Based on MetaNetX. Information about metabolites and reactions is provided by MNXref namespace.
An online API service endpoint can be found at https://api.dd-decaf.eu/id-mapper/query.
Example on how to find a match for the chemical with BIGG id nh3 in BioPath database:
In [1]: import requests
In [2]: query = {"ids": ["atp"], "db_from": "bigg", "db_to": "kegg", "type": "Metabolite"}
In [3]: requests.post("http://localhost:8000/query", json=query).json()
Out[3]: {"ids": {"atp": ["C00002", "D08646"]}}
The graph consists of large amount of connected components. A connected component is considered being one object: a metabolite or a reaction. Search is returning all the elements in the component with db_to database name.
Download and load the chemical references into the graph database (may take several hours):
curl -O https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_xref.tsv
docker-compose run --rm web python src/load_chem_xref.py
Start the application:
docker-compose up
To compile a new requirements file and then re-build the service with the new requirements, run:
make pip-compile build
id-mapper is licensed under the Apache License Version 2.0 (see LICENSE in source directory).