Unfound Genes Disrupt Transcripts

[emersonlebleu]

There appears to be a bug still if someone puts an unknown gene in the gene list.

I thought it was transcripts causing the issue but that may not be the case because if a transcript is not found there is logic for that.

[tonydisera]

Emerson, the geneinfo service now supports a lookup option. For example, if you want to determine if a gene name is valid, you can use this endpoint:

https://backend.iobio.io/geneinfo/lookup/MTHFR?searchAlias=last&exactMatch=true

response:
{"genes":[{"gene_name":"MTHFR"}]}

And there are variations on this API:

1. Multiple gene lookup
   https://backend.iobio.io/geneinfo/api/lookupGenes?genes=MTHFR,BRCA1&searchAlias=last&exactMatch=true
2. Partial name or case-insensitive matching
   https://backend.iobio.io/geneinfo/lookup/MTh?searchAlias=last&exactMatch=false
3. Only include matches from Gencode and RefSeq (exclude HGVS gene aliases)
   https://backend.iobio.io/geneinfo/lookup/MTHFR?searchAlias=none&exactMatch=true

The geneinfo service also provides a more detailed lookup that shows how many transcripts exists for refseq and gencode for the difference genome builds:

https://backend.iobio.io/geneinfo/lookupEntries/MTHFR

response:
"genes":[{"gene_name":"MTHFR","GRCh37":{"gencode":9,"refseq":2},"GRCh38":{"gencode":7,"refseq":12} .....

[tonydisera]

Also, I have a client-side javascript class called GeneModel used by multiple Vue.js components in gene.iobio. I'm in the process of simplifying this class, so I will make that a priority. We should try not to duplicate client-side or servier-side code/logic for gene name searching because it is quite involved when you take into account that a gene symbol may only have transcripts in refseq or gencode, or in genome build GRCh37, but not GRCh38. And then when you consider gene synonyms, it adds another layer of considerations/logic in client-side code.

[emersonlebleu]

I think that lookup will be great for my use case. I can do that with the inputted gene names to get my reliable set before I do any other processing with them.