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owlcollab / owltools

OWLTools
BSD 3-Clause "New" or "Revised" License
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Add or confirm support for GAF 2.2 to owltools #291

Open kltm opened 4 years ago

kltm commented 4 years ago

I believe that currently owltools would not support the upcoming GAF 2.2 spec particularly well. While the only material difference for the new spec is that many more qualifiers are allowed, eyeballing a few sections in owltools, it seems that often what is there for the qualifiers is hard-coded in.

For example, I've found possibly problematic sections in:

./OWLTools-Annotation/src/main/java/owltools/gaf/godb/GoMySQLDatabaseDumper.java:520:                               this.getTermInternalId("contributes_to"),
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/GpadGpiObjectsBuilder.java:304:         relation = "contributes_to";
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java:146:  contributesTo("contributes_to", "(contributes[_ ]to)"),
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java:371:  sb.append("contributes_to");
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/BuilderTools.java:404:  qualifiers.add("contributes_to");
./OWLTools-Annotation/src/main/java/owltools/gaf/parser/GafObjectsBuilder.java:257:         relation = "contributes_to";
./OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:391:    comb_aqual = comb_aqual + "contributes_to";
./OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:392:    annotation_doc.addField("qualifier", "contributes_to");
./Golr-Client/src/main/java/org/bbop/golr/java/RetrieveGolrAnnotations.java:97:else if ("contributes_to".equalsIgnoreCase(qualifier)) {

(obviously not exhaustive)

For our purposes, owltools can assume that the incoming files are "good" 2.2/2.1--we just want to make sure that the additional qualifiers can pass through where hard-coded lists now exist.