Converting Cas/Mesh/Chid Numbers Into Pubchems Cid'S
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13.8 years ago
Christiank ▴ 70

I use JoChem which gives me CAS, Mesh and/or CHID numbers to identify Drugs. I want to link those with PubChems CID's.

Does such a database already exist somewhere? If it doesn't how do I go about creating the link?

pubchem CAS • 8.1k views
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2
Entering edit mode
13.8 years ago

You can look for the CAS ids in PubChem and their download files, but the data there can be pretty dirty (e.g. a mixture might have all the CAS ids listed). If you're lucky, then you can make the link via ChemSpider.

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12.3 years ago
Pablacious ▴ 620

You can use an Entrez query to retrieve all PubChem compound (or substance) entries for a particular MeSH identifier. In this case you need to use the MeSH identifier that Entrez/NCBI uses, not the ones used by the National Library of Medicine MeSH download, which are different. For instance, for this small set of MeSH identifiers (in a shell script):

for i in 68001697 68020228 68020313 68045424 68006727 68007287 68004364; do
    curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=mesh&id=$i&db=pccompound" > pchem_compound_with_mesh_$i.xml
    sleep 15
done;

(in a shell script, the $i in the URL shown would be replaced by the things that you are iterating in the for using i variable). You can see each mesh id accessing ncbi like this: http://www.ncbi.nlm.nih.gov/mesh/68001697

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