Question

我想从xml文件（如下所示的示例文件）中读取PMID和作者姓氏

我正在获取PMID和姓氏，但是将循环作为PMID的次数，我想要1个PMID并有各自的姓氏

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE PubmedArticleSet SYSTEM "http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd">
<PubmedArticleSet>
<PubmedArticle>
    <MedlineCitation Status="MEDLINE" Owner="NLM">
        <PMID Version="1">2844048</PMID>
        <AuthorList CompleteYN="Y">
            <Author ValidYN="Y">
                <LastName>Guarner</LastName>
                <ForeName>J</ForeName>
                <Initials>J</Initials>
            </Author>
            <Author ValidYN="Y">
                <LastName>Cohen</LastName>
                <ForeName>C</ForeName>
                <Initials>C</Initials>
            </Author>
            <Author ValidYN="Y">
                <LastName>Mushi</LastName>
                <ForeName>E</ForeName>
                <Initials>F</Initials>
            </Author>
        </AuthorList>
    </MedlineCitation>
</PubmedArticle>
<PubmedArticle>
    <MedlineCitation Status="MEDLINE" Owner="NLM">
        <PMID Version="1">123456</PMID>
        <AuthorList CompleteYN="Y">
            <Author ValidYN="Y">
                <LastName>Smith</LastName>
                <ForeName>C</ForeName>
                <Initials>C</Initials>
            </Author>
            <Author ValidYN="Y">
                <LastName>Jones</LastName>
                <ForeName>E</ForeName>
                <Initials>F</Initials>
            </Author>
        </AuthorList>
    </MedlineCitation>
</PubmedArticle>
</PubmedArticleSet>

代码，我已经尝试

FN=[]
for pmid in root.iter('PMID'):
    print(pmid.text)
    for id in root.findall("./PubmedArticle/MedlineCitation/Article/AuthorList"):
        for f in id.findall("./Author/ForeName"):
            fn=f.text

            x= '{},{}'.format(i, fn)
            #print(x)
            FN.append(x)

预期产量

PMID               AUTHORS
2844048            'Guarner J J', 'Cohen C C'

Answer 1

我不知道您是否希望输出采用特定格式。但是，您可以尝试以下代码。输出为Dictionary，其中Keys为PMID，Values为Authors列表。

import xml.etree.ElementTree as ET
import pandas as pd
tree = ET.parse('E:\Python\DataFiles\PMID.xml') # change according to your location
authors_pmid = []
all_authors_pmid = []
root = tree.getroot()
for amedlinecitation in root.iter('MedlineCitation'): #PMID and Author are childs of MedlineCitation
    pmid = amedlinecitation.find('PMID').text
    for anauthor in amedlinecitation.iter('Author'): # for each amedlinecitation, find all its Authors
        author_name = anauthor.find('LastName').text # for each Author, find the LastName tag and extract its value
        authors_pmid = [pmid,author_name]
        all_authors_pmid.append(authors_pmid)
df = pd.DataFrame(all_authors_pmid,columns=['PMID','Author'])
print(df)

输出：

{'2844048': ['Guarner', 'Cohen', 'Mushi'], '123456': ['Smith', 'Jones']}

以下代码将使用Python数据框以表格形式给出输出。

import xml.etree.ElementTree as ET
import pandas as pd
tree = ET.parse('E:\Python\DataFiles\PMID.xml') # change according to your location
authors_pmid = []
all_authors_pmid = []
root = tree.getroot()
for amedlinecitation in root.iter('MedlineCitation'): #PMID and Author are childs of MedlineCitation
    pmid = amedlinecitation.find('PMID').text
    for anauthor in amedlinecitation.iter('Author'): # for each amedlinecitation, find all its Authors
        author_name = anauthor.find('LastName').text # for each Author, find the LastName tag and extract its value
        authors_pmid = [pmid,author_name]
        all_authors_pmid.append(authors_pmid)
df = pd.DataFrame(all_authors_pmid,columns=['PMID','Author'])
print(df)

输出：

      PMID   Author
0  2844048  Guarner
1  2844048    Cohen
2  2844048    Mushi
3   123456    Smith
4   123456    Jones

以上代码与第一个代码有何不同：

对于每对PMID和作者名称，它将创建一个列表。该列表名为authors_pmid。例如，['2844048'，'Guarner']，['2844048'，'Cohen']，['2844048'，'Mushi']，['123456'，'Smith']，['123456'，'Jones ']将是内部for循环的每次迭代期间列表变量authors_pmid中的值。
然后，上述每个列表将附加到由all_authors_pmid定义的最终列表中
此最终列表将是调用Dataframe构造函数以创建具有以下列名称的数据帧的数据输入：PMID和Author

无法从XML文件读取同级和同级的子级

1 个答案: