request 'targets' between 'drug' and 'gene'

[gloriachin]

I want to add predicates to the model.

'target': a subject (drug/small molecule) "target" an object (protein/gene) 'target by': a subject (protein/gene) is "targeted by" an object (drug/small molecule)

Example data to be models will be similar to the paper PMID: 27910877.

@sierra-moxon @cbizon

[gloriachin]

Here is an example graph I hope to add:

Subject.id: CHEMBL428647 Subject.name : Paclitaxel Subject.category: Drug

Object.id: NCBIgene:596 Object.category: Gene Object.symbol: BCL2
Object.name: BCL2 apoptosis regulator

Predicates: Targets @sierra-moxon

[ehinderer]

In this case, the "target" is not the direct physical interacting partner of the other member of the predicate. It may be pedantic, but we should probably specify what is allowable by a "targets" predicate. Paclitaxel binds the BCL2 protein if I'm not mistaken.

I bring this up in anticipation of future queries that may want to expand upon a question regarding what paclitaxel "targets." Maybe this would involve protein-protein interaction relations or metabolic relationships that a gene wouldn't connect up with.

[gloriachin]

"Efficacy target: ‘target’ refer to those proteins or other biomolecules (such as DNA, RNA, heparin and peptides) to which the drug directly binds, and which are responsible for the therapeutic efficacy of the drug. Biomolecules that the drug may also bind to, or be metabolized by, but which are not known to be responsible for its therapeutic effect, are not defined as targets. "

Reference: Santos, R., Ursu, O., Gaulton, A. et al. A comprehensive map of molecular drug targets. Nat Rev Drug Discov 16, 19–34 (2017). https://doi.org/10.1038/nrd.2016.230

[sierra-moxon]

Targets proposals for review Targets predicate - DM call summary of targets Targets publication highlights - Publication from Guangrong that established the definitions of “target” in the chemical->disease space and clarified the definition of “target” in the gene->disease space. Thoughts on ‘target’ in the context of biomedical sciences - Sandrine/MolePro’s use case for “targets” being too broadly applicable to be helpful and requesting “target” be a qualifier of some sort. Matt's landscape survey

More information can also be found in the predicate WG meeting minutes