msalvadores

import requests
import time
import pdb
import json
import sys
import urllib

FILE_NAME = "ontology_ids_and_parents.txt"
APIKEY = 'YOUR KEY'

msalvadores

<?xml version="1.0"?>

<!DOCTYPE rdf:RDF [
    <!ENTITY dcam "http://purl.org/dc/dcam/" >
    <!ENTITY dcterms "http://purl.org/dc/terms/" >
    <!ENTITY dcmitype "http://purl.org/dc/dcmitype/" >
    <!ENTITY dwc "http://rs.tdwg.org/dwc/terms/" >
    <!ENTITY dwctype "http://rs.tdwg.org/dwc/dwctype/" >
    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >

msalvadores

import sys
import urllib,urllib2
import traceback
import pdb
import time                                                
import json
import os

def query(q,epr,f='text/plain'):
    params = {'query': q}

msalvadores

import timeit

DATA = 'abcdef'

def bytearr():
    bytesn = 1024 * 1024 * 5
    s = bytearray(bytesn)
    i = 0 
    while i < bytesn:
        s[i] = DATA[i%len(DATA)]

msalvadores

require 'pry'

module Test
  module Settings
    def self.included(base)
      base.extend(ClassMethods)
    end

    module ClassMethods
      attr_accessor :settings

msalvadores

public ResultSet executeQuery(String queryString) throws Exception {
	 Query query = QueryFactory.create(queryString) ;

         QueryEngineHTTP qexec = QueryExecutionFactory.createServiceRequest(this.service, query)		                      
         qexec.addParam("apikey", this.apikey)
         ResultSet results = qexec.execSelect() ;
         return results;
}

msalvadores

import json,urllib2,urllib,traceback, sys 

def query(q,apikey,epr,f='application/json'):
    try:
        params = {'query': q, 'apikey': apikey}
        params = urllib.urlencode(params)
        opener = urllib2.build_opener(urllib2.HTTPHandler)
        request = urllib2.Request(epr+'?'+params)
        request.add_header('Accept', f)
        request.get_method = lambda: 'GET'

msalvadores

package test;

import java.io.PrintStream;

public class TestOutput {
	
	public static void outputFiltered(String label, PrintStream out) {
		for (byte b : label.getBytes()) {
			if (Character.isLetterOrDigit((char)b)) {
				out.print((char)b);

msalvadores

import json
import urllib2
import urllib
import traceback
import sys 

def query(q,apikey,epr,f='application/json'):
    """Function that uses urllib/urllib2 to issue a SPARQL query.
       By default it requests json as data format for the SPARQL resultset"""

msalvadores

#Ontology here http://protege.stanford.edu/ontologies/mappings/mappings.rdfs

<http://purl.bioontology.org/mapping/21d7a8e0-004d-012e-74a1-005056bd0010>
    <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_source_ontology_version> 40400 ;
    <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#created_in_target_ontology_version> 42693 ;
    <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#date> "2010-05-17T23:24:34Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
    <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source> "Application" ;
    <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_algorithm> "Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym." ;
    <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#mapping_source_contact_info> "support@bioontology.org" ;
    <http://protege.stanford.