Wikidata:Property proposal/Inhibitor (Biochemistry)
inhibitor of edit
Originally proposed at Wikidata:Property proposal/Natural science
| Description | protein for which this chemical compound acts as an inhibitor |
|---|---|
| Data type | Item |
| Domain | biology, chemistry |
| Allowed values | Wikidata items of instance of (P31)/subclass of (P279): chemical compound (Q11173) or protein (Q8054) |
| Example | vemurafenib (Q423111) → B-Raf proto-oncogene, serine/threonine kinase (Q21109218) |
| Source | Guide to Pharmacology, ChEMBL, BindingDB, PDB |
| Planned use | Several thousand chemical compound to protein relations should be imported |
- Motivation
We have been importing proteins, chemical compounds and the relations between those and have modeled the relation by using physically interacts with (P129) and qualifiers to indicate the type of relation (e.g. Activator, Inhibitor). This approach is not very convenient. It makes adding data by users more difficult, as well as querying the data with SPARQL and it also makes it impossible to properly map these relations to external resources/ontologies. Therefore, we talked to the folks from ChEMBL and they kindly provided us with their list of chemical compound - protein mechanistic relations. We are currently also getting these relations established in the Relation Ontology which allows for interoperability and direct integration of these relations Wikidata with the OBO world. This is a big advantage, as data contributions to Wikidata can easily disseminate into the OBO world, making community curation in WD even more valuable. In total, there are 29 relations, I will now just propose the 10 most important as properties. Sebotic (talk) 19:05, 6 February 2017 (UTC)
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- Discussion
- Given the way we currently name properties I would prefer "Biochemical Inhabitor" over "Inhibitor (Biochemistry)". Otherwise
Support ChristianKl (talk) 11:58, 8 February 2017 (UTC) - I welcome this proposal, so I certainly Support this proposal. However, I am wondering if we could rename it into "inhibits" (similar to encodes/encoded by) to have the directionality of the relationship explicit. --Andrawaag (talk) 19:39, 8 February 2017 (UTC)
- Support ArthurPSmith (talk) 19:07, 16 February 2017 (UTC)
- Support -Emitraka (talk) 20:02, 16 February 2017 (UTC)
- Support Gstupp (talk) 18:30, 7 March 2017 (UTC)
2019-10-14
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Dear all, for a project I'm (DeSl) currently working on, we would like to use the properties that came out of this discussion. The 10 selected relationship are now retrievable since they are linked to each other with the related property (P1659) claim. I want to add the subclass of (P279) + mechanism of action (Q3271540) claim as well (since I think it will make these properties and any additions easier to find for future modeling purposes, and to query which relationships WD is covering), however I got a issue when I added it to inhibitor of (P3776). Question 1: Is there any other way to connect these properties together ("instance of" "Wikidata property related to chemistry" is not detailed enough I believe). Question 2: if we're missing relationships for our project, should I propose them here (or somewhere else?). Question 3: what about all the relationships which are based on the old model (physically interacts with (P129) as predicate); should these be changed to fit with the properties from this proposal? Otherwise querying the data is still not so easy (especially if we are using two types of models). Hoping to hear your thoughts! DeSl (talk) 13:13, 14 October 2019 (UTC)