search

monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
56 stars 26 forks source link

Add Rhea: annotated biochemical reaction database ingest into dipper #533

Open putmantime opened 6 years ago

putmantime commented 6 years ago

Source Name: Rhea http://www.rhea-db.org/

Source Data Description: About
Rhea comes from a joint ISB and EMBL-EBI effort and annotates biochemical reactions including enzymes, kinetic data and participants (linking to ChEBI).

Scope of Ingest: ~10,500 reactions including links to various other entities (ChEBI, EC, UniProt, etc.) detailed here

Source Data Location: biopax2 dump: ftp://ftp.ebi.ac.uk/pub/databases/rhea/biopax/

Source Documentation:
Licensing (CC BY 4) About Updates in Rhea - an expert curated resource of biochemical reactions.

Additional Notes: With this data in monarch, we can make the enzyme to reaction connection through European Commision (EC) numbers that are already imported as xrefs from Kegg.
This allows querying for substrates and products of enzymatic reactions; especially useful in modeling microbiome interactions between host and microbes.

I have already done some parsing of the Rhea biopax2 dump using paxtools here

cmungall commented 6 years ago

do you plan to use GO here too? We have rhea xrefs and will be improving these by axiomatizing rhea

putmantime commented 6 years ago

@cmungall yes that's great, I didn't realize GO had Rhea xrefs

cmungall commented 5 years ago

yes, and @bgood is generating OWL with all of the reaction participants in it