Add more species - Githubissues

Reed-CompBio / protein-weaver

A web interface for ontology-based protein network visualization.

https://proteinweaver.reedcompbio.org/

GNU General Public License v3.0

2 stars 5 forks source link

Add more species #87

Open oliverfanderson opened 8 months ago

oliverfanderson commented 8 months ago

Suggestions:

[x] C. elegans
[ ] E. coli
[x] S. cerevisiae
[ ] Plant species: http://zzdlab.com/plappisite/index.php

ctrlaltaf commented 5 months ago

potentially import STRINGdb interactions that encompass a wide range of species

oliverfanderson commented 3 months ago

Arabidopsis thaliana (txid3702):

PPI data: http://zzdlab.com/plappisite/index.php
Reg data: https://agris-knowledgebase.org/downloads.html
PPI data: https://string-db.org/cgi/download?sessionId=bNGgCrkvD3Qk&species_text=Arabidopsis+thaliana
Will likely need to namespace map from Araport to access UniProt IDs for protein search: https://www.uniprot.org/id-mapping
https://www.arabidopsis.org/ does not allow to search using URL (that I can find)

oliverfanderson commented 3 months ago

Caenorhabditis elegans (txid6239):

PPI data: https://downloads.wormbase.org/species/c_elegans/annotation/interactions/ (also has genetic interactions)
String: https://string-db.org/cgi/download?sessionId=bcCxo57mYE8U&species_text=Caenorhabditis+elegans
Reg data: https://tflink.net/download/
Gene association data: https://downloads.wormbase.org/species/c_elegans/annotation/gene_association/
https://wormbase.org/species/c_elegans/gene/[wormbaseID] is a good URL for dynamic searches

oliverfanderson commented 3 months ago

Escherichia coli (txid 83333):

PPI data maybe only from STRING: https://string-db.org/cgi/download?sessionId=bcCxo57mYE8U&species_text=Escherichia+coli+K12
Reg data: https://regulondb.ccg.unam.mx/datasets
- Note: may also want set of Sigma Factors
Gene association: https://www.ebi.ac.uk/QuickGO/annotations?taxonId=83333&taxonUsage=descendants&geneProductSubset=Swiss-Prot&geneProductType=protein

oliverfanderson commented 3 months ago

Saccharomyces cerevisiae (txid 559292):

PPI data: https://downloads.thebiogrid.org/File/BioGRID/Latest-Release/BIOGRID-ORGANISM-LATEST.tab3.zip
- BioGRID has datasets for yeast but is strain specific to txid 559292
STRING: https://string-db.org/cgi/download?sessionId=btRmh6bhQhyl&species_text=Saccharomyces+cerevisiae
- Data not specific to strain (more general txid 4932)
Reg data: https://tflink.net/download/
- When I search the gene IDs it directs me to txid 559292. I believe that means it is the most studied strain and that we can likely assume our STRING data is for the same. We also may decide to not include the STRING data for this species if BioGRID has enough data.
GO data: redirects txid 4932 to txid 559292 https://www.ebi.ac.uk/QuickGO/annotations?taxonId=4932&taxonUsage=descendants&geneProductSubset=Swiss-Prot&geneProductType=protein

oliverfanderson commented 3 months ago

TFLink does not appear to encode information about the type of regulatory interaction (i.e., no suppression/activation info). To address this in styling, we will likely need a specific edge tip or color.

ctrlaltaf commented 3 months ago

Saccharomyces cerevisiae data added.

PPI data is from (biogrid) [https://downloads.thebiogrid.org/File/BioGRID/Latest-Release/BIOGRID-ORGANISM-LATEST.tab3.zip]
gene ontology annotations are from QuickGo [https://www.ebi.ac.uk/QuickGO/annotations?taxonId=4932&taxonUsage=descendants&geneProductSubset=Swiss-Prot&geneProductType=protein]()
regulatory data are from [https://tflink.net/download/]()
Physical Relationships = 167,876
Go annotations = 151,185
Regulatory relationships = 237,715