Search substance by external ID

[fbaensch-beilstein]

Hi folks,

due to our new feature in Beilstein Journals we would like to link from each submitted substance to the substance/compound entry in PubChem. Is it therefore possible to search for a substance via an external ID?

[nbehrnd]

Conceptual I can imagine to let pubchempy probe if a compound is indexed, e.g. by its SMILES string

Python 3.13.1 (main, Jan  3 2025, 10:26:34) [GCC 14.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pubchempy import get_compounds, Compound
>>> comps = get_compounds("c1ccncc1", "smiles")
>>> print(comps[0].cid)
1049

and then use this cid to concatenate this to yield an url of

https://pubchem.ncbi.nlm.nih.gov/compound/1049

to indicate the record of pyridine. Though at present (cf. #96) probably working only in Linux, you might include a PubChem key to increase the overall rate of application permitted by the database. Would this partially match your intent?

wheel corresponding to the pending pr (works only within Linux, e.g. Debian)

pubchempy-1.0.5a0-py3-none-any.whl.zip

[fbaensch-beilstein]

@nbehrnd Thanks for that nice work around and the idea with the PubChem key.

I have solved it a little differently:
The response of the request with the url https://www.ncbi.nlm.nih.gov/pcsubstance/?term=[our_id] is searched for the <title> tag that contains the SID. With the SID, if available, the CID can be queried via pcp.Substance.from_sid(sid).standardised_cid.

In this way, I can use the SID and CID to create links to the substance and, if present, to the compound.