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ClinVar.py
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__author__ = 'lario'
import csv
import re
import gc
import os, urllib, datetime, time, sys
import xml.etree.ElementTree as ET
import clinvar13
import visumpointGene
try:
from lxml import etree
print("running with lxml.etree")
except ImportError:
try:
# Python 2.5
import xml.etree.cElementTree as etree
print("running with cElementTree on Python 2.5+")
except ImportError:
try:
# Python 2.5
import xml.etree.ElementTree as etree
print("running with ElementTree on Python 2.5+")
except ImportError:
try:
# normal cElementTree install
import cElementTree as etree
print("running with cElementTree")
except ImportError:
try:
# normal ElementTree install
import elementtree.ElementTree as etree
print("running with ElementTree")
except ImportError:
print("Failed to import ElementTree from any known place")
MAIN_NAMESPACE = visumpointGene.VP
MAIN_NAMESPACESHORT = "VP"
ClinVar_NAMESPACE = MAIN_NAMESPACE
_goodchars=dict()
def safe_unicode(obj, *args):
""" return the unicode representation of obj """
try:
return unicode(obj, *args)
except UnicodeDecodeError:
# obj is byte string
ascii_text = str(obj).encode('string_escape')
return unicode(ascii_text)
def safe_str(obj):
""" return the byte string representation of obj """
try:
return str(obj).replace('\"','').replace('\\','/')
except UnicodeEncodeError:
# obj is unicode
return unicode(obj).encode('unicode_escape').replace('\"','').replace('\\','/')
def cleanString(msg):
'''
Author: Denis Barmenkov <[email protected]>
Date: 02-jul-2007
Write string to stdout.
On UnicodeEncodeError exception all the unsafe chars from string
replaced by its python representation
'''
global _goodchars
try:
return str(msg)
except UnicodeEncodeError:
# get error,
res=''
for i in list(msg):
# try to put unknown characters thru print statement:
if i not in _goodchars:
try:
print i # try print character, some extra trash on screen
# for each unknown printable character
_goodchars[i]=i # safe character, save it as is
except UnicodeEncodeError:
# format character as python string constant
code=ord(i)
if code < 256:
t='\\x%02x' % code # 8-bit value
elif code < 65536:
t='\\u%04x' % code # 16-bit value unicode
else:
t='\\U%08x' % code # other values as 32-bit unicode
_goodchars[i]=t # or '.' for readability ;-)
res+=_goodchars[i] # append to result
print res
def processClasses(stream = sys.stdout):
stream.write('VP:Citable\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Citations"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Citable"^^xsd:string .\n\n')
stream.write('VP:Referencable\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "References"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Referencable"^^xsd:string .\n\n')
# Symbolable
stream.write('VP:Symbolable\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Symbols"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Symbolable"^^xsd:string .\n\n')
#Attributable
stream.write('VP:Attributable\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Attributes associated"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Attributable"^^xsd:string .\n\n')
# Namable
stream.write('VP:Namable\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Names"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Names"^^xsd:string .\n\n')
stream.write('VP:ClinVarClass\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Clin Var Class"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Clin Var Class"^^xsd:string .\n\n')
stream.write('VP:Measurable\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Measurable"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Measurable"^^xsd:string .\n\n')
stream.write('VP:ReferenceAssertion\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "ReferenceAssertion"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "ReferenceAssertion"^^xsd:string .\n\n')
stream.write('VP:SequenceLocation\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "SequenceLocation"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "SequenceLocation"^^xsd:string .\n\n')
stream.write('VP:Attribute\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Attribute"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Attribute"^^xsd:string .\n\n')
stream.write('VP:AttributeSet\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "AttributeSet"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Attribute Set"^^xsd:string .\n\n')
stream.write('VP:MeasureRelationship\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "MeasureRelationship"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf VP:Citable , owl:Thing , VP:Referencable, VP:Symbolable;\n')
stream.write('\tskos:prefLabel "MeasureRelationship"^^xsd:string .\n\n')
stream.write('VP:Measure\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Measure"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf VP:Citable , owl:Thing , VP:Referencable , VP:Symbolable, VP:Namable;\n')
stream.write('\tskos:prefLabel "Measure"^^xsd:string .\n\n')
#Trait
stream.write('VP:Trait\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Trait"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf VP:Citable , owl:Thing , VP:Referencable , VP:Symbolable, VP:Namable;\n')
stream.write('\tskos:prefLabel "Trait"^^xsd:string .\n\n')
stream.write('VP:Citation\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Citation"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Citation"^^xsd:string .\n\n')
stream.write('VP:Symbol\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Symbol"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf VP:Citable , owl:Thing , VP:Referencable;\n')
stream.write('\tskos:prefLabel "Symbol"^^xsd:string .\n\n')
stream.write('VP:Reference\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Reference"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Reference"^^xsd:string .\n\n')
stream.write('VP:Name\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "Name"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf VP:Citable , owl:Thing , VP:Referencable;\n')
stream.write('\tskos:prefLabel "Name"^^xsd:string .\n\n')
stream.write('VP:ReferenceClinVarAssertion\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "ReferenceClinVarAssertion"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf VP:Citable , VP:Measurable, VP:Referencable, owl:Thing ;\n')
stream.write('\tskos:prefLabel "ReferenceClinVarAssertion"^^xsd:string .\n\n')
stream.write('VP:hasCitations\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Citable ;\n')
stream.write('\trdfs:label "has citations"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Citation ;\n')
stream.write('\tskos:prefLabel "has citations"^^xsd:string .\n\n')
stream.write('VP:hasSymbols\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Symbolable ;\n')
stream.write('\trdfs:label "has Symbol"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Symbol ;\n')
stream.write('\tskos:prefLabel "has Symbol"^^xsd:string .\n\n')
stream.write('VP:hasNames\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Namable ;\n')
stream.write('\trdfs:label "has Name"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Name ;\n')
stream.write('\tskos:prefLabel "has Name"^^xsd:string .\n\n')
#shasAttributeSet
stream.write('VP:hasAttributeSet\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Attributable ;\n')
stream.write('\trdfs:label "has AttributeSet"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:AttributeSet ;\n')
stream.write('\tskos:prefLabel "has AttributeSet"^^xsd:string .\n\n')
stream.write('VP:hasAttribute\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Attributable ;\n')
stream.write('\trdfs:label "has Attribure"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Attribute ;\n')
stream.write('\tskos:prefLabel "has Attribute"^^xsd:string .\n\n')
stream.write('VP:hasMeasures\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Measurable ;\n')
stream.write('\trdfs:label "has Measure"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Measure ;\n')
stream.write('\tskos:prefLabel "has Measure"^^xsd:string .\n\n')
stream.write('VP:hasMeasuresRelation\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Attributable ;\n')
stream.write('\trdfs:label "has MeasuresRelation"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:MeasureRelation ;\n')
stream.write('\tskos:prefLabel "has MeasuresRelation"^^xsd:string .\n\n')
stream.write('VP:hasTraits\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:ReferenceClinVarAssertion ;\n')
stream.write('\trdfs:label "has Traits"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Trait ;\n')
stream.write('\tskos:prefLabel "has Traits"^^xsd:string .\n\n')
stream.write('VP:hasReferences\n')
stream.write('\ta\towl:ObjectProperty ;\n')
stream.write('\trdfs:domain VP:Referencable ;\n')
stream.write('\trdfs:label "has Reference"^^xsd:string ;\n')
stream.write('\t rdfs:range VP:Reference ;\n')
stream.write('\tskos:prefLabel "has Reference"^^xsd:string .\n\n')
########################
stream.write('VP:ReferenceType\n')
stream.write('\ta\towl:Class ;\n')
stream.write('\trdfs:label "ReferenceType"^^xsd:string ;\n')
stream.write('\trdfs:subClassOf owl:Thing ;\n')
stream.write('\tskos:prefLabel "Reference Database Type"^^xsd:string .\n\n')
stream.write('VP:SO\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Sequence Ontology"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Sequence Ontology"^^xsd:string .\n')
stream.write('VP:dbSNP\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "dbSNP"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "dbSNP"^^xsd:string .\n')
stream.write('VP:OMIM\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "OMIM"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "OMIM"^^xsd:string .\n')
stream.write('VP:Gene\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Gene"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Gene"^^xsd:string .\n')
stream.write('VP:GR\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "GeneReviews"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "GeneReviews"^^xsd:string .\n')
stream.write('VP:GA\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Genetic Alliance"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Genetic Alliance"^^xsd:string .\n')
stream.write('VP:HP\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Human Phenotype Ontology"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Human Phenotype Ontology"^^xsd:string .\n')
stream.write('VP:MD\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "MedGen"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "MedGen"^^xsd:string .\n')
stream.write('VP:GTR\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Molecular Diagnostic Laboratory,Greenwood Genetic Center"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Molecular Diagnostic Laboratory,Greenwood Genetic Center"^^xsd:string .\n')
stream.write('VP:RD\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Office of Rare Diseases"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Office of Rare Diseases"^^xsd:string .\n')
stream.write('VP:OT\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Orphanet"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "Orphanet"^^xsd:string .\n')
stream.write('VP:RefSeq\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "RefSeq"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "RefSeq"^^xsd:string .\n')
stream.write('VP:SCT\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "SNOMED CT"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "SNOMED CT"^^xsd:string .\n')
stream.write('VP:dbVar\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "dbVar"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Reference ;\n')
stream.write('skos:prefLabel "dbVar"^^xsd:string .\n')
##########################################################
#Citations
stream.write('VP:PubMed\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "dbVar"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Citation ;\n')
stream.write('skos:prefLabel "dbVar"^^xsd:string .\n')
stream.write('VP:PMC\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "dbVar"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:Citation ;\n')
stream.write('skos:prefLabel "dbVar"^^xsd:string .\n')
stream.write('VP:General\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "General"^^xsd:string ;\n')
stream.write('skos:prefLabel "General"^^xsd:string .\n')
stream.write('VP:Review\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Review"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:General ;\n')
stream.write('skos:prefLabel "Review"^^xsd:string .\n')
stream.write('VP:Translational\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Translational/Evidence-based"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:General ;\n')
stream.write('skos:prefLabel "Translational/Evidence-based"^^xsd:string .\n')
stream.write('VP:PracticeGuideline\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "practice guideline"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:General ;\n')
stream.write('skos:prefLabel "practice guideline"^^xsd:string .\n')
##############
stream.write('VP:TraiType\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Type of Trait"^^xsd:string ;\n')
stream.write('skos:prefLabel "Type of Trait"^^xsd:string .\n')
stream.write('VP:Disease\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Type of Disease"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:TraiType ;\n')
stream.write('skos:prefLabel "Type of Disease"^^xsd:string .\n')
stream.write('VP:DrugResponse\n')
stream.write('a owl:Class ;\n')
stream.write('rdfs:label "Type of DrugResponse"^^xsd:string ;\n')
stream.write('rdfs:subClassOf VP:TraiType ;\n')
stream.write('skos:prefLabel "Type of DrugResponse"^^xsd:string .\n')
###############
# result = {
# 'a': lambda x: x * 5,
# 'b': lambda x: x + 7,
# 'c': lambda x: x - 2
# }[id](x)
# Select Case domain
# Case x<0 : y = -1
# Case 0<=x<1 : y = 0
# Case 1<=x<2 : y = 1
# Case 2<=x<3 : y = 2
# Case Else : y = 'n/a'
# End Select
def printHeader(outStream):
#outStream.write("@prefix :\t<http://www.ncbi.nlm.nih.gov/clinvar#> .\n")
outStream.write("@prefix %s: <%s/> .\n\n" % (MAIN_NAMESPACESHORT , MAIN_NAMESPACE))
outStream.write("@prefix skos:\t<http://www.w3.org/2004/02/skos/core#> .\n")
outStream.write("@prefix owl:\t<http://www.w3.org/2002/07/owl#> .\n")
outStream.write("@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\n")
outStream.write("@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n")
outStream.write("@prefix umls: <http://bioportal.bioontology.org/ontologies/umls/> .\n")
outStream.write("@prefix Hugo: <http://ncicb.nci.nih.gov/xml/owl/EVS/Hugo.owl/> .\n")
#http://ncicb.nci.nih.gov/genenames.org/HGNC.owl%23HGNC_1138%3E
outStream.write("@prefix HP: <http://purl.obolibrary.org/obo/> .\n")
#outStream.write("@prefix GO: <http://purl.obolibrary.org/obo/> .\n")
#outStream.write("@prefix PMID: <http://purl.obolibrary.org/obo/> .\n")
outStream.write("@prefix SO: <http://purl.obolibrary.org/obo/>.\n")
outStream.write("@prefix GN: <http://www.visumpoint.com/Gene/> .\n")
outStream.write("@prefix OMIM: <http://www.omim.org/entry/> .\n")
outStream.write("@prefix ORD: <http://www.visumpoint.com/ORD/> .\n")
outStream.write("@prefix SCT: <http://snomed.info/> .\n")
outStream.write("@prefix MG: <http://www.visumpoint.com/MedGen/> .\n")
outStream.write("@prefix dbSNP: <http://www.visumpoint.com/dbSNP/> .\n")
outStream.write("@prefix GR: <http://www.visumpoint.com/GeneReviews/> .\n")
outStream.write("@prefix OR: <http://www.visumpoint.com/Orphanet/> .\n")
outStream.write("@prefix SO: <http://www.visumpoint.com/SequenceOntology/> .\n")
outStream.write("@prefix RefSeq: <http://www.visumpoint.com/RefSeq/> .\n")
outStream.write("@prefix GL: <http://www.visumpoint.com/GeneticsLaboratory/> .\n")
#dbVar
outStream.write("@prefix dbVar: <http://www.visumpoint.com/dbVar/> .\n")
# Molecular Diagnostic Laboratory,Greenwood Genetic Center
outStream.write("@prefix MDL: <http://www.visumpoint.com/MolecularDiagnostic/> .\n")
#Human Phenotype Ontology
#outStream.write("@prefix HPO: <http://www.visumpoint.com/HumanPhenotypeOntology/> .\n")
outStream.write("@prefix HP: <http://www.visumpoint.com/HumanPhenotypeOntology/> .\n")
#GeneTests
outStream.write("@prefix GT: <http://www.visumpoint.com/GeneTests/> .\n")
#Genetics Home Reference
outStream.write("@prefix GH: <http://www.visumpoint.com/GeneticsHomeReference/> .\n")
#Emory Genetics Laboratory
outStream.write("@prefix EHL: <http://www.visumpoint.com/EmoryGeneticsLaboratory/> .\n")
#Counsyl
outStream.write("@prefix CL: <http://www.visumpoint.com/Counsyl/> .\n")
#Department of Clinical Immunology,Odense University Hospital
outStream.write("@prefix DCI: <http://www.visumpoint.com/DepartmentClinicalImmunology/> .\n")
#MeSH
outStream.write("@prefix MeSH: <http://www.visumpoint.com/MeSH/> .\n")
#Clinical Genomics,Maastricht University Medical Centre
outStream.write("@prefix CGM: <http://www.visumpoint.com/MeSH/> .\n")
#Michigan Medical Genetics Laboratories,University of Michigan
outStream.write("@prefix MMG: <http://www.visumpoint.com/MeSH/> .\n")
#InSiGHT
outStream.write("@prefix IS: <http://www.visumpoint.com/InSiGHT/> .\n")
#Department of Clinical Immunology,Odense University Hospital') :
outStream.write("@prefix DCL: <http://www.visumpoint.com/DepartmentClinicalImmunology/> .\n")
outStream.write("@prefix PubMed: <http://www.ncbi.nlm.nih.gov/pubmed/> .\n")
outStream.write("<%s>\n" % (MAIN_NAMESPACE))
outStream.write("\ta owl:Ontology ;\n")
outStream.write('\trdfs:comment "The File ontology defines the concepts and relationships related to the image file."^^xsd:string ;\n')
outStream.write("\towl:imports <%s> ;\n" % (visumpointGene.VP))
outStream.write('\towl:versionInfo "1.0"^^xsd:string .\n\n')
def processClinVarSet(clinVarSet, stream = sys.stdout):
ID = ""
if 'ID' in clinVarSet.attrib :
ClinVarAccession = clinVarSet.xpath('ReferenceClinVarAssertion[1]/ClinVarAccession[1]')
ACC = ClinVarAccession[0].attrib['Acc']
version = ClinVarAccession[0].attrib['Version']
type = ClinVarAccession[0].attrib['Type']
dateupdate = ClinVarAccession[0].attrib['DateUpdated']
ID = clinVarSet.attrib['ID']
#stream.write('VP:CV_%s\n' % (ID))
#print('VP:%s\n' % (ID))
stream.write('<%s/%s>\n' % (visumpointGene.VP,ACC))
print('VP:%s\n' % (ID))
stream.write('\ta VP:ClinVarClass ;\n')
title = clinVarSet.xpath('Title[1]')
if len(version) > 0 :
stream.write('\tVP:Version "%s"^^xsd:string ;\n' % version)
if len(type) > 0 :
stream.write('\tVP:Type "%s"^^xsd:string ;\n' % type)
if len(title) > 0 :
stream.write('\tVP:UpdateDate "%s"^^xsd:Date ;\n' % dateupdate)
if len(title) > 0 :
stream.write('\tVP:Title "%s"^^xsd:string ;\n' % safe_str((title[0].text)))
#stream.write('\trdfs:label "%s"^^xsd:string ;\n' % safe_str((title[0].text)))
#stream.write('\tskos:prefLabel"%s"^^xsd:string ;\n' % safe_str((title[0].text)))
recordStatus = clinVarSet.xpath('RecordStatus[1]')
if len(recordStatus) > 0 :
stream.write('\tVP:Status "%s"^^xsd:string ;\n' % safe_str((recordStatus[0].text)))
#stream.write('\trdfs:label "%s"^^xsd:string ;\n' % safe_str((recordStatus[0].text)))
#stream.write('\tskos:prefLabel"%s"^^xsd:string ;\n' % safe_str((recordStatus[0].text)))
referenceClinVarAssertion = clinVarSet.xpath('ReferenceClinVarAssertion[1]')
if len(referenceClinVarAssertion) > 0 :
processReferenceClinVarAssertion(referenceClinVarAssertion[0], stream)
#for clinVarAssertion in clinVarSet.xpath('ClinVarAssertion'):
# if('ID' in clinVarAssertion.attrib):
# stream.write('\tVP:ClinVarAssertion VP:%s; \n' % (clinVarAssertion.attrib['ID']))
#processReferenceClinVarAssertion(referenceClinVarAssertion[0],stream)
#clinVarAssertion = clinVarSet.xpath('ClinVarAssertion[1]')
#if len(clinVarAssertion) > 0 :
#processClinVarAssertion(clinVarAssertion[0],stream)
recordStatus = clinVarSet.xpath('RecordStatus[1]')
#if len(recordStatus) > 0 :
# stream.write('\tVP:RecordStatus "%s"^^xsd:string ;\n' % (recordStatus[0].text))
stream.write('.\t#ClinVarSet %s\n\n' % (ID))
def processSequenceLocation(sequence, stream = sys.stdout, tab = '\t'):
stream.write('%sVP:hasSequenceLocation\n' % (tab))
stream.write('%s\t [a\tVP:SequenceLocation;\n' % (tab));
if('Assembly' in sequence.attrib):
stream.write('%s\t\tVP:Assembly "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['Assembly'])))
if('Chr' in sequence.attrib):
stream.write('%s\t\tVP:Chr "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['Chr'])))
if('Accession' in sequence.attrib):
stream.write('%s\t\tVP:Accession "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['Accession'])))
if('outerStart' in sequence.attrib):
stream.write('%s\t\tVP:outerStart "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['outerStart'])))
if('innerStart' in sequence.attrib):
stream.write('%s\t\tVP:innerStart "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['innerStart'])))
if('start' in sequence.attrib):
stream.write('%s\t\tVP:start "%s"^^xsd:integer; \n' % (tab, safe_str(sequence.attrib['start'])))
if('stop' in sequence.attrib):
stream.write('%s\t\tVP:stop "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['stop'])))
if('innerStop' in sequence.attrib):
stream.write('%s\t\tVP:innerStop "%s"^^xsd:integer; \n' % (tab, safe_str(sequence.attrib['innerStop'])))
if('outerStop' in sequence.attrib):
stream.write('%s\t\tVP:outerStop "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['outerStop'])))
if('Strand' in sequence.attrib):
stream.write('%s\t\tVP:Strand "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['Strand'])))
if('variantLength' in sequence.attrib):
stream.write('%s\t\tVP:variantLength "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['variantLength'])))
if('referenceAllele' in sequence.attrib):
stream.write('%s\t\tVP:referenceAllele "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['referenceAllele'])))
if('AlternateAllele' in sequence.attrib):
stream.write('%s\t\tVP:AlternateAllele "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['AlternateAllele'])))
if('AssemblyAccessionVersion' in sequence.attrib):
stream.write('%s\t\tVP:AssemblyAccessionVersion "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['AssemblyAccessionVersion'])))
if('AssemblyStatus' in sequence.attrib):
stream.write('%s\t\tVP:AssemblyStatus "%s"^^xsd:string; \n' % (tab, safe_str(sequence.attrib['AssemblyStatus'])))
#stream.write('%s\t\tVP:Text "%s"^^xsd:string;\n' % (tab, sequence.text));
stream.write('%s\t];\t#Attribute\n' % (tab))
def processAttribute(attribute, stream = sys.stdout, tab = '\t'):
stream.write('%sVP:hasAttribute\n' % (tab))
stream.write('%s\t [a\tVP:Attribute;\n' % (tab))
if('Type' in attribute.attrib):
stream.write('%s\t\tVP:Type "%s"^^xsd:string; \n' % (tab, safe_str(attribute.attrib['Type'])))
if('Change' in attribute.attrib):
stream.write('%s\t\tVP:Change "%s"^^xsd:string; \n' % (tab, safe_str(attribute.attrib['Change'])))
stream.write('%s\t\tVP:Text "%s"^^xsd:string;\n' % (tab, safe_str(attribute.text)))
#stream.write('%s\t\trdfs:label "%s"^^xsd:string;\n' % (tab, safe_str(attribute.text)))
stream.write('%s\t];\t#Attribute\n' % (tab))
def processAttributeSet(attribtionSet, stream = sys.stdout, tab = '\t'):
stream.write('%sVP:hasAttributeSet\n' % (tab))
stream.write('%s\t [a\tVP:AttributeSet;\n' % (tab))
for attribute in attribtionSet.xpath('Attribute'):
processAttribute(attribute, stream, tab + '\t\t')
for citation in attribtionSet.xpath('Citation'):
processCitation(citation,stream,tab + '\t\t')
for reference in attribtionSet.xpath('XRef'):
processXRef(reference,stream,tab + '\t\t')
stream.write('%s\t];\t#AttribtionSet\n' % (tab))
def processMeasureRelationship(measureRelationship, stream = sys.stdout, tab = '\t'):
stream.write('%sVP:hasMeasuresRelationship\n' % (tab))
stream.write('%s\t [a\tVP:MeasureRelationship;\n' % (tab))
for symbol in measureRelationship.xpath('Symbol'):
processSymbol(symbol,stream,tab + '\t\t')
for name in measureRelationship.xpath('Name'):
processName(name,stream,tab + '\t\t')
for citation in measureRelationship.xpath('Citation'):
processCitation(citation,stream,tab + '\t\t')
for reference in measureRelationship.xpath('XRef'):
processXRef(reference,stream,tab + '\t\t')
stream.write('%s\t];\t#MeasureRelationship\n' % (tab))
def processMeasure(measure, stream = sys.stdout, tab = '\t'):
ID = ""
stream.write('%sVP:hasMeasures \n' % (tab))
stream.write('%s\t\t[a\tVP:Measure;\n' % (tab));
if('ID' in measure.attrib):
ID = safe_str(measure.attrib['ID'])
stream.write('%s\t\t\tVP:ID VP:CV_%s; \n' % (tab, ID))
if('Type' in measure.attrib):
stream.write('%s\t\t\tVP:MeasureType %s; \n' % (tab, MeasureType(safe_str(measure.attrib['Type']))))
stream.write('%s\t\t\trdfs:label "%s"^^xsd:string; \n' % (tab, safe_str(measure.attrib['Type'])))
for attributeSet in measure.xpath('AttributeSet'):
processAttributeSet(attributeSet,stream,tab + '\t\t\t')
for measureRelationship in measure.xpath('MeasureRelationship'):
processMeasureRelationship(measureRelationship,stream,tab + '\t\t\t')
for citation in measure.xpath('Citation'):
processCitation(citation,stream,tab + '\t\t\t')
for reference in measure.xpath('XRef'):
processXRef(reference,stream,tab + '\t\t\t')
for sequence in measure.xpath('SequenceLocation'):
processSequenceLocation(sequence,stream,tab + '\t\t\t')
stream.write('%s];\t #measure %s\n' % (tab,ID))
def MeasureType(measure):
if measure.startswith('Deletion'):
return "<http://purl.obolibrary.org/obo/SO_1000029>"
#Bret???
if measure.startswith('single nucleotide variant'):
return "VP:SingleNucleotideVariant"
if measure.startswith('Duplication"'):
return "<http://purl.obolibrary.org/obo/SO_1000038>"
if measure.startswith('Insert"'):
return "<http://purl.obolibrary.org/obo/SO_0000667>"
#Bret???
if measure.startswith('Indel"'):
return "VP:Indel"
#Bret???
if measure.startswith('Variation"'):
return "VP:Variation"
#translocation"
if measure.startswith('translocation"'):
return "<http://purl.obolibrary.org/obo/SO_1000035>"
#copy number loss - Bret
#copy number gain - - Bret
return '"%s"^^xsd:string' % measure
def processTrait(trait, stream = sys.stdout, tab = '\t'):
ID = ""
stream.write('%sVP:hasTraits \n' % (tab))
stream.write('%s\t\t[a\tVP:Trait;\n' % (tab))
if('ID' in trait.attrib):
ID = safe_str(trait.attrib['ID'])
stream.write('%s\t\t\tVP:ID VP:CV_%s; \n' % (tab, ID))
if('Type' in trait.attrib):
stream.write('%s\t\t\tVP:TraitType %s; \n' % (tab, TraitType(safe_str(trait.attrib['Type']))))
for citation in trait.xpath('Citation'):
processCitation(citation,stream,tab + '\t\t\t')
for symbol in trait.xpath('Symbol'):
processSymbol(symbol,stream,tab + '\t\t\t')
for name in trait.xpath('Name'):
processName(name,stream,tab + '\t\t\t')
for xref in trait.xpath('XRef'):
processXRef(xref,stream,tab +'\t\t\t')
stream.write('%s];\t #Trait %s\n' % (tab,ID))
def TraitType(trait):
if trait.startswith('Disease'):
return "VP:Disease"
if trait.startswith('Drug'):
return "VP:DrugResponse"
return "VP:%s" % trait
def getDBCitation(db,id, stream):
if db == 'Gene':
return '"%s"^^xsd:string' % (id)
if db == 'OMIM':
if special_match_num(id):
return '"%s"^^xsd:string' % (id)
else:
return ""
#SNOMED CT
if db == 'PubMed':
return "<http://www.ncbi.nlm.nih.gov/%s>" % (id)
if db == 'dbSNP':
return id
def processCitation(citation, stream = sys.stdout, tab = '\t'):
source = ''
id = citation.xpath('ID')
url = citation.xpath('URL')
citationText = citation.xpath('CitationText')
if len(id) > 0:
source = safe_str(id[0].attrib['Source'])
stream.write('%sVP:hasCitation \n' % (tab))
if source == 'PubMed':
stream.write('%s\t [a\tVP:PubMed;\n' % (tab))
if len(id) > 0:
stream.write('%s\t\t VP:ID <http://www.ncbi.nlm.nih.gov/pubmed/%s>;\n' % (tab, safe_str(id[0].text)))
if 'Source' in id[0].attrib :
stream.write('%s\t\t VP:Source "%s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source'])))
stream.write('%s\t\trdfs:label "%s : %s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source']), safe_str(id[0].text)))
elif source == 'pmc':
stream.write('%s\t [a\tVP:PMC;\n' % (tab))
if len(id) > 0:
stream.write('%s\t\t VP:ID <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC%s>;\n' % (tab, safe_str(id[0].text)))
if 'Source' in id[0].attrib :
stream.write('%s\t\t VP:Source "%s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source'])))
stream.write('%s\t\trdfs:label "%s : %s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source']), safe_str(id[0].text)))
elif source == 'OMIM':
stream.write('%s\t [a\tVP:OMIM;\n' % (tab))
if len(id) > 0:
stream.write('%s\t\t VP:ID <http://www.omim.org/entry/%s>;\n' % (tab, safe_str(id[0].text)))
if 'Source' in id[0].attrib :
stream.write('%s\t\t VP:Source "%s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source'])))
stream.write('%s\t\trdfs:label "%s : %s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source']), safe_str(id[0].text)))
else:
stream.write('%s\t [a\tVP:Citation;\n' % (tab))
if 'Abbrev' in citation.attrib :
stream.write('%s\t\t VP:Abbrev "%s"^^xsd:string;\n' % (tab, safe_str(citation.attrib['Abbrev'])))
if len(id) > 0:
if 'Source' in id[0].attrib :
stream.write('%s\t\t VP:Source "%s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source'])))
stream.write('%s\t\trdfs:label "%s : %s"^^xsd:string;\n' % (tab, safe_str(id[0].attrib['Source']), safe_str(id[0].text)))
stream.write('%s\t\t VP:ID "%s"^^xsd:string;\n' % (tab, safe_str(id[0].text)))
if 'Type' in citation.attrib :
stream.write('%s\t\t VP:Type %s;\n' % (tab, citationType(safe_str(citation.attrib['Type']))))
else:
stream.write('%s\t\t VP:Type VP:General;\n' % (tab))
#stream.write('%s\t\t VP:Type "%s"^^xsd:string;\n' % (tab, safe_str(citation.attrib['Type'])))
if len(url) > 0 :
stream.write('%s\t\t VP:URL <%s>;\n' % (tab, url[0].text))
if len(citationText) > 0:
stream.write('%s\t\t VP:CitationText "%s"^^xsd:string;\n' % (tab, citationText[0].text))
stream.write('%s\t];\t#Citation\n' % (tab))
def citationType(citation):
if citation.startswith('Translational'):
return "VP:Translational"
if citation.startswith('review'):
return "VP:Review"
if citation.startswith('PracticeGuideline'):
return "VP:practice"
return "VP:General"
def processSymbol(symbol, stream = sys.stdout, tab = '\t'):
stream.write('%sVP:hasSymbols \n' % (tab))
stream.write('%s\t[a\tVP:Symbol;\n' % (tab))
for xref in symbol.xpath('XRef'):
processXRef(xref,stream,tab + '\t\t')
element = symbol.xpath("ElementValue[1]")
if len(element) > 0 :
if 'Type' in element[0].attrib :
#stream.write('%s\t\tVP:Type "%s"^^xsd:string;\n' % (tab, safe_str(element[0].attrib['Type'])))
stream.write('%s\t\tVP:Type %s;\n' % (tab, visumpointGene.ontologyClass(safe_str(element[0].attrib['Type']))))
stream.write('%s\t\tVP:ID %s;\n' % (tab,visumpointGene.symbol(visumpointGene.strip(safe_str(element[0].text)))))
stream.write('%s\t\tVP:Text "%s"^^xsd:string;\n' % (tab, safe_str(element[0].text)))
stream.write('%s\t\trdfs:label "%s"^^xsd:string;\n' % (tab, safe_str(element[0].text)))
stream.write('%s\t\tskos:prefLabel "%s"^^xsd:string;\n' % (tab, safe_str(element[0].text)))
stream.write('%s\t];\t#Symbol\n' % (tab))
def getDBReferenceNamespace(db):
if db == 'Gene':
return 'GN'
if db == 'OMIM':
return 'OMIM'
#SNOMED CT
if db == 'SNOMED CT':
return 'SCT'
if db == 'dbSNP':
return 'dbSNP'
#Office of Rare Diseases
if db == 'Office of Rare Diseases':
return 'ORD'
#MedGen
if db == 'MedGen':
return 'MG'
#GeneReviews
if db == 'GeneReviews':
return 'GR'
#'Genetic Alliance'
if db == 'Genetic Alliance':
return ''
# 'Orphanet'
if db == 'Orphanet':
return 'OR'
# 'Sequence Ontology'
if db == 'Sequence Ontology':
return 'SO'
# 'Genetics Laboratory,Cambridge University Hospitals (Addenbrooke\\'s)'
if db.startswith('Genetics Laboratory,Cambridge') :
return 'GL'
if db.startswith('RefSeq') :
return 'RefSeq'
#dbVar
if db.startswith('dbVar') :
return 'dbVar'
# Molecular Diagnostic Laboratory,Greenwood Genetic Center
if db.startswith('Molecular Diagnostic Laboratory') :
return 'MDL'
#Human Phenotype Ontology
if db.startswith('Human Phenotype Ontology') :
return 'HP'
#GeneTests
if db.startswith('GeneTests') :
return 'GT'
#Genetics Home Reference
if db.startswith('Genetics Home Reference') :
return 'GH'
#Emory Genetics Laboratory
if db.startswith('Emory Genetics Laboratory') :
return 'EHL'
#Counsyl
if db.startswith('Counsyl') :
return 'CL'
#Department of Clinical Immunology,Odense University Hospital
if db.startswith('Department of Clinical Immunology,Odense University Hospital') :
return 'DCL'
#MeSH
if db.startswith('MeSH') :
return 'MeSH'
#Clinical Genomics,Maastricht University Medical Centre
if db.startswith('Clinical Genomics,Maastricht University Medical Centre'):
return 'CGM'
#Michigan Medical Genetics Laboratories,University of Michigan
if db.startswith('Michigan Medical Genetics Laboratories,University of Michigan'):
return 'MMG'
#InSiGHT
if db.startswith('InSiGHT') :
return 'IS'
#1234:Genetics Laboratory
if db.startswith('1234:Genetics Laboratory') :
return 'GL'
print(">>>>>>>>>>>>> %s" % (db))
return ''
def getDBReferenceDEAD(db,id):
if db == 'Gene':
return id
if db == 'OMIM':
return id
#SNOMED CT
if db == 'SCT':
return id
if db == 'dbSNP':
return id
#Office of Rare Diseases
if db == 'Office of Rare Diseases':
return id
#MedGen
if db == 'MG':
return id
#GeneReviews
if db == 'GeneReviews':
return '"%s"^^xsd:string' % (id)
if db.startswith('SO'):
return id
#return id[3:]
return '"%s : %s"^^xsd:string' % (db, id)
def getCleanDBID(db,id):
if db == 'Gene':
return id
if db == 'OMIM':
if special_match_num(id):
return id
else:
return ""
#SNOMED CT
if db == 'SNOMED CT':
return id
if db == 'dbSNP':
return id
#Office of Rare Diseases
if db == 'Office of Rare Diseases':
return id
#MedGen
if db == 'MG':
return id[2:]
#GeneReviews
if db == 'GeneReviews':
return '"%s"^^xsd:string' % (id)
if db.startswith('SO'):
return id[3:]
if db.startswith('HP'):
if id.startswith('HP'):
return "HP_%s" % (id[3:])
else:
return id
if db.startswith("RefSeq"):
return id[0:id.index(".")]
#return id[0:id.index(":")]
if db.startswith('DV'):
return id
if db.startswith('ORD'):
return id
if db.startswith('SCT'):
return id
if db.startswith('MDL'):
return id
if db.startswith('GR'):
return id
if db.startswith('OR'):
return id
if db.startswith('GN'):
return id
return ''
def getDBReference(db,id):
if db == 'Gene':
return '"%s"^^xsd:string' % (id)
if db == 'OMIM':
if special_match_num(id):
return '<%s/%s>' % (visumpointGene.OMIM,id)
else:
return ""
#SNOMED CT
if db == 'SNOMED CT' or db.startswith('SCT'):
return "<http://snomed.info/id/%s>" % (id)
if db == 'dbSNP':
return id
#Office of Rare Diseases
if db == 'Office of Rare Diseases':
return '"%s"^^xsd:string' % (id)
#MedGen
if db == 'MG':
return '"%s"^^xsd:string' % (id)
#GeneReviews
if db == 'GeneReviews':
return '"%s"^^xsd:string' % (id)
if db.startswith('SO'):
return '"%s"^^xsd:string' % (id[3:])
if db.startswith('HP'):
if id.startswith('HP'):
return "<http://purl.obolibrary.org/obo/HP_%s>" % (id[3:])
else:
return id
if db.startswith("RefSeq"):
return '"%s"^^xsd:string' % (id) #(id[0:id.index(".")])
if db.startswith('DV'):
return '"%s"^^xsd:string' % (id)
if db.startswith('ORD'):
return '"%s"^^xsd:string' % (id)
if db.startswith('MDL'):
return '"%s"^^xsd:string' % (id)
if db.startswith('GR'):
return '"%s"^^xsd:string' % (id)
if db.startswith('OR'):