# Saved by TopBraid on Tue Nov 01 08:23:32 EET 2011
# baseURI: http://purl.org/varioml/pathogenicity/skos/1.0/
# imports: http://purl.org/dc/elements/1.1/
# imports: http://www.w3.org/2004/02/skos/core

@prefix dc:      <http://purl.org/dc/elements/1.1/> .
@prefix dct:     <http://purl.org/dc/terms/> .
@prefix owl:     <http://www.w3.org/2002/07/owl#> .
@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos:    <http://www.w3.org/2004/02/skos/core#> .
@prefix vml:     <http://purl.org/varioml/pathogenicity/skos/1.0/> .
@prefix xml:     <http://www.w3.org/XML/1998/namespace> .
@prefix xs:      <http://www.w3.org/2001/XMLSchema> .
@prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .

<http://purl.org/varioml/pathogenicity/skos/1.0/>
      rdf:type owl:Ontology ;
      owl:imports <http://www.w3.org/2004/02/skos/core> , <http://purl.org/dc/elements/1.1/> .

vml:p_9991
      rdf:type skos:TopConcept ;
      skos:inScheme vml:g2p , vml:cmgs_vgl_5, vml:acmg_2007 ;
      skos:prefLabel "Pathogenecity"@en .

# CMGS 5 concept scheme
#  1 Certainly not pathogenic
#  2 Unlikely to be pathogenic but cannot be formally proven
#  3 Likely to be pathogenic but cannot be formally proven
#  4 Certainly pathogenic
#  5 Unknown 


# http://demo.semantic-web.at:8080/SkosServices/check

vml:cmgs_vgl_5
      rdf:type skos:ConceptScheme ;
      dc:creator "Juha Muilu <juha.muilu@helsinki.fi>" ;
      dc:description "Pathogenicity terms adopted from Alamut. Terms are based on publication 'Practice guidelines for the Interpretation and Reporting of Unclassified Variants (UVs) in Clinical Molecular Genetics'" ;
      dc:title "CMGS_VGL_5 Pathogenicity terms" .

vml:p_0001
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:exactMatch vml:p_1001; # g2p non pathogenic
      skos:inScheme vml:cmgs_vgl_5 ;
      skos:prefLabel "Certainly not pathogenic"@en .

vml:p_0002
      rdf:type skos:Concept ;
      skos:prefLabel "Unlikely pathogenic"@en ;
      skos:broader vml:p_9991 ;
      skos:exactMatch vml:p_1004; # probably not pathogenic
      skos:inScheme vml:cmgs_vgl_5 ;
      skos:altLabel "Unlikely to be pathogenic but cannot be formally proven"@en .

vml:p_0003
      rdf:type skos:Concept ;
      skos:prefLabel "Likely pathogenic"@en ;
      skos:broader vml:p_9991 ;
      skos:exactMatch vml:p_1005; # probably pathgenic
      skos:inScheme vml:cmgs_vgl_5 ;
      skos:altLabel "Likely to be pathogenic but cannot be formally proven"@en .

vml:p_0004
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:exactMatch vml:p_1003; # pathogenic
      skos:inScheme vml:cmgs_vgl_5 ;
      skos:prefLabel "Certainly pathogenic"@en .


vml:p_0005
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:cmgs_vgl_5 ;
      skos:closeMatch vml:p_1006, vml:p_1002, vml:p_3001,vml:p3_3002; # unclassified and not-known
      skos:prefLabel "Unknown"@en .



vml:cmgs_vgkl_5_list
      rdf:type skos:OrderedCollection ;
      skos:memberList (vml:p_0001 vml:p_0002 vml:p_0003 vml:p_0004 vml:p_0005) .

#
# Gen2pen concept scheme
#
# Non-pathogenic
# Not known
# Pathogenic
# Probably not pathogenic
# Probably pathogenic
# Unclassified

vml:g2p
      rdf:type skos:ConceptScheme ;
      dc:creator "Juha Muilu <juha.muilu@helsinki.fi>" ;
      dc:description "Pathogenicity terms developed in gen2phen program based on the LOVD 2.0" ;
      dc:title "Gen2phen pathogenicity terms" .

vml:p_1001
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:hiddenLabel "Non patogenic"@en ;
      skos:inScheme vml:g2p ;
      skos:prefLabel "Non-pathogenic"@en .


vml:p_1002
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:hiddenLabel "Not-known"@en ;
      skos:inScheme vml:g2p ;
      dc:description "Variant is known but it not reported to be pathogenic" ;
      skos:altLabel "Not known to be pathogenic"@en ;
      skos:prefLabel "Not known"@en .

vml:p_1003
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:g2p ;
      skos:prefLabel "Pathogenic"@en .

vml:p_1004
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:prefLabel "Probably not pathogenic"@en ;
      skos:inScheme vml:g2p .

vml:p_1005
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:prefLabel "Probably pathogenic"@en ;
      skos:inScheme vml:g2p .

vml:p_1006
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:g2p ;
      dc:description "Variant is new and pathogenicity is unclassified" ;
      skos:prefLabel "Unclassified"@en .

vml:g2p_list
      rdf:type skos:OrderedCollection ;
      skos:memberList (vml:p_1001 vml:p_1002 vml:p_1003 vml:p_1004 vml:p_1005 vml:p_1006) .
      
      
vml:acmg_2007
      rdf:type skos:ConceptScheme ;
      dc:creator "Juha Muilu <juha.muilu@helsinki.fi>" ;
      dc:description "Pathogenicity terms defined in ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007" ;
      dc:bibliographicCitation "doi:10.1097/GIM.0b013e31816b5cae" ;
      dc:title "ACGM pathogenicity terms" .

vml:p_2001
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:acmg_2007 ;
      skos:exactMatch vml:p_1003; # pathogenic
#      skos:altLabel "Reported and recognized to be causative";
      skos:prefLabel "Sequence variation is previously reported and is a recognized cause of the disorder"@en .

vml:p_2002
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:acmg_2007 ;
      skos:exactMatch vml:p_1005; # probably pathogenic
#      skos:altLabel "Unreported and expected to be causative by type";
      skos:prefLabel "Sequence variation is previously unreported and is of the type which is expected to cause the disorder"@en .

vml:p_2003
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:acmg_2007 ;
      skos:exactMatch vml:p_1006 ; # unclassified
#      skos:altLabel "Unreported and pathogenicity is not known by type";
      skos:prefLabel "Sequence variation is previously unreported and is of the type which may or may not be causative of the disorder"@en .

vml:p_2004
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:acmg_2007 ;
      skos:closeMatch vml:p_1004  ; # g2p probably not pathogenic     
#      skos:altLabel "Unreported and probably not causative";
      skos:prefLabel "Sequence variation is previously unreported and is probably not causative of disease"@en .

vml:p_2005
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:exactMatch vml:p_1001 ; # g2p non pathogenic
      skos:inScheme vml:acmg_2007 ;
 #     skos:altLabel "Reported and recognized to be neutral";
      skos:prefLabel "Sequence variation is previously reported and is a recognized neutral variant"@en .

vml:p_2006
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:acmg_2007 ;
      skos:closeMatch vml:p_1004  ; # g2p probably not pathogenic     (can we  say this ? this not exactMatch )
  #    skos:altLabel "Not expected to be causative, but is accociated with clinical presentation";
      skos:prefLabel "Sequence variation is not known or expected to be causative of disease, but is found to be associated with a clinical presentation"@en .

vml:acmg_2007_list
      rdf:type skos:OrderedCollection ;
      skos:memberList (vml:p_2001 vml:p_2002 vml:p_2003 vml:p_2004 vml:p_2005 vml:p_2006) .
      

vml:dbsnp
      rdf:type skos:ConceptScheme ;
      dc:creator "Juha Muilu <juha.muilu@helsinki.fi>" ;
      dc:description "Clinical significance terms defined in dbSNP" ;
      dc:url "http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html";
      dc:bibliographicCitation "doi:10.1097/GIM.0b013e31816b5cae" ;
      dc:title "dbSNP - Clinical significance terms" .

vml:p_3001
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:prefLabel "unknown"@en .

vml:p_3002
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:prefLabel "untested"@en .

vml:p_3003
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:exactMatch vml:p_1001; # g2p non pathogenic
      skos:prefLabel "non-pathogenic"@en .

vml:p_3004
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:exactMatch vml:p_1004  ; # g2p probably not pathogenic     
      skos:prefLabel "probable-non-pathogenic"@en .

vml:p_3005
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:exactMatch vml:p_1005; # probably pathogenic
      skos:prefLabel "probable-pathogenic"@en .

vml:p_3006
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:exactMatch vml:p_1003; # pathogenic
      skos:prefLabel "pathogenic"@en .

vml:p_3007
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:prefLabel "drug-response"@en .

vml:p_3008
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:prefLabel "histocompatibility"@en .

vml:p_3009
      rdf:type skos:Concept ;
      skos:broader vml:p_9991 ;
      skos:inScheme vml:dbsnp ;
      skos:prefLabel "other"@en .

vml:dbsnp_list
      rdf:type skos:OrderedCollection ;
      skos:memberList (vml:p_3001 vml:p_3002 vml:p_3003 vml:p_3004 vml:p_3005 vml:p_3006 vml:p_3007 vml:p_3008 vml:p_3009) .