Add more species

[oliverfanderson]

Suggestions:

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

[ctrlaltaf]

potentially import STRINGdb interactions that encompass a wide range of species

[oliverfanderson]

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]

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]

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]

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]

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]

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