Biopython Class Instance - Output From Entrez.Read: I Don'T Know How To Manipulate The Output

Question

[Wheaton Little]

I am trying to download some xml from Pubmed - no problems there, Biopython is great. The problem is that I do not really know how to manipulate the output. I want to put most of the parsed xml into a sql database, but I'm not familiar with the output. For some things I can call the parsed xml like a dictionary, but for others it doesn't seem that straight forward.

from Bio import Entrez
Entrez.email="[e-mail]"
import sqlite3 as lite
handle=Entrez.efetch(db='pubmed',id='22737229', retmode='xml')
record = Entrez.read(handle)

If I want to find the title I can do this:

title=record[0]['MedlineCitation']['Article']['ArticleTitle']

But the type of the parsed object is a class:

>>> type(record)
<class 'Bio.Entrez.Parser.ListElement'>
>>>r=record[0]
>>>type(r)
<class 'Bio.Entrez.Parser.DictionaryElement'>
>>> r.keys()
[u'MedlineCitation', u'PubmedData']

Which makes me think there must be a much easier way of doing this than using it as a dictionary. But when I try:

>>> r.MedlineCitation

Traceback (most recent call last):
  File "<pyshell#67>", line 1, in <module>
    r.MedlineCitation
AttributeError: 'DictionaryElement' object has no attribute 'MedlineCitation'

It doesn't work. I can obviously use it as a dictionary, but then I run into problems later.

The real problem is trying to get certain information from the record when using it like a dictionary:

>>> record[0]['MedlineCitation']['PMID']
StringElement('22737229', attributes={u'Version': u'1'})

Which means that I can't just plop (that's a technical term ;) it into my sql database but need to convert it:

>>> t=record[0]['MedlineCitation']['PMID']
>>> t
StringElement('22737229', attributes={u'Version': u'1'})
>>> int(t)
22737229
>>> str(t)
'22737229'

All in all I am glad for the depth of information that Entrez.read() provides but I am not sure how to easily use the information in the resulting class instance.

Cheers

Wheaton

[Pierre Lindenbaum]

I would use XSLT to insert pubmed-xml into a database, not python.

[Wheaton Little]

Sadly I have no knowledge of XSLT, but I've used python and the sqlite3 module before.

[Pierre Lindenbaum]

I can show a quick example , what's the schema of your database ?

Answer 1

[bow]

The elements you see there are subclasses of Python's built-in types. You can use this information to check the type and perform any necessary casting prior to storing them in your database.

>>> pmid = record[0]['MedlineCitation']['PMID']
>>> pmid.__class__.__bases__
(<type 'str'>,)
>>> isinstance(pmid, basestring)
True

By the way, what do you mean by "I can obviously use it as a dictionary, but then I run into problems later."? The r[0] object you're using is a subclass of Python's built-in dictionary (in similar flavor to the example I've shown above), so it should be straightforward to treat it as a dictionary.

EDIT: There seems to be something wrong with the display. The line after pmid.__class__.__bases__ above is supposed to show (<type 'str',)

[Wheaton Little]

what I mean by "problems later" is this piece here:

>>> t=record[0]['MedlineCitation']['PMID'] 
>>> t
StringElement('22737229', attributes={u'Version': u'1'})
>>> int(t)
22737229
>>> str(t)
'22737229'

I can't just dump the value into sql because of the attribute

[bow]

Hmm..you can convert them based on the parent class into a built-in Python type, right?

[Damian Kao]

You've kinda already solved the problem. You can recast the object as scalar ints or strings and dump that into the sql database.

[Wheaton Little]

True. I can do it, it just isn't pretty. I thought maybe since someone took the time to put it in this structure there must be a really easy way of dealing with it. Maybe not though