解析 PubMed 数据并从多个文件中提取多列

Question

我有多个来自 PubMed 的 xml 文件。几个文件是here.

如何解析它并在单个数据框中获取这些列。如果一篇文章有多个作者，我希望将它们作为单独的行

预期产出（应包括所有作者）：

Title  Year ArticleTitle     LastName ForeName
Nature 2021 Inter-mosaic ... Roy      Suva
Nature 2021 Inter-mosaic ... Pearson  John
Nature 2021 Neural dynamics  Pearson  John
Nature 2021 Neural dynamics  Mooney   Richard

Answer 1

首先，你想要的是可行的。像这样的东西应该适用于你的第二个文件，你可以通过用 for 循环包装代码来添加其他文件：

from lxml import etree
import pandas as pd

doc = etree.parse('file.xml')

columns = ['Title','ArticleDate','ArticleTitle','LastName','ForeName']
title = doc.xpath(f'//{columns[0]}/text()')[0]
year = doc.xpath(f'//{columns[1]}//Year/text()')[0]
article_title = doc.xpath(f'//{columns[2]}/text()')[0]
rows = []
for auth in doc.xpath('//Author'):
    last_name = auth.xpath(f'{columns[3]}/text()')[0]
    fore_name = auth.xpath(f'{columns[4]}/text()')[0]
    rows.append([title,year,article_title,last_name,fore_name])
pd.DataFrame(rows,columns=columns)

输出（34671166.xml）：

    Title   ArticleDate     ArticleTitle    LastName    ForeName
0   Nature  2021    Neural dynamics underlying birdsong practice a...   Singh Alvarado  Jonnathan
1   Nature  2021    Neural dynamics underlying birdsong practice a...   Goffinet    Jack
2   Nature  2021    Neural dynamics underlying birdsong practice a...   Michael     Valerie
3   Nature  2021    Neural dynamics underlying birdsong practice a...   Liberti     William
4   Nature  2021    Neural dynamics underlying birdsong practice a...   Hatfield    Jordan
5   Nature  2021    Neural dynamics underlying birdsong practice a...   Gardner     Timothy
6   Nature  2021    Neural dynamics underlying birdsong practice a...   Pearson     John
7   Nature  2021    Neural dynamics underlying birdsong practice a...   Mooney  Richard

话虽如此，我不确定每个作者在单独一行中的数据框是否适合您拥有的数据类型。在此示例中，由于您有 8 co-authors，因此文章标题等信息不必要地重复了 8 次。你可以给每个作者一组单独的专栏，但是如果文章有 3 或 10 个 co-authors...

，你就会遇到问题

解析 PubMed 数据并从多个文件中提取多列

Parsing PubMed data and extracting multiple columns from multiple files

python

xml

parsing

pubmed