Converting Cas/Mesh/Chid Numbers Into Pubchems Cid'S
2
1
Entering edit mode
14.6 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 • 8.5k views
ADD COMMENT
2
Entering edit mode
14.6 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.

ADD COMMENT
0
Entering edit mode
13.1 years ago
Pablacious ▴ 630

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

ADD COMMENT

Login before adding your answer.

Traffic: 2855 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6