Beispiel #1
0
def get_disease_specific_drugs(parser, selected_drugs, phenotypes):
    import text_utilities
    disease_to_drugs = {}
    indication_to_diseases = {}
    for drug, indication in parser.drug_to_indication.iteritems():
        if drug not in selected_drugs:
            continue
        if indication is None:
            continue
        #if any(map(lambda x: x is not None, [ exp.search(indication) for exp in exps ])):
        #disease = keywords[0]
        #disease_to_drugs.setdefault(disease, set()).add(drug)
        #for disease, exp in zip(phenotypes, exps):
        #    if exp.search(indication.lower()) is not None:
        #	disease_to_drugs.setdefault(disease, set()).add(drug)
        indication = indication.lower()
        for disease in phenotypes:
            #if all([ indication.find(word.strip()) != -1 for word in disease.split(",") ]):
            #	disease_to_drugs.setdefault(disease, set()).add(drug)
            values = text_utilities.tokenize_disease_name(disease)
            #print disease, values
            indication_to_diseases.setdefault(indication, set())
            if all([indication.find(word.strip()) != -1 for word in values]):
                #print disease, drug
                disease_to_drugs.setdefault(disease, set()).add(drug)
                indication_to_diseases.setdefault(indication,
                                                  set()).add(disease)
            else:
                values = text_utilities.tokenize_disease_name(
                    disease.replace("2", "II"))
                if all(
                    [indication.find(word.strip()) != -1 for word in values]):
                    disease_to_drugs.setdefault(disease, set()).add(drug)
                    indication_to_diseases.setdefault(indication,
                                                      set()).add(disease)
                else:
                    values = text_utilities.tokenize_disease_name(
                        disease.replace("1", "I"))
                    if all([
                            indication.find(word.strip()) != -1
                            for word in values
                    ]):
                        disease_to_drugs.setdefault(disease, set()).add(drug)
                        indication_to_diseases.setdefault(indication,
                                                          set()).add(disease)
    # Print non-matching indications #!
    for indication, diseases in indication_to_diseases.iteritems():
        if len(diseases) == 0:
            continue
            print indication.encode('ascii', 'ignore')
        elif indication.find(" not ") != -1 or indication.find(
                " except ") != -1:
            continue
            print diseases, indication.encode('ascii', 'ignore')
    #print disease_to_drugs["diabetes mellitus, type 2"]
    return disease_to_drugs
Beispiel #2
0
def get_disease_specific_drugs(parser, selected_drugs, phenotypes):
    import text_utilities
    disease_to_drugs = {}
    indication_to_diseases = {}
    for drug, indication in parser.drug_to_indication.iteritems():
	if drug not in selected_drugs:
	    continue
	if indication is None:
	    continue
	#if any(map(lambda x: x is not None, [ exp.search(indication) for exp in exps ])):
	    #disease = keywords[0]
	    #disease_to_drugs.setdefault(disease, set()).add(drug)
	#for disease, exp in zip(phenotypes, exps):
	#    if exp.search(indication.lower()) is not None:
	#	disease_to_drugs.setdefault(disease, set()).add(drug)
	indication = indication.lower()
	for disease in phenotypes:
	    #if all([ indication.find(word.strip()) != -1 for word in disease.split(",") ]):
	    #	disease_to_drugs.setdefault(disease, set()).add(drug)
	    values = text_utilities.tokenize_disease_name(disease)
	    #print disease, values
	    indication_to_diseases.setdefault(indication, set())
	    if all([ indication.find(word.strip()) != -1 for word in values ]):
		#print disease, drug
		disease_to_drugs.setdefault(disease, set()).add(drug)
		indication_to_diseases.setdefault(indication, set()).add(disease)
	    else:
		values = text_utilities.tokenize_disease_name(disease.replace("2", "II"))
		if all([ indication.find(word.strip()) != -1 for word in values ]):
		    disease_to_drugs.setdefault(disease, set()).add(drug)
		    indication_to_diseases.setdefault(indication, set()).add(disease)
		else:
		    values = text_utilities.tokenize_disease_name(disease.replace("1", "I"))
		    if all([ indication.find(word.strip()) != -1 for word in values ]):
			disease_to_drugs.setdefault(disease, set()).add(drug)
			indication_to_diseases.setdefault(indication, set()).add(disease)
    # Print non-matching indications #!
    for indication, diseases in indication_to_diseases.iteritems():
	if len(diseases) == 0:
	    continue
	    print indication.encode('ascii','ignore')
	elif indication.find(" not ") != -1 or indication.find(" except ") != -1:
	    continue
	    print diseases, indication.encode('ascii','ignore')
    #print disease_to_drugs["diabetes mellitus, type 2"] 
    return disease_to_drugs
Beispiel #3
0
def convert_fda_name_to_mesh(disease, mesh_name_to_ids):
    phenotype = None
    disease = disease.replace("^s", "").replace("'s","")
    if disease in mesh_name_to_ids:
        phenotype = disease
    return phenotype
    # Get words skipping disease / disorder / syndrome / plural / 's
    values = text_utilities.tokenize_disease_name(disease, exact=False)
    val_and_phenotypes = []
    for mesh_name in mesh_name_to_ids:
        val = sum([ mesh_name.lower().find(word.strip()) != -1 for word in values ])
        #print mesh_name, val
        if val > len(values) / 2.0:
            #print mesh_name, disease
            val_and_phenotypes.append((float(val)/len(mesh_name.split()), mesh_name))
    #print values, val_and_phenotypes
    if len(val_and_phenotypes) > 0:
        val_and_phenotypes.sort()
        phenotype = val_and_phenotypes[-1][1]
    return phenotype
Beispiel #4
0
def convert_fda_name_to_mesh(disease, mesh_name_to_ids):
    phenotype = None
    disease = disease.replace("^s", "").replace("'s", "")
    if disease in mesh_name_to_ids:
        phenotype = disease
    return phenotype
    # Get words skipping disease / disorder / syndrome / plural / 's
    values = text_utilities.tokenize_disease_name(disease, exact=False)
    val_and_phenotypes = []
    for mesh_name in mesh_name_to_ids:
        val = sum(
            [mesh_name.lower().find(word.strip()) != -1 for word in values])
        #print mesh_name, val
        if val > len(values) / 2.0:
            #print mesh_name, disease
            val_and_phenotypes.append(
                (float(val) / len(mesh_name.split()), mesh_name))
    #print values, val_and_phenotypes
    if len(val_and_phenotypes) > 0:
        val_and_phenotypes.sort()
        phenotype = val_and_phenotypes[-1][1]
    return phenotype