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geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
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Improve amigo xrefs page to better clarify the nature of the synonyms #697

Open kltm opened 10 months ago

kltm commented 10 months ago

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 would like to fix this.

For example, maybe instead of 

[LocusID](https://amigo.geneontology.org/xrefs#LocusID)
NCBI Gene

Site
    http://www.ncbi.nlm.nih.gov/ 
Object
    gene 
Example ID
    NCBI_Gene:4771 
URL syntax
    https://www.ncbi.nlm.nih.gov/gene/[example_id] 
URL example
    https://www.ncbi.nlm.nih.gov/gene/4771

We could have:

NCBIGene (with synonym [LocusID](https://amigo.geneontology.org/xrefs#LocusID))
NCBI Gene

Site
    http://www.ncbi.nlm.nih.gov/ 
Object
    gene 
Example ID
    NCBI_Gene:4771 
URL syntax
    https://www.ncbi.nlm.nih.gov/gene/[example_id] 
URL example
    https://www.ncbi.nlm.nih.gov/gene/4771
kltm commented 10 months ago

Noting that I think this might be due to AmiGO still using xref_abbs somehow? The "best" thing would likely be to unsure that we are using the YAML, then iterate for the template and nest (and link) the synonyms there.