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 requests
import time
import pdb
import json
import sys
import urllib

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

msalvadores

/* 
code to get all var names hanging from a rasqal_expression 
author: Manuel Salvadores (msalvadores@gmail.com)
*/

static void get_var_names(rasqal_expression *e,GList **list_vars) {
        GList *l = *list_vars;
        if (!e) return;
        if (e->literal != NULL) {
            rasqal_literal *lit  = e->literal;

msalvadores

@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix def: <http://foo.com/def/> .
@prefix id: <http://foo.com/id/> .

############################################################
#####              RDFS SCHEMA
############################################################

########  rdfs:subClassOf hierarchy

msalvadores

#stackoverflow answer http://stackoverflow.com/questions/6225590/python-find-occurrences-of-strings-from-a-reference-file-within-an-input-file

def count_line_occurrences(ref_list,input_list):
  line_counter = {}
  # Initialization
  for ref_line in ref_list:
    ref_line = ref_line.rstrip()
    line_counter[ref_line] = 0
  for input_line in input_list:
      input_line = input_line.rstrip()

msalvadores

package ncbo.proto;

import java.io.FileInputStream;
import java.net.URI;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Properties;

import edu.stanford.smi.protegex.owl.database.creator.OwlDatabaseCreator;
import edu.stanford.smi.protegex.owl.model.OWLModel;

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.

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

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,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'