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 |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | capture | range |
owl:ObjectProperty | bed | domain |
owl:DatatypeProperty | name | domain |
Class : Gender
Name | Value |
---|---|
label | Gender |
label | Genre |
subClassOf | http://www.w3.org/2002/07/owl#Thing |
comment | Sample's gender |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | gender | range |
owl:NamedIndividual | Undefined | type |
owl:NamedIndividual | Male | type |
Class : Project
Name | Value |
---|---|
label | Project |
subClassOf | http://www.w3.org/2002/07/owl#Thing |
comment | Placeholder for grouping BAM,VCF,Samples, ... |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | sample | domain |
owl:DatatypeProperty | name | domain |
Class : Fastq
Name | Value |
---|---|
label | Fastq |
subClassOf | File |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | sample | domain |
Class : Reference
Name | Value |
---|---|
label | Reference |
subClassOf | File |
comment | Fasta Reference name indexed with samtools faidx |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | reference | range |
owl:DatatypeProperty | buildVersion | domain |
owl:DatatypeProperty | ncbiTaxonId | domain |
Class : Sample
Name | Value |
---|---|
label | Sample |
subClassOf | http://www.w3.org/2002/07/owl#Thing |
comment | A Sample sequenced, genotyped |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | gender | domain |
owl:ObjectProperty | sample | range |
owl:ObjectProperty | hasParent | domain |
owl:ObjectProperty | hasParent | range |
owl:DatatypeProperty | name | domain |
Class : BED
Name | Value |
---|---|
label | BED |
subClassOf | File |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | bed | range |
owl:ObjectProperty | reference | domain |
Class : Bam
Name | Value |
---|---|
label | Bam |
subClassOf | File |
comment | A BAM file sorted and indexed with samtools |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | capture | domain |
owl:ObjectProperty | sample | domain |
owl:ObjectProperty | reference | domain |
Class : File
Name | Value |
---|---|
label | File |
subClassOf | http://www.w3.org/2002/07/owl#Thing |
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 |
Class : VCF
Name | Value |
---|---|
label | VCF |
subClassOf | File |
comment | A VCF file indexed with tabix |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | sample | domain |
owl:ObjectProperty | reference | domain |
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 |
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 |
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 |
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 |
Object Properties
ObjectProperty : gender
Name | Value |
---|---|
label | gender |
subPropertyOf | http://www.w3.org/2002/07/owl#topObjectProperty |
range | Gender |
domain | Sample |
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 |
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 |
ObjectProperty : bed
Name | Value |
---|---|
label | bed |
comment | Associated BED file |
subPropertyOf | http://www.w3.org/2002/07/owl#topObjectProperty |
domain | Capture |
range | BED |
ObjectProperty : hasMother
Name | Value |
---|---|
label | hasMother |
subPropertyOf | hasParent |
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 |
ObjectProperty : hasParent
Name | Value |
---|---|
label | hasParent |
subPropertyOf | http://www.w3.org/2002/07/owl#topObjectProperty |
domain | Sample |
range | Sample |
Type | Class | Property |
---|---|---|
owl:ObjectProperty | hasMother | subPropertyOf |
owl:ObjectProperty | hasFather | subPropertyOf |
ObjectProperty : hasFather
Name | Value |
---|---|
label | hasFather |
subPropertyOf | hasParent |
NamedIndividual
NamedIndividual : Recalibrate
Name | Value |
---|---|
label | Recalibrate |
NamedIndividual : ****
Name | Value |
---|
NamedIndividual : RealignAroundIndels
Name | Value |
---|---|
label | RealignAroundIndels |
NamedIndividual : Undefined
Name | Value |
---|---|
type | Gender |
label | Undefined |
NamedIndividual : Male
Name | Value |
---|---|
type | Gender |
label | Male |
isDefinedBy | https://en.wikipedia.org/wiki/Male |
NamedIndividual : MarkDuplicates
Name | Value |
---|---|
label | MarkDuplicates |