Question: Converting Cas/Mesh/Chid Numbers Into Pubchems Cid'S
gravatar for Christiank
9.0 years ago by
Christiank70 wrote:

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?

ADD COMMENTlink written 9.0 years ago by Christiank70
gravatar for Michael Kuhn
9.0 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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 COMMENTlink written 9.0 years ago by Michael Kuhn5.0k
gravatar for Pablacious
7.5 years ago by
Cambridge, UK
Pablacious610 wrote:

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 "$i&db=pccompound" > pchem_compound_with_mesh_$i.xml
    sleep 15

(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 accesing ncbi like this:

ADD COMMENTlink modified 7 months ago by RamRS21k • written 7.5 years ago by Pablacious610
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