[Biopython] Parsing XML returned by efetch from the Journals database

[Michiel de Hoon]

Dear users,

The parser in Bio.Entrez can parse any XML returned by the Entrez E-utilities as long as the corresponding DTD is available (which are included with each release of Biopython). One corner case is efetch results from the Journals database. Officially, efetch from the Journals database does not generate output in the XML format, but only plain text or HTML. However, when requesting XML explicitly from Entrez, in practice it does return an XML-like output. Our parser in Bio.Entrez is able to parse this XML, but it requires several hacks in the parser code.

To make the parser more stable for other XML documents, I'd like to remove these hacks. Currently is anybody using Bio.Entrez to parse XML returned by efetch from the Journals database?

--Michiel.