Ontology describing NGS experiments
Currently hosted on web-protege: http://webprotege.stanford.edu/#Edit:projectId=b4960e4f-b237-4261-bca1-5cd9869557af
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
```
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
```
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, ...
```
Name | Value |
---|
label | Fastq |
subClassOf | File |
In range:
Type | Class | Property |
---|
owl:ObjectProperty | sample | domain |
**XML**:
```xml
Fastq
```
Name | Value |
---|
label | Reference |
subClassOf | File |
comment | Fasta Reference name indexed with samtools faidx |
In range:
**XML**:
```xml
Reference
Fasta Reference name indexed with samtools faidx
```
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
```
Name | Value |
---|
label | BED |
subClassOf | File |
In range:
Type | Class | Property |
---|
owl:ObjectProperty | bed | range |
owl:ObjectProperty | reference | domain |
**XML**:
```xml
BED
```
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
```
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
```
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
```
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
```
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
```
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
```
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
```
Name | Value |
---|
label | gender |
subPropertyOf | http://www.w3.org/2002/07/owl#topObjectProperty |
range | Gender |
domain | Sample |
**XML**:
```xml
gender
```
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
```
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
```
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
```
Name | Value |
---|
label | hasMother |
subPropertyOf | hasParent |
**XML**:
```xml
hasMother
```
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
```
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
```
Name | Value |
---|
label | hasFather |
subPropertyOf | hasParent |
**XML**:
```xml
hasFather
```
Name | Value |
---|
label | Recalibrate |
**XML**:
```xml
Recalibrate
```
**XML**:
```xml
```
Name | Value |
---|
label | RealignAroundIndels |
**XML**:
```xml
RealignAroundIndels
```
Name | Value |
---|
type | Gender |
label | Undefined |
**XML**:
```xml
Undefined
```
**XML**:
```xml
Male
```
Name | Value |
---|
label | MarkDuplicates |
**XML**:
```xml
MarkDuplicates
```