{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [], "source": [ "from __future__ import print_function\n", "\n", "import csv\n", "import sys\n", "import xml.etree.ElementTree as ET\n", " \n", "import pandas as pd\n", "import requests\n", "\n", "if sys.version_info.major == 2:\n", " from StringIO import StringIO\n", "else:\n", " from io import StringIO" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "def get_psiquic(service, query, full_url=False, **kwargs):\n", " kwargs['format'] = kwargs.get('format', 'tab27')\n", " if full_url:\n", " req = requests.get('%s%s' % (service, query), params=kwargs)\n", " else:\n", " server = 'http://www.ebi.ac.uk/Tools/webservices/psicquic'\n", " req = requests.get('%s/%s/%s' % (server, service, query), params=kwargs)\n", " if not req.ok:\n", " req.raise_for_status()\n", " return req.content" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", " | name | \n", "org_url | \n", "
---|---|---|
1 | \n", "BioGrid | \n", "http://www.thebiogrid.org/ | \n", "
2 | \n", "bhf-ucl | \n", "http://www.ucl.ac.uk/functional-gene-annotation/cardiovascular/projects | \n", "
3 | \n", "ChEMBL | \n", "http://www.ebi.ac.uk/chembl | \n", "
4 | \n", "DIP | \n", "http://dip.doe-mbi.ucla.edu/ | \n", "
5 | \n", "HPIDb | \n", "http://www.agbase.msstate.edu/hpi/main.html | \n", "
6 | \n", "InnateDB | \n", "http://www.innatedb.com | \n", "
7 | \n", "IntAct | \n", "http://www.ebi.ac.uk/intact | \n", "
8 | \n", "mentha | \n", "http://mentha.uniroma2.it/ | \n", "
9 | \n", "MPIDB | \n", "http://jcvi.org/mpidb/ | \n", "
11 | \n", "MatrixDB | \n", "http://matrixdb.ibcp.fr/ | \n", "
12 | \n", "MINT | \n", "http://mint.bio.uniroma2.it/ | \n", "
13 | \n", "Reactome | \n", "http://www.reactome.org/ | \n", "
14 | \n", "Reactome-FIs | \n", "http://www.reactome.org/ | \n", "
16 | \n", "BIND | \n", "http://www.baderlab.org | \n", "
17 | \n", "Interoporc | \n", "http://biodev.extra.cea.fr/interoporc | \n", "
20 | \n", "I2D-IMEx | \n", "http://ophid.utoronto.ca/ | \n", "
21 | \n", "InnateDB-IMEx | \n", "http://www.innatedb.ca/ | \n", "
22 | \n", "MolCon | \n", "http://www.molecularconnections.com | \n", "
23 | \n", "UniProt | \n", "http://www.uniprot.org | \n", "
24 | \n", "MBInfo | \n", "http://www.mechanobio.info/ | \n", "
25 | \n", "BindingDB | \n", "http://www.bindingdb.org | \n", "
26 | \n", "VirHostNet | \n", "http://pbildb1.univ-lyon1.fr/virhostnet | \n", "
28 | \n", "Spike | \n", "None | \n", "