Question: Converting Cas/Mesh/Chid Numbers Into Pubchems Cid'S
1
gravatar for Christiank
9.0 years ago by
Christiank70
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?

• 4.3k views
ADD COMMENTlink written 9.0 years ago by Christiank70
2
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
0
gravatar for Pablacious
7.5 years ago by
Pablacious610
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 "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 accesing ncbi like this: http://www.ncbi.nlm.nih.gov/mesh/68001697

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