python - Parsing PubMed Central XML using Biopython Bio Entrez parse -


I am trying to parse piamped central XML files which are using the Bioethon Bio Enter Pars function. What I have done: 

  bio import from Entrez for xmlfile in glob.glob ('samplepmcxml.xml'): print xmlfile fh = open (xmlfile, "r") in the record Record = Entrance purse (handle) for record: Print record

I get the following: read_xml (fh, outfp) fh.close () def read_xml (handle, out) error: 

  Tracebacks (the most recent call final): The file "3parse_info_from_pmc_nxml.py", line 78, & lt; Module & gt; Read_xml (FH, Outfip) file "3parse_info_from_pmc_nxml.py", line 10, for record in read_xml: file "/usr/lib/pymodules/python2.6/Bio/Entrez/Parser.py", line 137, pars In Self.parser.Parse (text, false) file "/usr/lib/pymodules/python2.6/Bio/Entrez/Parser.py", in line 165, startNamespaceDeclHandler raises NotImplementedError ("Bio.Entrez Parser handled XML data Can not be used which can use XML namespaces) "NotImplementedError: Bio.Entrez Parser can not handle XML data that uses XML namespaces

I already have ar Chivearticle.dtd file is downloaded. Are there any other DTD files that need to be installed which will describe the schema of PMC files? Has anyone successfully used the Bio Entres function or any other method to parse PMC articles?

Thank you for your help!

Import from XMLMinidom data = minidom.parse ("pmc_full.xml") to 

 . 
 Now what data you want to extract based on, dive into XML and it's fun: 
 
  for the title in the data. Elements biathagnam ("article-title"): .childNodes for nodes in the title: if node. NodeType == Node. TEXT_NODE: Print node data

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