🧬 Wikidata Orthologs Bot 🤖

This repository uses hatch to easily handle scripts and virtual environments. Checkout the pyproject.toml file for more details on the scripts available.

You can also just install dependencies with pip install . and run the python script in src

Add orthologs from OMA

Extension of SuLab OrthologBot.py to include OMA orthologs and references to the OMA browser (e.g. https://omabrowser.org/oma/vps/P04637/).

Define the Wikidata bot username and password in a .env file at the root of the repository:

WDUSER=BOT_USERNAME
WDPASS=BOT_PASSWORD

Run mapping script without writing to Wikidata, will generate a CSV file with all orthologs:

hatch run oma

Note

Takes about 34h to run

Run the mapping script with writing to Wikidata enabled:

hatch run oma --write

Warning

It currently does not check if the OMA browser reference already exists in Wikidata, so it might create duplicates references if ran multiple times with --write enabled.

TODO: add logic that checks if the OMA browser reference has already been added

SPARQL query to check for OMA references in https://query.wikidata.org:

SELECT (COUNT(?ortho) as ?count) WHERE {
  ?ortho pr:P248 wd:Q7104801 .
}

See also

We use WikidataIntegrator to interact with WikiData.

https://github.com/BgeeDB/Wikidata_BgeeDB-bot