使用解析PubMed中心XML

Question

我试图使用Biopython的Biopython解析函数解析PubMed中央XML文件。这就是我迄今为止尝试过的：

from Bio import Entrez
for xmlfile in glob.glob ('samplepmcxml.xml'):
   print xmlfile
   fh = open (xmlfile, "r")
   read_xml (fh, outfp)
   fh.close()

def read_xml (handle, outh):
   records = Entrez.parse(handle)
   for record in records:
      print record

我得到了以下错误：

Traceback (most recent call last):
File "3parse_info_from_pmc_nxml.py", line 78, in <module>
read_xml (fh, outfp)
File "3parse_info_from_pmc_nxml.py", line 10, in read_xml
for record in records:
File "/usr/lib/pymodules/python2.6/Bio/Entrez/Parser.py", line 137, in parse
self.parser.Parse(text, False)
File "/usr/lib/pymodules/python2.6/Bio/Entrez/Parser.py", line 165, in startNamespaceDeclHandler
raise NotImplementedError("The Bio.Entrez parser cannot handle XML data that make use of XML namespaces")
NotImplementedError: The Bio.Entrez parser cannot handle XML data that make use of XML namespaces

我已经下载了archivearticle.dtd文件。是否还有其他需要安装的DTD文件来描述PMC文件的架构？是否有人成功地使用Bio函数或任何其他方法来解析PMC文章？

谢谢你的帮忙!

Answer 1

使用另一个解析器，如迷你型

from xml.dom import minidom

data = minidom.parse("pmc_full.xml")

现在，根据您想要提取的数据，深入研究XML并从中获得乐趣：

for title in data.getElementsByTagName("article-title"):
    for node in title.childNodes:
        if node.nodeType == node.TEXT_NODE:
            print node.data