Add B. Subtilis data - Githubissues

Reed-CompBio / protein-weaver

A web interface for ontology-based protein network visualization.

https://proteinweaver.reedcompbio.org/

GNU General Public License v3.0

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Add B. Subtilis data #39

Closed annaritz closed 8 months ago

annaritz commented 8 months ago

Add PPI and regulatory interaction data.

annaritz commented 8 months ago

Here's one source: SubtiWiki has an exports page.

From their paper: "Currently, we have expanded the data to >5950 and >2660 experimentally validated regulatory and protein–protein interactions, respectively"

annaritz commented 8 months ago

Here's a list of GO terms for B. subtilis: https://bsubcyc.org/BSUB/class-tree?object=Gene-Ontology-Terms. From BSubCyc.

annaritz commented 8 months ago

What we just went through:

We looked up all the B. subtilis GO annotations in AmiGO.
We downloaded that file, there were full names & UniProt IDs.
If uniprot or bsubcyc has a Uniprot-to-BSUB mapping or a common-name to identifier mapping, we should be OK.

oliverfanderson commented 8 months ago

Our GO annotations file seems to only have the entry for GO qualifier for about 50 of the entries, the rest are blank. I will move forward with this for now but either we may lack qualifiers for some of the B sub entries or we need to find an additional data source.

oliverfanderson commented 8 months ago

We have the ability to add a symbol and common name search for the B. Subtilis data since we have two multiple naming conventions. E.g. Leucine--tRNA ligase & LeuS.