先程の質問と似ているがxmlファイルのデータの抽出

Question

<passage> <infon key="section_type">ABSTRACT</infon> <infon key="type">abstract</infon> <offset>81</offset> <text>Neurologic complications of COVID-19 infection have been recently described and include dizziness, headache, loss of taste and smell, stroke, and encephalopathy. Brain MRI in these patients have revealed various findings including ischemia, hemorrhage, inflammation, and demyelination. In this article, we report a case of critical illness-associated cerebral microbleeds identified on MRI in a patient with severe COVID-19 infection and discuss the potential etiologies of these neuroimaging findings.</text> 　<annotation id="20">
<infon key="identifier">9606</infon>
<infon key="type">Species</infon>
<location offset="262" length="8"/>
<text>patients</text>　　　　　　　　　　　　　　
<passage>

ソースコード
import xml.etree.ElementTree as ET
tree = ET.parse('result.xml')
root=tree.getroot()

試したこと

pythonでxmlファイルのannotationのtextの部分を無視してNeurologicの部分のtextの抽出って可能なのでしょうか?

Comments

[1T2R3M4]

https://qiita.com/15698-sai/questions/bc5c8fe07be96aebedfd
以下ご対応ください。
https://teratail.com/help#posted-otherservice

Answer 1

BioC XML の場合、sentence や relation タグが含まれる場合があります。例えば以下の様にです。

result.xml

<passage>
  <infon key="section_type">ABSTRACT</infon>
  <infon key="type">abstract</infon>
  <offset>81</offset>
  <text>Neurologic complications of COVID-19 ... </text>
  <annotation id="20">
    <infon key="identifier">9606</infon>
    <infon key="type">Species</infon>
    <location offset="262" length="8"/>
    <text>patients</text>
  </annotation>
  <sentence>
    <infon key="type">original sentence</infon>
    <offset>70</offset>
    <text>Active Raf-1 phosphorylates and activates the mitogen-activated protein ... </text>
  </sentence>
</passage>

以下は lxml - Processing XML and HTML with Python モジュールを使う場合です。

from lxml import etree as ET

tree = ET.parse('result.xml')
root = tree.getroot()
texts = [t.text for t in root.findall('.//text') if t.getparent().tag != 'annotation']
print(texts)

#
['Neurologic complications of COVID-19 ...', 'Active Raf-1 phosphorylates and activates the mitogen-activated protein ...']

Comments

[123478]

result.xml
<passage>
<infon key="authors">Gupta NA, Lien C, Iv M, </infon>
<offset>0</offset>
<text>Critical illness-associated cerebral microbleeds in severe COVID-19 infection </text>
<infon key="section_type">ABSTRACT</infon>
<infon key="type">abstract</infon>
<offset>81</offset>
<text>Neurologic complications of COVID-19 ... </text>
<annotation id="20">
<infon key="identifier">9606</infon>
<infon key="type">Species</infon>
<location offset="262" length="8"/>
<text>patients</text>
</annotation>
<passage>

先程のコードだとCritical illness-associatedの文が含まれてしまうんですがどうするればよいでしょうか.

[shiracamus]

そのxml、最後の<passage>は</passage>なのでは？
動作確認したxmlでしょうか？

[123478]

</passsage>ですね.ダウンロードした容量の大きいXMLファイルの一部分を切り取ったものになります.

[melian]

> 先程のコードだとCritical illness-associatedの文が含まれてしまうんですが

annotation タグの外側にありますので含まれることになります。

[123478]

そうなんですね.ありがとうございます.

Answer 2

<passage>
  <infon key="section_type">ABSTRACT</infon>
  <infon key="type">abstract</infon> <offset>81</offset>
  <text>Neurologic complications of COVID-19 infection have been recently described and include dizziness, headache, loss of taste and smell, stroke, and encephalopathy. Brain MRI in these patients have revealed various findings including ischemia, hemorrhage, inflammation, and demyelination. In this article, we report a case of critical illness-associated cerebral microbleeds identified on MRI in a patient with severe COVID-19 infection and discuss the potential etiologies of these neuroimaging findings.</text>
  <annotation id="20">
    <infon key="identifier">9606</infon>
    <infon key="type">Species</infon>
    <location offset="262" length="8"/>
    <text>patients</text>
  </annotation>
</passage>

import xml.etree.ElementTree as ET

tree = ET.parse('result.xml')
root = tree.getroot()
text = root.find('.//text')
print("textがありません" if text is None else text.text)

Neurologic complications of COVID-19 infection have been recently described and include dizziness, headache, loss of taste and smell, stroke, and encephalopathy. Brain MRI in these patients have revealed various findings including ischemia, hemorrhage, inflammation, and demyelination. In this article, we report a case of critical illness-associated cerebral microbleeds identified on MRI in a patient with severe COVID-19 infection and discuss the potential etiologies of these neuroimaging findings.

Comments

[123478]

import xml.etree.ElementTree as ET
tree = ET.parse('result.xml')
root=tree.getroot()
print(root.find('text').text)
これだとAttributeError: 'NoneType' object has no attribute 'text'
というエラーが出てしまうのですがどうすればよいでしょうか

[shiracamus]

上記のxmlはタグが不完全なのでxmlを修正しました。
示されたコードを実行してみましたが、表示されましたよ。