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ialbert / genescape-central

Gene Ontology subgraph visualizations
MIT License
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Support other gene identifiers #7

Open j-andrews7 opened 2 months ago

j-andrews7 commented 2 months ago

Gene symbols are fickle beasts and subject to change. Support for converting other identifiers (Entrez, Ensembl) to their gene symbol on the fly would be ideal, as I know the GO annotations themselves prefer the symbol be used.

ialbert commented 2 months ago

Here the issue is that this tool works off gene ontology data. We build upon of what they publish and how they chose to map a symbol to a gene ontology. We use the symbols the Gene Ontology Consortium selected to annotate the data.

I also hate converting between gene ids, but it is not tools like this where we need to demand that gene id conversion happens automatically.

These conversions should happen much earlier via authoritative processes where we know there is ongoing oversight that the mappings are correct and most up to date.

By the time someone needs a tool like GeneScape they should have a table where the genes are mapped to GO symbols as well. The GeneScape symbols are in my opinion the closest to how biologists think about problems as these symbols have names that relate to functions.

ialbert commented 2 months ago

I could not make the additional symbols work, but I have added three more genomes by default and now the system includes, human, mouse, rat, drosophila and zebrafisth