Web scraping table from UniProt database-CodePudding

I have a list of UniProt IDs and would like to use BeautifulSoup to scrap a table containing the structure information. The url I am using is as follows: https://www.uniprot.org/uniprot/P03496, with accession "P03496".

A snippet of the html code is as follows.

<div >
    <div >
        <div  id="structure">
            <protvista-uniprot-structure accession="P03468">
                <div >
                    <div  protvista-uniprot-structure__table">
                        <protvista-datatable >
                            <table>...</table>
                        </protvista-datatable>
                    </div>
                </div>
            </protvista-uniprot-structure>
        </div>
    </div>
</div>

The information I require is contained between the <table>...</table> tag.

I tried

from bs4 import BeautifulSoup
import requests

url='https://www.uniprot.org/uniprot/P03468'
r=requests.get(url)
url=r.content
soup = BeautifulSoup(url,'html.parser')
soup.find("protvista-datatable", {"class": "feature"})
print(soup)

CodePudding user response：

Content is provided dynamically and is not contained in your soup if you take a deeper look. It do not need BeautifulSoupto get data, your tabel is based on, simply use their api / rest interface to get structured data as JSON:

import requests
url='https://rest.uniprot.org/uniprot/P03468'
## fetch the json response
data = requests.get(url).json()
## pick needed data e.g. 
data['uniProtKBCrossReferences']

Output

[{'database': 'EMBL',
  'id': 'J02146',
  'properties': [{'key': 'ProteinId', 'value': 'AAA43412.1'},
   {'key': 'Status', 'value': '-'},
   {'key': 'MoleculeType', 'value': 'Genomic_RNA'}]},
 {'database': 'EMBL',
  'id': 'AF389120',
  'properties': [{'key': 'ProteinId', 'value': 'AAM75160.1'},
   {'key': 'Status', 'value': '-'},
   {'key': 'MoleculeType', 'value': 'Genomic_RNA'}]},
 {'database': 'EMBL',
  'id': 'EF467823',
  'properties': [{'key': 'ProteinId', 'value': 'ABO21711.1'},
   {'key': 'Status', 'value': '-'},
   {'key': 'MoleculeType', 'value': 'Genomic_RNA'}]},
 {'database': 'EMBL',
  'id': 'CY009446',
  'properties': [{'key': 'ProteinId', 'value': 'ABD77678.1'},
   {'key': 'Status', 'value': '-'},
   {'key': 'MoleculeType', 'value': 'Genomic_RNA'}]},
 {'database': 'EMBL',
  'id': 'K01031',
  'properties': [{'key': 'ProteinId', 'value': 'AAA43415.1'},
   {'key': 'Status', 'value': '-'},
   {'key': 'MoleculeType', 'value': 'Genomic_RNA'}]},
 {'database': 'RefSeq',
  'id': 'NP_040981.1',
  'properties': [{'key': 'NucleotideSequenceId', 'value': 'NC_002018.1'}]},
 {'database': 'PDB',
  'id': '6WZY',
  'properties': [{'key': 'Method', 'value': 'X-ray'},
   {'key': 'Resolution', 'value': '1.50 A'},
   {'key': 'Chains', 'value': 'C=181-190'}]},...]