Integration of text mining data (GW)

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Integration of text mining data (GW) #1716

Closed ReneRanzinger closed 1 month ago

ReneRanzinger commented 2 months ago

Integrate the text mining data produced by Robels pipeline into the GlyGen release. Frontend wise that should have little impact since it just more data. How do we deal with the case that your and Vijays pipeline produced:

the same results
slightly different results

This is also related to documenting the algorithm used (#1717) in the frontend.

rykahsay commented 1 month ago

@katewarner @ubhuiyan ... please add the following step as part of the downloads that should be done in every release (including now), which will be one of the inputs for the *_proteoform_glycosylation_sites_literature_mining.csv dataset files:

$ cp /data/shared/lmsite/generated/predicted/glycosylation_sites_lmsite.csv /data/shared/glygen/downloads/lit_min/current/

ubhuiyan commented 1 month ago

@rykahsay Appears the glycosylation_sites_lmsite.csv file is locked. Could you give me permissions?

[sbhuiyan28@glygen-vm-dev ~]$ ll /data/shared/lmsite/generated/predicted/
total 81
-rw-r--r--. 1 rykahsay glygen 164193 Sep 23 13:31 glycosylation_sites_lmsite.csv

ubhuiyan commented 1 month ago

I was able to copy it regardless. It's also been updated in the documentation.