Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 7
Description
GOAL: To get the STRING DB
https://string-db.org/cgi/input?sessionId=bODA2Ie6lzxH&input_page_show_search=on
To play nice with our tomato data. According to Kelsey, this worked at one point with SOly IDs. But recently, with a version update, she has not been able to get STRING to work.
We will test various data inputs to see what can it will accept. If all fail, we ping them and ask what is up!!!
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
Gramene is integrated into interpro.
Gramene contains SolyIds!!
So we can use Uniprot to go from SolyID to UniprotID, which is acceptable in string.
But how do we do this easily?
I am exploring still.
| Sprint | Spring 6 [ 215 ] | Spring 7 [ 216 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
I have generated 3hr and 8hr STRING images and popped them into the google slides.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
SolyIDs no longer work.
Solgenomics.net is currently borken!!! So we can't use any resource from there for now (I emailed Cornell and asked what is up with being down)
There is an API and how to retrieve from it here:
https://string-db.org/help/api/
It will accept our amino acid sequences. So we could send queries this way.
Another possibility is to feed our solyIds into DAVID and get uniprot IDs maybe that way?