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

Name	Value
label	Capture
subClassOf	http://www.w3.org/2002/07/owl#Thing
comment	A capture design

In range:

Type	Class	Property
owl:ObjectProperty	capture	range
owl:ObjectProperty	bed	domain
owl:DatatypeProperty	name	domain

**XML**: ```xml Capture A capture design ```

Class : Gender

Name	Value
label	Gender
label	Genre
subClassOf	http://www.w3.org/2002/07/owl#Thing
comment	Sample's gender

In range:

Type	Class	Property
owl:ObjectProperty	gender	range
owl:NamedIndividual	Undefined	type
owl:NamedIndividual	Male	type

**XML**: ```xml Gender Genre Sample's gender ```

Class : Project

Name	Value
label	Project
subClassOf	http://www.w3.org/2002/07/owl#Thing
comment	Placeholder for grouping BAM,VCF,Samples, ...

In range:

Type	Class	Property
owl:ObjectProperty	sample	domain
owl:DatatypeProperty	name	domain

**XML**: ```xml Project Placeholder for grouping BAM,VCF,Samples, ... ```

Class : Fastq

Name	Value
label	Fastq
subClassOf	File

In range:

Type	Class	Property
owl:ObjectProperty	sample	domain

**XML**: ```xml Fastq ```

Class : Reference

Name	Value
label	Reference
subClassOf	File
comment	Fasta Reference name indexed with samtools faidx

In range:

Type	Class	Property
owl:ObjectProperty	reference	range
owl:DatatypeProperty	buildVersion	domain
owl:DatatypeProperty	ncbiTaxonId	domain

**XML**: ```xml Reference Fasta Reference name indexed with samtools faidx ```

Class : Sample

Name	Value
label	Sample
subClassOf	http://www.w3.org/2002/07/owl#Thing
comment	A Sample sequenced, genotyped

In range:

Type	Class	Property
owl:ObjectProperty	gender	domain
owl:ObjectProperty	sample	range
owl:ObjectProperty	hasParent	domain
owl:ObjectProperty	hasParent	range
owl:DatatypeProperty	name	domain

**XML**: ```xml Sample A Sample sequenced, genotyped ```

Class : BED

Name	Value
label	BED
subClassOf	File

In range:

Type	Class	Property
owl:ObjectProperty	bed	range
owl:ObjectProperty	reference	domain

**XML**: ```xml BED ```

Class : Bam

Name	Value
label	Bam
subClassOf	File
comment	A BAM file sorted and indexed with samtools

In range:

Type	Class	Property
owl:ObjectProperty	capture	domain
owl:ObjectProperty	sample	domain
owl:ObjectProperty	reference	domain

**XML**: ```xml Bam A BAM file sorted and indexed with samtools ```

Class : File

Name	Value
label	File
subClassOf	http://www.w3.org/2002/07/owl#Thing

In range:

Type	Class	Property
owl:DatatypeProperty	path	domain
owl:Class	Fastq	subClassOf
owl:Class	Reference	subClassOf
owl:Class	BED	subClassOf
owl:Class	Bam	subClassOf
owl:Class	VCF	subClassOf

**XML**: ```xml File ```

Class : VCF

Name	Value
label	VCF
subClassOf	File
comment	A VCF file indexed with tabix

In range:

Type	Class	Property
owl:ObjectProperty	sample	domain
owl:ObjectProperty	reference	domain

**XML**: ```xml VCF A VCF file indexed with tabix ```

Properties

DataType Properties

DatatypeProperty : buildVersion

Name	Value
label	buildVersion
range	http://www.w3.org/2001/XMLSchema#token
subPropertyOf	http://www.w3.org/2002/07/owl#topDataProperty
domain	Reference

**XML**: ```xml buildVersion ```

DatatypeProperty : path

Name	Value
label	path
comment	The path to the file
range	http://www.w3.org/2001/XMLSchema#normalizedString
subPropertyOf	http://www.w3.org/2002/07/owl#topDataProperty
domain	File

**XML**: ```xml path The path to the file ```

DatatypeProperty : name

Name	Value
label	name
label	nom
range	http://www.w3.org/2001/XMLSchema#string
subPropertyOf	http://www.w3.org/2002/07/owl#topDataProperty
domain	Capture
domain	Project
domain	Sample

**XML**: ```xml name nom ```

DatatypeProperty : ncbiTaxonId

Name	Value
label	ncbiTaxonId
range	http://www.w3.org/2001/XMLSchema#positiveInteger
subPropertyOf	http://www.w3.org/2002/07/owl#topDataProperty
domain	Reference

**XML**: ```xml ncbiTaxonId ```

Object Properties

ObjectProperty : gender

Name	Value
label	gender
subPropertyOf	http://www.w3.org/2002/07/owl#topObjectProperty
range	Gender
domain	Sample

**XML**: ```xml gender ```

ObjectProperty : capture

Name	Value
label	capture
comment	Associated design for exome capture
subPropertyOf	http://www.w3.org/2002/07/owl#topObjectProperty
range	Capture
domain	Bam

**XML**: ```xml capture Associated design for exome capture ```

ObjectProperty : sample

Name	Value
label	sample
comment	Link to a Sample
subPropertyOf	http://www.w3.org/2002/07/owl#topObjectProperty
domain	Project
domain	Fastq
range	Sample
domain	Bam
domain	VCF

**XML**: ```xml sample Link to a Sample ```

ObjectProperty : bed

Name	Value
label	bed
comment	Associated BED file
subPropertyOf	http://www.w3.org/2002/07/owl#topObjectProperty
domain	Capture
range	BED

**XML**: ```xml bed Associated BED file ```

ObjectProperty : hasMother

Name	Value
label	hasMother
subPropertyOf	hasParent

**XML**: ```xml hasMother ```

ObjectProperty : reference

Name	Value
label	reference
comment	Associated Reference
subPropertyOf	http://www.w3.org/2002/07/owl#topObjectProperty
range	Reference
domain	BED
domain	Bam
domain	VCF

**XML**: ```xml reference Associated Reference ```

ObjectProperty : hasParent

Name	Value
label	hasParent
subPropertyOf	http://www.w3.org/2002/07/owl#topObjectProperty
domain	Sample
range	Sample

In range:

Type	Class	Property
owl:ObjectProperty	hasMother	subPropertyOf
owl:ObjectProperty	hasFather	subPropertyOf

**XML**: ```xml hasParent ```

ObjectProperty : hasFather

Name	Value
label	hasFather
subPropertyOf	hasParent

**XML**: ```xml hasFather ```

NamedIndividual

NamedIndividual : Recalibrate

Name	Value
label	Recalibrate

**XML**: ```xml Recalibrate ```

NamedIndividual : ****

Name	Value

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

NamedIndividual : RealignAroundIndels

Name	Value
label	RealignAroundIndels

**XML**: ```xml RealignAroundIndels ```

NamedIndividual : Undefined

Name	Value
type	Gender
label	Undefined

**XML**: ```xml Undefined ```

NamedIndividual : Male

Name	Value
type	Gender
label	Male
isDefinedBy	https://en.wikipedia.org/wiki/Male

**XML**: ```xml Male ```

NamedIndividual : MarkDuplicates

Name	Value
label	MarkDuplicates

**XML**: ```xml MarkDuplicates ```