt:  rhea.obo
	blip-findall -r go  -consult util/card_report.pro summary/4 -no_pred -label -use_tabs  > $@
go-rhea-xref-summary-2.rpt:  rhea.obo
	blip-findall -r go  -consult util/card_report.pro summary_level_2/4 -no_pred -label -use_tabs  > $@

rhea-chebi.tbl: 
	blip-findall  -i rhea-pathway_db.pro -r chebi  -consult util/xpgen.pro rhea_chebi/4 -label > $@

#########################################
#
# Reactions
#

# convert Rhea BioPAX to blipkit pathway model
# sometimes fails?
rhea-pathway_db.pro: rhea-biopax_lite.owl
	blip -i $< -f rdf -u biopax2_bridge_to_pathway io-convert -to pathway_db:pro > $@.tmp && ./util/fix-bp-uris.pl $@.tmp > $@

# ** rheax = RHEA, aXiomatized **

# translate pathway model to blipkit obo model
rheax-ontol_db.pro: 
	blip-findall -r chebi  -i rhea-pathway_db.pro  -consult util/xpgen.pro wfacts > $@

# logical definitions. E.g:
# [Term]
# id: RHEA:28425
# comment: RHEA:IUBMB=false
# intersection_of: GO:0003824 
# intersection_of: has_substance_bag CHEBIX:15377-2.0-58349-1.0-60954-1.0 ! water-2.0 + NADP(3-)-1.0 + 2-hydroxy-2-methylbutanenitrile-1.0
# intersection_of: has_substance_bag CHEBIX:15378-1.0-15379-1.0-57783-1.0-61136-1.0 ! hydron-1.0 + dioxygen-1.0 + NADPH(4-)-1.0 + (Z)-2-methylbutanal oxime-1.0
rheax.obo: rheax-ontol_db.pro
	blip -i $< io-convert -to obo -o $@

rheax.owl: rheax.obo
	owltools $< -o -f manchester $@

# chebi without relationships
chebi_lite.obo:
	owltools $(OBO)/chebi.owl --make-subset-by-properties // -o -f obo $@

# subset of chebi_lite required to axiomatize rheax
chebi_import.owl: rheax.owl chebi_lite.obo
	owltools $< chebi_lite.obo --add-imports-from-supports --extract-module -s $(OBO)/chebi.owl -c --extract-mingraph  --set-ontology-id $(OBO)/go/extensions/$@ -o file://`pwd`/$@

# MERGED
rhea-plus.owl: rhea.obo rheax.owl
	owltools --create-ontology $(OBO)/rhea.owl $< rheax.owl chebi_import.owl --merge-support-ontologies -o -f functional $@

# transformed version of MF ontology, with xrefs to RHEA turned into equivalence axioms
mf.obo:
	blip ontol-query -r go -query "belongs(ID,molecular_function)" -to obo > $@.tmp && perl -npe 's@xref: RHEA@equivalent_to: RHEA@' $@.tmp >$@
#mf.owl: mf.obo
#	owltools $< --remove-dangling -o mf.owl

mf-rhea-equiv.obo: mf.obo
	obo-grep.pl -r equivalent_to mf.obo | obo-filter-tags.pl -t equivalent_to -t id - | perl -npe 's@ontology: go@ontology: go/extensions/mf-rhea-equiv@' > $@
mf-rhea-equiv.owl: mf-rhea-equiv.obo
	owltools $< -o -f functional $@.tmp && grep -v ^Declaration $@.tmp | grep -v ^AnnotationAssertion > $@


rhea_import.owl: mf.obo rhea-plus.owl
	owltools $< rhea-plus.owl --add-imports-from-supports --extract-module -s $(OBO)/rhea.owl -c  --set-ontology-id $(OBO)/go/extensions/$@ -o file://`pwd`/$@

mf-plus.owl: mf.obo rhea_import.owl
	owltools $< rhea_import.owl --merge-support-ontologies -o -f functional $@

#mf-inf.obo: mf-plus.owl
#	owltools $< --assert-inferred-subclass-axioms --allowEquivalencies --markIsInferred -o -f obo --no-check $@

# todo - fix owltools - merged sets should not have 1 member - causes problems for functional writer
mf-merged.owl: mf-plus.owl
	owltools $< --merge-equivalent-classes -f RHEA -t GO --remove-dangling -o  $@

mf-inf.obo: mf-merged.owl
	owltools $< --assert-inferred-subclass-axioms --allowEquivalencies --markIsInferred -o -f obo --no-check $@


#########################################
#
# Derived Reports
#
mf-connections.rpt: rheax.obo
	blip-findall -consult util/connections.pro -i $< -r go mfconnected/3 -label -no_pred > $@

mf-connections.obo: mf-connections.rpt
	cut -f1,2 $< | tbl2obolinks.pl -k --rel connected_to $< > $@