This is a Wikidata bot that will take information from Reactome and create/update pages in Wikidata.
##Code
The bot is written in Python (requires v 3) and makes use of the WikidataIntegrator developed by the Su Lab.
It is based on the wikipathways\_wikidata\_bot used for Wikidata entry written for Wikipathways.
python ReactomeBot.py wikidata_username wikidata_password (inputfilename)
The code requires an comma separated value (.csv) file where each line refers to a Wikidata entry. The entries expected are:
Species_code,Reactome_Id,Name,Description,[publication1;publication2;..],goterm,None
where
- Species_code is the three letter abbreviation of the species used by Reactome e.g. HSA
- Reactome_Id is the Reactome Stable Indentifier for the pathway
- Name the Reactome Display Name
- Description a sentence based on Name stating that this is an instance of this pathway in the given species
- [publication1;..] a semi-colon separated list of the pmid URL of each referenced publication
- goterm teh relevant term as GO:nnnn
- None - to indicate the end of the entry
- Once we have a Reactome ID property in Wikidata this needs to be added.
- Add support for identifying parent and child pathways that could be added to WSD as 'has part' and 'part of' properties.
- Add support for adding reactome 'Reactions' that are not full pathways in the database.