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Add Apollo link-outs to transcript and protein features #351

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mpoelchau opened this issue Sep 20, 2022 · 1 comment
Open

Add Apollo link-outs to transcript and protein features #351

mpoelchau opened this issue Sep 20, 2022 · 1 comment
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@mpoelchau
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We'd like to add link-outs, similar to the existing Apollo link-outs to the genome reference, to transcript and protein features. The idea would be to build Apollo URLs with the subject sequence ID in the location component of the URL.

Related but a separate issues: We'd also have to modify our genomics-workspace ingest procedures to use fasta files with just the transcript and protein accession in the defline; process our existing GW content in this manner as well; and ensure that all transcript and protein features are indexed in Apollo. (In the meantime it might be nice if we could control which organisms/files had linkouts).

@mpoelchau
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@trentwyman here is a blast results page where the correct sseqid is listed - let's use the example XP_049805619.1: https://i5k.nal.usda.gov/webapp/blast/task/c89c13c507d64a91a85f5dec4d18e4ea

Screenshot with the example sseqid highlighted:

Screen Shot 2022-10-03 at 11 39 26 AM

Here is the Apollo URL that would need to be generated from the example sseqid XP_049805619.1 and organism Schistocerca_nitens: https://apollo.nal.usda.gov/apollo/Schistocerca_nitens/jbrowse/index.html?loc=XP_049805619.1

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