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ropensci / webchem

Chemical Information from the Web
https://docs.ropensci.org/webchem
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Any way to search by Mass? #382

Open mr-september opened 2 years ago

mr-september commented 2 years ago

For example, like this for PubChem: http://www.cheminfo.org/Chemistry/Database/PubChem/Search_by_exact_mass_in_PubChem/index.html

stitam commented 2 years ago

Thanks @mr-september for opening this issue. I think this functionality is not yet implemented in webchem, but PubChem does have a solution that might be relevant called PUG VIEW Annotations: https://pubchemdocs.ncbi.nlm.nih.gov/pug-view#_Toc495044630.

For molecular weight, the url would look like this: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading/JSON?heading=Molecular%20Weight

While the results are not filtered to a required range, you can extract the values and filter yourself. Since the format is JSON, extracting the data should be relatively simple. Does this help your problem?

@Aariq, my understanding is that with annotation, we could query any section on a PubChem page (similarly to pc_sect()) and then get the values in that section for all (?) PubChem entries. This mechanism is different from most other webchem functions where we query a compound or a list of compounds but the output looks quite useful. Do you think it would be worth implementing annotations as a new feature?

Aariq commented 2 years ago

I'm not sure... The cheminfo link above seems very helpful, but I'm not sure recreating that is 100% in scope for webchem. Definitely something to consider for the future though.

mr-september commented 2 years ago

Thanks for the replies.

@stitam would that PUG_REST api essentially return all entries with known Molecular Weight? Is that how a post-hoc filtering can work?

I found another database that was promising, but doesn't seem to have public-facing APIs... yet... HMDB, last known effort in setting up an API was in 2016. I've contacted HMDB's maintainers, hoping they just haven't publicly documented it yet.

stitam commented 2 years ago

Another alternative could be ChemSpider. With this API you can filter by mass:

https://developer.rsc.org/docs/compounds-v1-trial/1/types/FilterByIntrinsicPropertyRequestMass

webchem includes a number of ChemSpider functions, but it does not implement this API because it is not 100% in scope for webchem, as @Aariq mentioned.