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SynBioHub / synbiohub-plugins

This is a repository that gives an overview of existing plugins and allows people to request new plugins.
BSD 3-Clause "New" or "Revised" License
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Uniprot Submit Plugin #1

Open JMante1 opened 4 years ago

JMante1 commented 4 years ago

What kind of plugin are you requesting? Submit

Is your plugin request related to a workflow problem? Please describe. Currently there are many proteins stored in https://www.uniprot.org/ however getting the protein and genetic information from uniprot to sbol for use with tools like sbolcanvas is very difficult

Describe the solution you'd like It would be very nice to be able to submit the uniprot id (e.g. P42212 for GFP https://www.uniprot.org/uniprot/P42212) and have the genomic DNA pulled as well as a protein object created in sbol.

Describe alternatives you've considered Currently it is possible to go to the page and pull the genbank for the protein and dna sequence and then link the two manually and add the genbank as a source.

Additional context The sequences associated with the protein are found in this section image

Note that one protein may have different sequence variants image

Additionally most/many proteins from uniprot link out to protein db. (e.g. gfp: https://www.rcsb.org/structure/5B61) which contains additional references and information.