[Biopython] Entrez.efetch problem when querying pccompound database

Fri Oct 29 11:26:30 UTC 2010

Hi,

I'm using BioPython to query the NCBI pccompound database.
I'm trying to retrieve the molecular weight of a compound given its
InChIKey.
Gettting the ID of the compound with esearch works fine. For instance:

Entrez.esearch(db="pccompound",
term='"BSYNRYMUTXBXSQ-UHFFFAOYSA-N"[InChIKey]')

However, when I try to retrieve the record's content with efetch from the ID
returned by esearch, like this:

Entrez.efetch(db="pcassay", id="2244")

I get the following response:

++++++++++

<html>
<body>
<br/><h2>Error occurred: Report 'ASN1' not found in 'pccompound'
presentation</h2><br/><ul title="some params from request:">
<li>db=pccompound</li>
<li>query_key=</li>
<li>report=</li>
<li>dispstart=</li>
<li>dispmax=</li>
<li>mode=html</li>
<li>WebEnv=</li>
</ul>
<br/><b>pmfetch need params:</b><br/><br/>
<li>(id=NNNNNN[,NNNN,etc]) or (query_key=NNN, where NNN - number in the
history, 0 - clipboard content for current database)</li>
<li>db=db_name (mandatory)</li>
<li>report=[docsum, brief, abstract, citation, medline, asn.1, mlasn1,
uilist, sgml, gen] (Optional; default is asn.1)</li>
<li>mode=[html, file, text, asn.1, xml] (Optional; default is html)</li>
<li>dispstart - first element to display, from 0 to count - 1, (Optional;
default is 0)</li>
<li>dispmax - number of items to display (Optional; default is all elements,
from dispstart)</li>
<br/>See <a href="
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
">help</a>.</body>
</html>

++++++++++++++++++++++++++++++++++++++++++++

I've tried to use other return types and return modes, like for instance

Entrez.efetch(db="pcassay", id="2244", rettype="abstract", retmode="text")

but I have not succeeded in retrieveing this compound's record's content.
Many thanks for any help on how to retrieve information on a compound from
pccompound.

Best wishes

Saikari