Annotate Reactome using offline database files

[iromeo]

Current impl of annotate_reactome.py requires access reactome.org website.
Reactome IDs -> Pathways titles annotator could use cached databases downloaded from rectome.org: /mnt/stripe/bio/genomes/ReactomePathways.txt

[iromeo]

Also think of other available annotations and how we can use them.

[iromeo]

Gene to Reactome mapping:
“The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. “

Pathways: ReactomePathways.txt
Reactions: Ensembl2ReactomeReactions.txt, UniProt2ReactomeReactions.txt, miRBase2ReactomeReactions.txt
Associations with other annotations:

• Ensembl: Ensembl2Reactome.txt/ Ensembl2Reactome_All_Levels.txt (the lowest level pathway diagram or subset of the pathway / all level pathway diagrams), Ensembl2ReactomeReactions.txt (reaction events)
• NCBI: NCBI2Reactome.txt/ NCBI2Reactome_All_Levels.txt
• PMIDS: ReactionPMIDS.txt
• OMIM: Reactome2OMIM.txt
• UniProt: UniProt2Reactome.txt / UniProt2Reactome_All_Levels.txt, UniProt2ReactomeReactions.txt
• MiRBase: miRBase2Reactome.txt/miRBase2Reactome_All_Levels.txt, miRBase2ReactomeReactions.txt
• misc, see all list at https://reactome.org/download-data

Pathways 2 Gene mapping: ReactomePathways.gmt
For some reason some pathways missed in ReactomPathays.txt, e.g. R-HSA-157052

[iromeo]

Open Question: Should we consider Reactions or Pathways

(Reactions are not included in Pathways and visa versa)

• Seems we can get genes involved in Reactions only using Ensembl/NCBI/UniProt-2ReactomeReactions.txt. There aren't file like ReactomePathways.gmt.
• *2ReactomeReactions.txt can be used in GSE analysis, although most likely it is covered by Enricher, or similar services.

[iromeo]

Also I think Gene mapping could be done using Ensembl2*.txt file, not manually

[olegs]

@iromeo Please recheck and close if necessary.