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geneontology
AmiGO is the public interface for the Gene Ontology.
It would be really useful if this were possible. it would provide an immediate way for the community to look up the GO data assigned to their own papers. Especially...
This past week I was using AmiGO to download annotation files. I see why this is happening, but I find it very annoying that the default download does NOT include...
Currently, entries in db-xrefs.yaml and presented in the amigo /xrefs page as if they were "top-level" entries, which can cause confusion for some users (re: discussion w/ @pgaudet ). We...
Currently, as an apparent result of #620 (specifically https://github.com/geneontology/amigo/commit/65be1caa3fb2d8c21df81b1337753343e20a28b6 and possibly part of https://github.com/geneontology/amigo/commit/7b4ff9ed294ed3ebaf43d1c9fe37035d77b89f9e from #634). The fix to this is one of the following: 1. do a mini-refactor so...
Hello, I'm trying to use term matrix, but I get an error with the "pair wise entity search" this is the URL it's trying to access https://amigo.geneontology.org/amigo/search/bioentity?q=*:*&fq=taxon_subset_closure_label:%22Eukaryota%22&fq=taxon_subset_closure_label:%22Vertebrata%20%3Cvertebrates%3E%22&fq=taxon_subset_closure_label:%22Homo%20sapiens%22&fq=type:%22protein%22&fq=isa_partof_closure:%22GO:0000940%22&fq=isa_partof_closure:%22GO:0048870%22 
`npx gulp load-ontology-purge-safe` results in a shell syntax error (`/bin/sh: 1: Syntax error: Unterminated quoted string`), due to a stray leftover single-quote at this line: https://github.com/geneontology/amigo/blob/6e83d501812b34ad1e4bca99be5fbf725fbee893/gulpfile.js#L427
The reference page http://amigo.geneontology.org/amigo/reference/PMID:30352852 displays the article title as '[object Object]' rather than 'Evolutionarily conserved Tbx5- Wnt2/2b pathway orchestrates cardiopulmonary development'.
This was a suggestion from Chris. Presumably the UI would be identical to what was added to GP pages, the only difference being which API is called to populate the...
From https://github.com/geneontology/amigo/issues/559#issuecomment-1421718871 From the managers' call, people were interested in taking a look at an AmiGO instance with a limited load. Essentially: * keep * ncbitaxon * eco * drop...
Playing around on all the live instances, it seems like it cannot even find the file, even if it's fed a hard-coded path. Very weird, as the file is clearly...
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AmiGO is the public interface for the Gene Ontology.