[BioPython] Medline records

Thomas Elliott telliott at hsc.wvu.edu
Fri Dec 8 18:58:40 UTC 2006


Hi,

I started playing with Biopython again.  Glad to see it is still  
active.   I love Python.

Some issues came up in parsing Medline records according to the  
tutorial.

It wasn't obvious which variables exist to be queried on a record.   
The tutorial example gives title, authors, and source only.

I tried looking at the code.  There are terms in NLMMedlineXML.py  
that look like they should work, but which raise AttributeError (e.g.  
journal and date_created).

I finally looked in the keys to __dict__ for a  record.  I found  
'year' there, but record.year seems to be always empty, or rather it  
is a blank string.

• record.title_abbreviation is actually the abbreviated journal name.
• record.volume_issue gives only the volume, not the issue.
• record.journal_title_code is always a blank string.

Not sure what the right way is to do this.  I guess it would be  
helpful to know which file of the source I should be looking at for  
variable names.

Tom Elliott



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