Use new support for prefixes in OBO format - WIP.

Makefile

@@ -88,7 +88,7 @@ include Makefile-gafs
 # The default owltools expansion makes this an OBO PURLs
 # We then "reverse" this with some hacky regexes...
 neo.owl: neo.obo
-	owltools $< -o $@.tmp && ./bin/fix-obo-uris.pl $@.tmp > $@.tmp2 && mv $@.tmp2 $@
+	robot convert -i $< -o $@.tmp -f owl && mv $@.tmp $@
 
 Makefile-gafs: datasets.json
 	./build-neo-makefile.py -i $< > $@.tmp && mv $@.tmp $@
@@ -110,7 +110,5 @@ rnacentral.gpi: rnacentral.gpi.gz
 target/neo-rnac.obo: rnacentral.gpi.gz
 	gzip -dc $< | ./rnacgpi2obo.pl > $@.tmp && mv $@.tmp $@
 
-target/xneo-%.owl: target/neo-%.obo
-	owltools $< -o $@.tmp && mv $@.tmp $@
-target/neo-%.owl: target/xneo-%.owl
-	./bin/fix-obo-uris.pl $< >  $@.tmp && mv $@.tmp $@
+target/neo-%.owl: target/neo-%.obo
+	robot convert -i $< -o $@.tmp -f owl && mv $@.tmp $@

gaf2obo.pl

@@ -5,6 +5,8 @@
 my $spn = 'generic';
 my $ontid;
 my $isoform_only = 0;
+open my $fh, '<', 'prefixes.obo.txt' or die "error opening prefixes.obo.txt: $!";
+my $prefixes = do { local $/; <$fh> };
 
 while (@ARGV) {
     my $opt = shift @ARGV;
@@ -24,6 +26,8 @@
 
 my $is_rat = $spn eq 'Rnor';
 
+print "format-version: 1.2\n";
+print $prefixes;
 print "ontology: go/noctua/$ontid\n";
 print "\n";
 

gpi2obo.pl

@@ -6,6 +6,8 @@
 my $fill_p = 0; # fill unknown species name with taxon id
 my $ontid;
 my $isoform_only = 0;
+open my $fh, '<', 'prefixes.obo.txt' or die "error opening prefixes.obo.txt: $!";
+my $prefixes = do { local $/; <$fh> };
 
 while (@ARGV) {
     my $opt = shift @ARGV;
@@ -26,6 +28,8 @@
     $ontid = $spn;
 }
 
+print "format-version: 1.2\n";
+print $prefixes;
 print "ontology: go/noctua/$ontid\n";
 print "\n";
 

prefixes.obo.txt

@@ -0,0 +1,15 @@
+idspace: AGI_LocusCode http://arabidopsis.org/servlets/TairObject?type=locus&name=
+idspace: ComplexPortal https://www.ebi.ac.uk/complexportal/complex/
+idspace: dictyBase http://identifiers.org/dictybase.gene/
+idspace: FB http://identifiers.org/flybase/
+idspace: GR_protein http://identifiers.org/uniprot/
+idspace: MGI http://identifiers.org/mgi/
+idspace: PomBase http://identifiers.org/pombase/
+idspace: RGD http://identifiers.org/rgd/
+idspace: RNAcentral http://rnacentral.org/rna/
+idspace: SGD http://identifiers.org/sgd/
+idspace: TAIR_locus http://identifiers.org/tair.locus/
+idspace: UniProtKB http://identifiers.org/uniprot/
+idspace: WB http://identifiers.org/wormbase/
+idspace: Xenbase http://identifiers.org/xenbase/
+idspace: ZFIN http://identifiers.org/zfin/

rnacgpi2obo.pl

@@ -18,8 +18,12 @@
 );
 
 my %tm = map {($_=>1)} @taxa;
-
 
+open my $fh, '<', 'prefixes.obo.txt' or die "error opening prefixes.obo.txt: $!";
+my $prefixes = do { local $/; <$fh> };
+
+print "format-version: 1.2\n";
+print $prefixes;
 print "ontology: go/noctua/rnac\n";
 print "\n";