In [1]:

    

from __future__ import print_function

import csv
import sys
import xml.etree.ElementTree as ET
    
import pandas as pd
import requests

if sys.version_info.major == 2:
    from StringIO import StringIO
else:
    from io import StringIO


    

In [2]:

    

def get_psiquic(service, query, full_url=False, **kwargs):
    kwargs['format'] = kwargs.get('format', 'tab27')
    if full_url:
        req = requests.get('%s%s' % (service, query), params=kwargs)
    else:
        server = 'http://www.ebi.ac.uk/Tools/webservices/psicquic'
        req = requests.get('%s/%s/%s' % (server, service, query), params=kwargs)
    if not req.ok:
        req.raise_for_status()
    return req.content


    

In [3]:

    

def get_databases(db_xml):
    for service in db_xml:
        for elem in service:
            ns_clean_tag = elem.tag[elem.tag.find('}') + 1:]
            if ns_clean_tag == 'name':
                name = elem.text
            elif ns_clean_tag == 'active':
                active = False if elem.text == 'false' else True
            elif ns_clean_tag == 'restUrl':
                rest_url = elem.text
            elif ns_clean_tag == 'restExample':
                example = elem.text
            elif ns_clean_tag == 'organizationUrl':
                org_url = elem.text
            else:
                pass  # there are a few more
        yield {'name': name, 'active': active, 'org_url': org_url,
               'example': example, 'rest_url': rest_url}

dbs_xml = get_psiquic('registry', 'registry', action='STATUS', format='xml')
dbs_xml_parsed = ET.fromstring(dbs_xml)
dbs = pd.DataFrame.from_records(get_databases(dbs_xml_parsed))

pd.options.display.max_colwidth = 100
active_dbs = dbs[dbs.active==True]
active_dbs.drop(['active', 'example', 'rest_url'], 1)


    

    
Out[3]:






  

    

      

      
name
      
org_url
    
  
  

    

      
1
      
BioGrid
      
http://www.thebiogrid.org/
    
    

      
2
      
bhf-ucl
      
http://www.ucl.ac.uk/functional-gene-annotation/cardiovascular/projects
    
    

      
3
      
ChEMBL
      
http://www.ebi.ac.uk/chembl
    
    

      
4
      
DIP
      
http://dip.doe-mbi.ucla.edu/
    
    

      
5
      
HPIDb
      
http://www.agbase.msstate.edu/hpi/main.html
    
    

      
6
      
InnateDB
      
http://www.innatedb.com
    
    

      
7
      
IntAct
      
http://www.ebi.ac.uk/intact
    
    

      
8
      
mentha
      
http://mentha.uniroma2.it/
    
    

      
9
      
MPIDB
      
http://jcvi.org/mpidb/
    
    

      
11
      
MatrixDB
      
http://matrixdb.ibcp.fr/
    
    

      
12
      
MINT
      
http://mint.bio.uniroma2.it/
    
    

      
13
      
Reactome
      
http://www.reactome.org/
    
    

      
14
      
Reactome-FIs
      
http://www.reactome.org/
    
    

      
16
      
BIND
      
http://www.baderlab.org
    
    

      
17
      
Interoporc
      
http://biodev.extra.cea.fr/interoporc
    
    

      
20
      
I2D-IMEx
      
http://ophid.utoronto.ca/
    
    

      
21
      
InnateDB-IMEx
      
http://www.innatedb.ca/
    
    

      
22
      
MolCon
      
http://www.molecularconnections.com
    
    

      
23
      
UniProt
      
http://www.uniprot.org
    
    

      
24
      
MBInfo
      
http://www.mechanobio.info/
    
    

      
25
      
BindingDB
      
http://www.bindingdb.org
    
    

      
26
      
VirHostNet
      
http://pbildb1.univ-lyon1.fr/virhostnet
    
    

      
28
      
Spike
      
None
    
  

In [4]:

    

req = get_psiquic('intact/webservices/current/search/query', 'tp53', format='count')
print(req)
for index, db in active_dbs.iterrows():
    req = get_psiquic(db['rest_url'], 'query/tp53', full_url=True, format='count')
    count = int(req)
    print('DB: %s, count: %d' % ( db['name'], count))


    

    




4802
DB: BioGrid, count: 2375
DB: bhf-ucl, count: 14
DB: ChEMBL, count: 80
DB: DIP, count: 0
DB: HPIDb, count: 74
DB: InnateDB, count: 136
DB: IntAct, count: 4802
DB: mentha, count: 3217
DB: MPIDB, count: 0
DB: MatrixDB, count: 0
DB: MINT, count: 2158
DB: Reactome, count: 0
DB: Reactome-FIs, count: 369
DB: BIND, count: 47
DB: Interoporc, count: 0
DB: I2D-IMEx, count: 194
DB: InnateDB-IMEx, count: 5
DB: MolCon, count: 18
DB: UniProt, count: 438
DB: MBInfo, count: 0
DB: BindingDB, count: 0
DB: VirHostNet, count: 0
DB: Spike, count: 450

In [5]:

    

req = get_psiquic('intact/webservices/current/search/query', 'tp53',
                  firstResult=0, maxResults=1000)
answer = csv.reader(StringIO(req), delimiter='\t')
db_types = set()
for record in answer:
    db_types.add(record[0].split(':')[0])
    db_types.add(record[1].split(':')[0])
print(db_types)


    

    




set(['uniprotkb', 'ddbj/embl/genbank', '-', 'ensembl', 'intact', 'chebi'])

In [ ]: