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geneontology / noctua-form-legacy

Simple annoton editor workbench for Noctua.
BSD 3-Clause "New" or "Revised" License
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Searching ontology synonyms #53

Closed vanaukenk closed 6 years ago

vanaukenk commented 6 years ago

It would be helpful if the GO term autocomplete allowed for searching on synonyms.

The display would include both the main term name and the synonym, perhaps something like this if the curator searched for 'receptor binding':

GO:0005102 signaling receptor binding (syn: receptor binding)

This is a more general issue and may relate to this ticket here: https://github.com/geneontology/noctua/issues/257

tmushayahama commented 6 years ago

@cmungall @kltm @thomaspd any comment on this?

kltm commented 6 years ago

This is supported by the backend. The issue is likely with the hard-coded queries in the code that you inherited.

tmushayahama commented 6 years ago

@kltm the graph doesn't do it either

kltm commented 6 years ago

It is in AmiGO and AFAICT it works in Noctua too, at least in some cases. "Cajal body" (http://amigo.geneontology.org/amigo/term/GO:0015030) can be found in the "Add individual" autocomplete with the synonym "Gems". Similarly in the "Add annoton" cellular_component autocomplete.

thomaspd commented 6 years ago

From the curators, was the request for synonyms for ontology terms, or was it for gene name synonyms? I think it might be for gene names/symbols.

vanaukenk commented 6 years ago

The original request was for ontology term synonyms.
In Seth's case of searching on 'Gems' the 'Cajal body' synonym is found in the form, the graph, and AmiGO. In the use case that led to this ticket, though, we were searching with 'receptor binding' which didn't get us to 'signaling receptor binding' but maybe this is because the list of terms that contains the 'receptor binding' string in name, synonyms or definition is long while the list of terms containing 'Gems' in the name, synonyms or definition is very short.