User:ProteinBoxBot/Gene-drug links

Objective

This bot function should add and update Wikidata items for Gene <> drug links.

Introduction

This bot is part of a family of bots to capture and maintain Genes, Diseases and Drugs in Wikidata. Originally started with the [[1]] where Genes and Proteins were added to Wikidata, the project gradually evolved in adding Diseases, Drugs and the relationships between the three.

Properties

In order to characterize the binding of a drug to its target, the property physically interacts with (P129) should be used. The property fits well, as it describes the interaction of 2 organic molecules, either polymer-polymer (nucleic acids, proteins, sugars) or polymer-small molecule interactions. 'Interacts with' should be on Wikidata protein items and also on the respective drug (small molecule items/peptides/antibodies). To describe the immediate effect of this interaction, a qualifier should be used. The most appropriate qualifier is has use (P366) on protein items. For the Wikidata drug items, the qualifier P794 (P794) should be used together with physically interacts with (P129).

Allowed values for the has use (P366) and P794 (P794) qualifiers:

• agonist (Q389934)
• antagonist (Q410943)
• ligand (Q899107)
• enzyme inhibitor (Q427492)
• allosteric modulator (Q2649417)

Data sources

For this effort, we currently retrieve data mostly from IUPHAR. In the future, we also plan on adding assay data from PubChem.

Additional data sources to be considered are listed at http://thinklab.com/discussion/incorporating-drugcentral-data-in-our-network/186

Output

The bot will add new gene<>drug links in its source databases to Wikidata. It will also modify existing Wikidata gene and drug items if new information becomes available in the mentioned data sources.

Reporting queries

link