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README.md

ngs-ontology

Ontology describing NGS experiments

Currently hosted on web-protege: http://webprotege.stanford.edu/#Edit:projectId=b4960e4f-b237-4261-bca1-5cd9869557af

Classes

Class : Capture

NameValue
labelCapture
subClassOfhttp://www.w3.org/2002/07/owl#Thing
commentA capture design
In range:
TypeClassProperty
owl:ObjectPropertycapturerange
owl:ObjectPropertybeddomain
owl:DatatypePropertynamedomain
**XML**: ```xml Capture A capture design ```

Class : Gender

NameValue
labelGender
labelGenre
subClassOfhttp://www.w3.org/2002/07/owl#Thing
commentSample's gender
In range:
TypeClassProperty
owl:ObjectPropertygenderrange
owl:NamedIndividualUndefinedtype
owl:NamedIndividualMaletype
**XML**: ```xml Gender Genre Sample's gender ```

Class : Project

NameValue
labelProject
subClassOfhttp://www.w3.org/2002/07/owl#Thing
commentPlaceholder for grouping BAM,VCF,Samples, ...
In range:
TypeClassProperty
owl:ObjectPropertysampledomain
owl:DatatypePropertynamedomain
**XML**: ```xml Project Placeholder for grouping BAM,VCF,Samples, ... ```

Class : Fastq

NameValue
labelFastq
subClassOfFile
In range:
TypeClassProperty
owl:ObjectPropertysampledomain
**XML**: ```xml Fastq ```

Class : Reference

NameValue
labelReference
subClassOfFile
commentFasta Reference name indexed with samtools faidx
In range:
TypeClassProperty
owl:ObjectPropertyreferencerange
owl:DatatypePropertybuildVersiondomain
owl:DatatypePropertyncbiTaxonIddomain
**XML**: ```xml Reference Fasta Reference name indexed with samtools faidx ```

Class : Sample

NameValue
labelSample
subClassOfhttp://www.w3.org/2002/07/owl#Thing
commentA Sample sequenced, genotyped
In range:
TypeClassProperty
owl:ObjectPropertygenderdomain
owl:ObjectPropertysamplerange
owl:ObjectPropertyhasParentdomain
owl:ObjectPropertyhasParentrange
owl:DatatypePropertynamedomain
**XML**: ```xml Sample A Sample sequenced, genotyped ```

Class : BED

NameValue
labelBED
subClassOfFile
In range:
TypeClassProperty
owl:ObjectPropertybedrange
owl:ObjectPropertyreferencedomain
**XML**: ```xml BED ```

Class : Bam

NameValue
labelBam
subClassOfFile
commentA BAM file sorted and indexed with samtools
In range:
TypeClassProperty
owl:ObjectPropertycapturedomain
owl:ObjectPropertysampledomain
owl:ObjectPropertyreferencedomain
**XML**: ```xml Bam A BAM file sorted and indexed with samtools ```

Class : File

NameValue
labelFile
subClassOfhttp://www.w3.org/2002/07/owl#Thing
In range:
TypeClassProperty
owl:DatatypePropertypathdomain
owl:ClassFastqsubClassOf
owl:ClassReferencesubClassOf
owl:ClassBEDsubClassOf
owl:ClassBamsubClassOf
owl:ClassVCFsubClassOf
**XML**: ```xml File ```

Class : VCF

NameValue
labelVCF
subClassOfFile
commentA VCF file indexed with tabix
In range:
TypeClassProperty
owl:ObjectPropertysampledomain
owl:ObjectPropertyreferencedomain
**XML**: ```xml VCF A VCF file indexed with tabix ```

Properties

DataType Properties

DatatypeProperty : buildVersion

NameValue
labelbuildVersion
rangehttp://www.w3.org/2001/XMLSchema#token
subPropertyOfhttp://www.w3.org/2002/07/owl#topDataProperty
domainReference
**XML**: ```xml buildVersion ```

DatatypeProperty : path

NameValue
labelpath
commentThe path to the file
rangehttp://www.w3.org/2001/XMLSchema#normalizedString
subPropertyOfhttp://www.w3.org/2002/07/owl#topDataProperty
domainFile
**XML**: ```xml path The path to the file ```

DatatypeProperty : name

NameValue
labelname
labelnom
rangehttp://www.w3.org/2001/XMLSchema#string
subPropertyOfhttp://www.w3.org/2002/07/owl#topDataProperty
domainCapture
domainProject
domainSample
**XML**: ```xml name nom ```

DatatypeProperty : ncbiTaxonId

NameValue
labelncbiTaxonId
rangehttp://www.w3.org/2001/XMLSchema#positiveInteger
subPropertyOfhttp://www.w3.org/2002/07/owl#topDataProperty
domainReference
**XML**: ```xml ncbiTaxonId ```

Object Properties

ObjectProperty : gender

NameValue
labelgender
subPropertyOfhttp://www.w3.org/2002/07/owl#topObjectProperty
rangeGender
domainSample
**XML**: ```xml gender ```

ObjectProperty : capture

NameValue
labelcapture
commentAssociated design for exome capture
subPropertyOfhttp://www.w3.org/2002/07/owl#topObjectProperty
rangeCapture
domainBam
**XML**: ```xml capture Associated design for exome capture ```

ObjectProperty : sample

NameValue
labelsample
commentLink to a Sample
subPropertyOfhttp://www.w3.org/2002/07/owl#topObjectProperty
domainProject
domainFastq
rangeSample
domainBam
domainVCF
**XML**: ```xml sample Link to a Sample ```

ObjectProperty : bed

NameValue
labelbed
commentAssociated BED file
subPropertyOfhttp://www.w3.org/2002/07/owl#topObjectProperty
domainCapture
rangeBED
**XML**: ```xml bed Associated BED file ```

ObjectProperty : hasMother

NameValue
labelhasMother
subPropertyOfhasParent
**XML**: ```xml hasMother ```

ObjectProperty : reference

NameValue
labelreference
commentAssociated Reference
subPropertyOfhttp://www.w3.org/2002/07/owl#topObjectProperty
rangeReference
domainBED
domainBam
domainVCF
**XML**: ```xml reference Associated Reference ```

ObjectProperty : hasParent

NameValue
labelhasParent
subPropertyOfhttp://www.w3.org/2002/07/owl#topObjectProperty
domainSample
rangeSample
In range:
TypeClassProperty
owl:ObjectPropertyhasMothersubPropertyOf
owl:ObjectPropertyhasFathersubPropertyOf
**XML**: ```xml hasParent ```

ObjectProperty : hasFather

NameValue
labelhasFather
subPropertyOfhasParent
**XML**: ```xml hasFather ```

NamedIndividual

NamedIndividual : Recalibrate

NameValue
labelRecalibrate
**XML**: ```xml Recalibrate ```

NamedIndividual : ****

NameValue
**XML**: ```xml ```

NamedIndividual : RealignAroundIndels

NameValue
labelRealignAroundIndels
**XML**: ```xml RealignAroundIndels ```

NamedIndividual : Undefined

NameValue
typeGender
labelUndefined
**XML**: ```xml Undefined ```

NamedIndividual : Male

NameValue
typeGender
labelMale
isDefinedByhttps://en.wikipedia.org/wiki/Male
**XML**: ```xml Male ```

NamedIndividual : MarkDuplicates

NameValue
labelMarkDuplicates
**XML**: ```xml MarkDuplicates ```

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