search

geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
29 stars 17 forks source link

In Annotation search, Ontology (aspect) filter only has one letter for aspect #279

Open elserj opened 9 years ago

elserj commented 9 years ago

It would be better if it had the whole text for the aspect, it would be much clearer if the full text was there, ie. Biological Process rather than P.

Mostly an issue for us downstream with the additional aspects we host. Hard to know which letter corresponds to which aspect.

kltm commented 9 years ago

amigo and solr don't really care what's in there--it's all just strings. This is coming from one of the columns of the GAFs, as reproduced with the getAspect() function in owltools.

I'm not sure what the consequences would be in changing that, but I imagine minor to none.

kltm commented 9 years ago

Tagging @cmungall and @hdietze in case there is some use I'm not thinking of here.

cmungall commented 9 years ago

Not sure if PAINT uses it, but otherwise I think it would be better to expand this.

The wider context for Justin's request is I suspect other amigo installations will want a wider range of ontologies here. We should check the loader behavior - does it just pass through the obo namespace is it's not in the hardcoded GO mapping?

Ultimately people will want to use the relationship type rather than aspect here, it's more meaningful. http://www.geneontology.org/specifications/gpad/gpad-1.html#default-annotation-relations

On 10 Nov 2015, at 17:31, kltm wrote:

Tagging @cmungall and @hdietze in case there is some use I'm not thinking of here.

Reply to this email directly or view it on GitHub: https://github.com/geneontology/amigo/issues/279#issuecomment-155625784

kltm commented 9 years ago

Talked with @elserj , will probably just add additional ontology information to the schema and the loader. See ont-config.yaml.

kltm commented 9 years ago

The fix will entail adding a new field (or fields) to the schema, in addition to a new load line to the owltools loader (GafDocumentLoader ?).