Wikidata:Property proposal/biological target

biological target

Originally proposed at Wikidata:Property proposal/Natural science

   Not done

Description	the target of an antibody, inhibitor or receptor blocker
Data type	String
Domain	gene therapy (Q213901), antibody (Q79460), microorganism (Q39833), cluster of differentiation (Q1103544), gene (Q7187)
Allowed values	medication (Q12140), protein (Q8054), signaling receptor (Q208467)
Example 1	Enbrel (Q29005794) → tumor necrosis factor (Q21173843)
Example 2	pembrolizumab (Q13896859) → programmed cell death 1 (Q21208025)
Example 3	erlotinib (Q418369) → epidermal growth factor receptor (Q424401)
Example 4	entacapone (Q416444) → catechol-O-methyltransferase (Q94291140)
Example 5	moclobemide (Q421934) → monoamine oxidase (Q410867)
Example 6	lonafarnib (Q3258910) → protein farnesyltransferase (Q410994)
Source	https://en.wikipedia.org/wiki/Biological_target
Planned use	filling in the biological targets of a lot of drugs and other biologically active substances
See also	enzyme inhibitor (Q427492)

Motivation

As of now, there's no generic way to add the biological target of an antibody or an enzyme inhibitor or other substance in an adequate way. For enzyme inhibitors, the 'has role'/'of' statement is used sometimes, e.g. lonafarnib (Q3258910)subject has role (P2868)enzyme inhibitor (Q427492)of (P642)protein farnesyltransferase (Q410994) is used, but this isn't really great. For one, this doesn't quite work for antibodies and works even less for gene therapies. There ought to be a single property that collects all biological targets: gene targets (for silencers, suppressors and gene therapies), receptor targets (for receptor blockers), enzyme targets (for enzyme inhibitors), protein targets (for monoclonals) and extraneous targets, e.g. obiltoxaximab for anthrax. Ari T. Benchaim ^(talk) 16:02, 2 July 2021 (UTC)

Discussion

This is wrong. There is physically interacts with (P129), inhibitor of (P3776), agonist of (P3772), inverse agonist of (P9275) and others. Therefore  Oppose. --SCIdude (talk) 09:28, 8 July 2021 (UTC)

BTW, your usage of monoamine oxidase (Q410867) and other enzyme classes in your example would be wrong as well, because no small molecule would be able to act on a whole class of enzymes. But you are not the only one making this error. --SCIdude (talk) 09:58, 8 July 2021 (UTC)

I understand. How would that cover something like partial agonists, which are both agonists and inhibitors? What about selective response modulators, which are agonists in some tissues and inhibitors in others? And, of course, the gene therapy aspect still stands: valoctocogene roxaparvovec has a clear biological target (the F8 protein) but is neither an inhibitor, nor an agonist, nor does it actually physically interact with the existing F8 protein in any meani]]'ngful sense. So does the issue of CAR-T drugs: in no commonly used sense of the word is a CAR-T therapy against something an inhibitor. Same goes for some antisense therapies. Consider volanesorsen: it is not, in the classical sense, an inhibitor or an agonist. However, the biological target (apo-C3) is clear. It's not that it physically interacts with (P129) apolipoprotein C3 (Q4068038), but that it interferes with its synthesis. Which would technically mean it interferes with mRNA, which is true enough but not particularly useful. Ari T. Benchaim ^(talk) 23:46, 14 July 2021 (UTC)

So we are talking now about a much smaller subset of applications. For special purposes there is always the possibility to create a class item and make the substance an instance or subclass of it. Also, the last cases you mention, intentionally would inhibit a process, i.e. expression of some protein. You will find that the GO hierarchy provides a remarkably fine-grained ontology of processes that could be used as value for an inhibits statement. Because, the same way that giving an mRNA as target is not enlightening, the same way it is for the translated protein. On the other hand, what do we really know which RNA entities are transcribed, apart from the target mRNA? Would it not be most correct to give the actual binding partner? --SCIdude (talk) 04:48, 15 July 2021 (UTC)

From a very strictly biomechanistic point of view, you're entirely right, of course. On the other hand, at least in the therapeutics context, there's a relatively good and unambiguous meaning of what a drug's biological target is. It would be useful to be able to see, say, all drugs that target TNF-alpha, or identify targets that are currently drugged by less than n substances. From a regulatory perspective, this would be a really useful property to have, even if it is not as precise as GO. Ari T. Benchaim ^(talk) 13:48, 23 July 2021 (UTC)

•  Not done, no consensus of proposed property at this time based on the above discussion. Regards, ZI Jony ^(Talk) 06:06, 19 August 2021 (UTC)