将 XML 文件转换为 Python 中的列表列表

Question

我有一个来自HMDB 的数据集Saliva Metabolites 数据。

此数据是一个 XML 文件。我想要做的是将此 XML 文件转换为 Python 中的列表列表（嵌套列表），但是，我不希望列表中的所有节点。

已编辑：这是一种代谢物的部分数据示例

<?xml version="1.0" encoding="UTF-8"?>
<hmdb xmlns="http://www.hmdb.ca">
<metabolite>
  <version>4.0</version>
  <creation_date>2005-11-16 15:48:42 UTC</creation_date>
  <update_date>2019-01-11 19:13:56 UTC</update_date>
  <accession>HMDB0000001</accession>
  <status>quantified</status>
  <secondary_accessions>
    <accession>HMDB00001</accession>
    <accession>HMDB0004935</accession>
    <accession>HMDB0006703</accession>
    <accession>HMDB0006704</accession>
    <accession>HMDB04935</accession>
    <accession>HMDB06703</accession>
    <accession>HMDB06704</accession>
  </secondary_accessions>
  <name>1-Methylhistidine</name>
  <cs_description>1-Methylhistidine, also known as 1-mhis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine has been found in human muscle and skeletal muscle tissues, and has also been detected in most biofluids, including cerebrospinal fluid, saliva, blood, and feces. Within the cell, 1-methylhistidine is primarily located in the cytoplasm. 1-Methylhistidine participates in a number of enzymatic reactions. In particular, 1-Methylhistidine and Beta-alanine can be converted into anserine; which is catalyzed by the enzyme carnosine synthase 1. In addition, Beta-Alanine and 1-methylhistidine can be biosynthesized from anserine; which is mediated by the enzyme cytosolic non-specific dipeptidase. In humans, 1-methylhistidine is involved in the histidine metabolism pathway. 1-Methylhistidine is also involved in the metabolic disorder called the histidinemia pathway.</cs_description>
  <description>One-methylhistidine (1-MHis) is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into b-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.</description>
  <synonyms>
    <synonym>(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoic acid</synonym>
    <synonym>1-Methylhistidine</synonym>
    <synonym>Pi-methylhistidine</synonym>
    <synonym>(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoate</synonym>
    <synonym>1 Methylhistidine</synonym>
    <synonym>1-Methyl histidine</synonym>
  </synonyms>
  <chemical_formula>C7H11N3O2</chemical_formula>
  <smiles>CN1C=NC(C[C@H](N)C(O)=O)=C1</smiles>
  <inchikey>BRMWTNUJHUMWMS-LURJTMIESA-N</inchikey>
<diseases>
    <disease>
      <name>Kidney disease</name>
      <omim_id/>
      <references>
        <reference>
          <reference_text>McGregor DO, Dellow WJ, Lever M, George PM, Robson RA, Chambers ST: Dimethylglycine accumulates in uremia and predicts elevated plasma homocysteine concentrations. Kidney Int. 2001 Jun;59(6):2267-72.</reference_text>
          <pubmed_id>11380830</pubmed_id>
        </reference>
        <reference>
          <reference_text>Ehrenpreis ED, Salvino M, Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40.</reference_text>
          <pubmed_id>11418788</pubmed_id>
        </reference>
        <reference>
         </reference>
      </references>
    </disease>
    <disease> 

导入文件：

import xml.etree.ElementTree as et

data1 = et.parse('D:/path/to/Tal/my/HMDB/DataSets/saliva_metabolites/saliva_metabolites.xml')
root = data1.getroot()

现在，不确定如何选择特定节点。意思是，我的目标是创建一个代谢物列表，列表中的每个代谢物都将包含一个节点列表（例如，<accession>、<name>、<synonyms> 和 <diseases_name>）

反过来，这些元素将包含另一个列表（例如，在<synonyms> 内部将有一个值名称列表，或者在<diseases_name> 内部将是疾病名称列表，每个疾病将包含一个pub_id 列表值）。

# To access the 4'th node of the first metabolit

>>  root[0][3].text
'HMDB0000001'

其中root[0][3] 代表<accession> 节点。

尝试使用 print 运行循环，所以我会理解循环的输出，但收到了 None 的列表

for node in root:
    print(node.find('accession'))
None
None
None
None
None
.
.
.

也试过了

>> root.findall('./metabolite/accession')
[]

但是收到了空括号

我尝试的第一个代谢物的同义词列表：

>> root[0][9].text
'\n    '

# This gave the first value of synonyms
root[0][9][0].text
'\n    '

我用这些问题找到了答案：

1. How do I parse XML in Python?
2. how to create a list of elements from an XML file in python
3. Python: XML file to pandas dataframe
4. Convert XML into Lists of Tags and Values with Python
5. Generating nested lists from XML doc

任何提示、想法都会有所帮助，感谢您的宝贵时间

Answer 1

您忽略了 XML 中的命名空间。

<hmdb xmlns="http://www.hmdb.ca">

表示没有<hmdb> 元素。 <hmdb> 在http://www.hmdb.ca 命名空间中。因为它是这个元素的默认命名空间，所以所有后代元素都在同一个命名空间中，除非它们覆盖它。

所以这个

root.findall('./metabolite/accession')

不会返回任何内容，因为您在错误的命名空间中搜索。

为方便起见，让我们在 http://www.hmdb.ca 命名空间中搜索，并为其提供句柄 h：

ns = {
    "h": "http://www.hmdb.ca"
}

accession = root.findall('./h:metabolite/h:accession', ns)
print(accession)

这会找到一个元素（查看它在打印时如何明确表示命名空间）：

[<Element '{http://www.hmdb.ca}accession' at 0x03E6E7B0>]

您可以在 ElementTree 中使用相同的显式语法，但它很快就会变得笨拙：

t.findall('./{http://www.hmdb.ca}metabolite/{http://www.hmdb.ca}accession')

prefix: 的较短（和标准）语法更易于使用。