Question: Get Accession Numbers For Chemicals? (Database Crossreference Identifiers)
2
gravatar for Lo Sauer
7.3 years ago by
Lo Sauer160
Lo Sauer160 wrote:

Dear all, Chemspider lists an impressive array of ID's for other databases (without specifying which accession-Id belongs to which DB. -> rub it in CS :) )

e.g. Aspririn

Q: What projects are out there that provide, downloadable or otherwise(webservice), the resolution of chemical names into a comprehensive list of accession Id's. Ideally accession IDs for the major webservices out there. Pubchem does so to a limited degree (under the category 'Classification').

PS: My response from Chemspider, specifically inquiring ONLY the accession lists: "We don't make our database available as a download."

Thanks.


Update 05/05/'12

This service solved the issue - for the field of metabolomics: Chemical ID Resolver

ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 7.3 years ago by Lo Sauer160
2
gravatar for Chris Evelo
7.3 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

We have a metabolite database for [?]BridgeDB[?] that contains identifiers based on HMDB and Chebi. You can see what it does and does not link to in [?]WikiPathways[?] since we use it in there. We in fact do have a version with ChemSpider IDs for the same metabolites (so not all the other in ChemSpider), but I am not sure that is part of the released sets yet. If you like it you can install a local webserver instance of BridgeDB or use the Java code.

ADD COMMENTlink written 7.3 years ago by Chris Evelo9.9k

A pathway-wiki, great idea. PS: The file named 'metabolites' consists out of HMDB's metabolites+SMILES? Do you offer an SQL Dump?

ADD REPLYlink modified 6.8 years ago • written 7.3 years ago by Lo Sauer160
1
gravatar for Pablacious
7.3 years ago by
Pablacious610
Cambridge, UK
Pablacious610 wrote:

You can use the EBI's ChEBI (Chemical Entities of Biological Interest) Web Service access to do a text search in the fields name and/or synonyms. This will retrieve a list of IDs, for each one of them you can retrieve the complete entity (with various names, synonyms, cross references to other databases, chemical structure, etc). The initial query also has a score associated to the text search, so you could filter by that or choose the top n results.

Check:

http://www.ebi.ac.uk/chebi/webServices.do

you can even try the methods in the web page, before deciding if you want to use the SOAP web service.

You can also use the NCI Cactvs Chemical Resolver:

http://cactus.nci.nih.gov/chemical/structure

This is a plain HTTP request.

ADD COMMENTlink written 7.3 years ago by Pablacious610

thanks, but my intend is to have a local database for xref's. But this seems promising: ftp://ftp.ebi.ac.uk/pub/databases/chebi/generic_dumps/names.sql

ADD REPLYlink written 7.3 years ago by Lo Sauer160
1
gravatar for Anon
7.3 years ago by
Anon10
Anon10 wrote:

Chemical name and chemical structure associations are available on the PubChem FTP site.
You can also get the CID/SID associations on their FTP site.

ADD COMMENTlink written 7.3 years ago by Anon10

thanks, but could you point me to the pubchem xref-list if available, starting here: ftp://ftp.ncbi.nlm.nih.gov/pubchem/ ...

ADD REPLYlink written 7.3 years ago by Lo Sauer160
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