jPOST RDF Ontology
type: Ontology
imports: sio-release.owl
creator: Yuki Moriya
description: jPOST RDF ontology
license: http://creativecommons.org/publicdomain/zero/1.0/
version info: 0.13

cell line
type: ObjectProperty
domain: Sample
range: Cell line
description: Property that describes the cell line of sample.

disease
type: ObjectProperty
domain: Sample
description: Property that describes the disease of sample.

disease class
type: ObjectProperty
domain: Sample
description: Property that describes the disease class of sample.

enzyme
type: ObjectProperty
domain: Enzyme/Modification
range: Enzyme
description: Property that describes the used enzyme to convert proteins into peptides

fixed modification
type: ObjectProperty
domain: Enzyme/Modification
range: Fixed modification
description: Property that describes the amino acid mass modifications applied universally.

has database sequence
type: ObjectProperty
domain: Protein
comment: has protein sequence entry in database.

has dataset
type: ObjectProperty
range: jPOST dataset
comment: jPOST project has a dataset.

has enzyme/modification
type: ObjectProperty
domain: Profile
range: Enzyme/Modification

has fractionation
type: ObjectProperty
domain: Profile
range: Fractionation

has fractionation type
type: ObjectProperty
domain: Fractionation
range: Fractionation type

has indistinguishable peptide at MS level
type: ObjectProperty
domain: Unique peptide
range: Unique peptide

has leading protein
type: ObjectProperty
domain: Protein
range: Protein

has modification
type: ObjectProperty
domain: Peptide
range: UNIMOD_0
range: MOD_00000
comment: amino acid sequence has a modification.

has LC/MS/MS mode
type: ObjectProperty
domain: Profile
range: MS instrument mode

has peptide
type: ObjectProperty
domain: Class
  union of: jPOST dataset
  union of: Peptide evidence
range: Peptide
comment: Dataset and peptide evidence has a peptide.

has peptide evidence
type: ObjectProperty
domain: Protein
range: Peptide evidence

has plex
type: ObjectProperty
domain: Profile
range: Plex

has profile
type: ObjectProperty
domain: Class
  union of: jPOST dataset
  union of: Raw data
range: Profile

has protein
type: ObjectProperty
domain: jPOST dataset
range: Protein
comment: Dataset has a protein.

has PSM
type: ObjectProperty
range: Peptide spectrum match
comment: Peptide has a PSM

has raw data
type: ObjectProperty
range: Raw data
comment: jPOST project has a LC-MS/MS raw data.

has sample
type: ObjectProperty
domain: Profile
range: Sample

has sequence
type: ObjectProperty
domain: Class
  union of: Peptide
  union of: Protein
comment: has amino acid sequence.

has spectrum
type: ObjectProperty
range: Spectrum
comment: PSM has a spectrum

in plex
type: ObjectProperty
domain: Relative quantitative value
range: Plex

in protein group
type: ObjectProperty
domain: Protein
range: Protein group
comment: Pataset in a protein group.

in raw data
type: ObjectProperty
range: Raw data
comment: Peptide in a LC-MS/MS raw data.

instrument
type: ObjectProperty
domain: Class
  union of: jPOST dataset
  union of: MS instrument mode
description: Property that describes instrument on which the data has been generated.

instrument mode
type: ObjectProperty
domain: MS instrument mode
range: Instrument mode
description: Property that describes the mode of mass spectrometer.

instrument purpose
type: ObjectProperty
domain: MS instrument mode
range: Instrument purpose
description: Property that describes the purpose of mass spectrometry.

modification class
type: ObjectProperty
range: Modifiaction class
description: Property that describes the modification type.

organ
type: ObjectProperty
domain: Sample
range: Organ
description: Property that describes the organ of sample.

quantification method
type: ObjectProperty
domain: MS instrument mode
range: Quantification platform
description: Property that describes the platform of quantification method.
description: Property that describes the quantification method.
label: quantification platform

representative PSM
type: ObjectProperty
domain: Peptide spectrum match
range: boolean
description: Representative PSM flag in a peptide sequence-level

sample type
type: ObjectProperty
domain: Sample
range: Sample type
description: Property that describes the sample type of sample.

species
type: ObjectProperty
domain: Class
  union of: jPOST dataset
  union of: Enzyme/Modification
  union of: Sample
description: Property that describes the species from which the data has been generated.

tissue
type: ObjectProperty
domain: Sample
range: Tissue
description: Property that describes the tissue of sample.

variable modification
type: ObjectProperty
domain: Enzyme/Modification
range: Variable modification
description: Property that describes the possible amino acid mass modifications

has post residue
type: DatatypeProperty
domain: Peptide evidence
range: string
comment: post residue of matched region

has pre residue
type: DatatypeProperty
domain: Peptide evidence
range: string
comment: pre residue of matched region

modification site
type: DatatypeProperty
range: string
description: Property that describes the amino acid mass modifications site.

fractions
type: DatatypeProperty
domain: Fractionation type
range: integer
description: Property describes the number of fractions.

replicates
type: DatatypeProperty
domain: Fractionation type
range: integer
description: Property describes the number of replicates.

plex number
type: DatatypeProperty
domain: MS instrument mode
range: integer
description: Property that describes the number of plex.

Absolute quantitative value
type: Class
subclass of: Quantitative value

Calculated mass-to-charge ratio
type: Class
subclass of: Mass-to-charge ratio
description: Calculated monoisotopic mass[obo:MS_1000225]-to-charge[obo:MS_1000041] ratio of mass spectrum.

Cell line
type: Class
subclass of: Sample
description: cell line of sample.

jPOST dataset
type: Class
subclass of: jPOST entry
subclass of: SIO_000089
description: a jPOST entry describing a dataset.

Dataset statistic
type: Class
description: Statistic of proteomics dataset

Disease
type: Class
subclass of: Sample
description: disease type of sample.

Enzyme
type: Class
subclass of: Enzyme/Modification
description: a used enzyme to convert proteins into peptides.

Enzyme/Modification
type: Class
subclass of: Profile
description: metadata of enzymes and modifications.

Experimental mass-to-charge ratio
type: Class
subclass of: Mass-to-charge ratio
description: Experimental monoisotopic mass[obo:MS_1000225]-to-charge[obo:MS_1000041] ratio of mass spectrum.

Fixed modification
type: Class
subclass of: Modification type
description: an amino acid mass modification applied universally.

Fractionation
type: Class
subclass of: Profile
description: metadata of sample fractionation processes.

Fractionation type
type: Class
subclass of: Fractionation
description: fractionation process type, such as subcellular, protein and peptide-level.

Subcellular fractionation
type: Class
subclass of: Fractionation type
description: subcellular-level fractionation process.

Protein fractionation
type: Class
subclass of: Fractionation type
description: protein-level fractionation process.

Peptide fractionation
type: Class
subclass of: Fractionation type
description: peptide-level fractionation process.

Instrument mode
type: Class
subclass of: MS instrument mode
description: instrument mode of mass spectromerter.

Instrument purpose
type: Class
subclass of: MS instrument mode
description: purpose of mass spectrometry.

jPOST controlled vocabulary
type: Class
description: root node for terms relating to the description of jPOST.

Instrument mode vocabulary
type: Class
subclass of: jPOST controlled vocabulary
description: root node for terms relating to the description of instrument modes.

Purpose vocabulary
type: Class
subclass of: jPOST controlled vocabulary
description: root node for terms relating to the description of instrument purposes.

Quantification platform vocabulary
type: Class
subclass of: jPOST controlled vocabulary
description: root node for terms relating to the description of quntification platforms.

DDA-high res.
type: Class
subclass of: Instrument mode vocabulary
type: NamedIndividual
type: Instrument mode
description: Data-dependent acquisition high resoluiton mode of mass spectrometer.

DDA-low res.
type: Class
subclass of: Instrument mode vocabulary
type: NamedIndividual
type: Instrument mode
description: Data-dependent acquisition low resoluiton mode of mass spectrometer.

DIA
type: Class
subclass of: Instrument mode vocabulary
type: NamedIndividual
type: Instrument mode
description: Data-independent acquisition mode of mass spectrometer.

Target
type: Class
subclass of: Instrument mode vocabulary
type: NamedIndividual
type: Instrument mode
description: Target mode of mass spectrometer.

Qualification
type: Class
subclass of: Purpose vocabulary
type: NamedIndividual
type: Instrument purpose

Absolute quantification
type: Class
subclass of: Purpose vocabulary
type: NamedIndividual
type: Instrument purpose

Relative quantification
type: Class
subclass of: Purpose vocabulary
type: NamedIndividual
type: Instrument purpose

Spectra count
type: Class
subclass of: Quantification platform vocabulary
type: NamedIndividual
type: Quantification platform

Precursor ion label free
type: Class
subclass of: Quantification platform vocabulary
type: NamedIndividual
type: Quantification platform

Precursor ion stable isotope labeling
type: Class
subclass of: Quantification platform vocabulary
type: NamedIndividual
type: Quantification platform

Product ion (reporter quantification)
type: Class
subclass of: Quantification platform vocabulary

Fragment ion (stable isotope labeling)
type: Class
subclass of: Quantification platform vocabulary
type: NamedIndividual
type: Quantification platform

Fragment ion (label-free)
type: Class
subclass of: Quantification platform vocabulary
type: NamedIndividual
type: Quantification platform

Sample vocabulary
type: Class
subclass of: jPOST controlled vocabulary
description: root node for terms relating to the description of sample.

Normal
type: Class
subclass of: Sample vocabulary
description: non-disease sample.

Other disease
type: Class
subclass of: Sample vocabulary
description: disease sample excludes cancer, nervous system disease, metabolic disease , cardiovascular system disease, infectious disease and immune system disease.

Modification class vocabulary
type: Class
subclass of: jPOST controlled vocabulary
description: root node for terms relating to the description of modification class based on unimod.

Post-translational
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Co-translational
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Pre-translational
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Chemical derivative
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Artefact
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

N-linked glycosylation
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

O-linked glycosylation
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Other glycosylation
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Synth. pep. protect. gp.
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Isotopic label
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Non-standard residue
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Multiple
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Other
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

AA substitution
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Cross-link
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

CID cleavable cross-link
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Photo cleavable cross-link
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Other cleavable cross-link
type: Class
subclass of: Modification class vocabulary
type: NamedIndividual
type: Modifiaction class

Unit
type: Class
subclass of: jPOST controlled vocabulary

Femtomole per picoliter
type: Class
subclass of: Unit
description: femtomole [obo:UO_0000043] per picoliter [obo:UO_0000103]
preferred label: fmol/pl

jPOST entry
type: Class
description: root node of jPOST entries.

jPOST score
type: Class
subclass of: Measurement value
description: jPOST result score for PSM

Mass-to-charge ratio
type: Class
subclass of: Measurement value
description: Mass[obo:MS_1000225]-to-charge[obo:MS_1000041] ratio of mass spectrum.

Matching type
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a matching ion type of PSM based on the sequence, PTMs and the charge, as a unit for calculating peptide FDR.

Measurement value
type: Class
description: Measurement value for mass spectrometry-based proteomics

Modification
type: Class
subclass of: jPOST entry
description: amin acid mass modification

Modifiaction class
type: Class
subclass of: Enzyme/Modification
description: A type of amino asid mass modification based on unimod

MS instrument mode
type: Class
subclass of: Profile
description: metadata of MS instrument.

Number of leading proteins
type: Class
subclass of: Dataset statistic
description: Number of leading protein (obo:MS_1002401) infered from proteins in a dataset

Number of matched proteins
type: Class
subclass of: Dataset statistic
description: Number of proteins matched with at least one peptide in a dataset

Number of peptides
type: Class
subclass of: Dataset statistic
description: Number of peptides in a dataset

Number of proteins with unique peptide
type: Class
subclass of: Dataset statistic
description: Number of proteins matched with at least one unique peptide in a dataset

Number of PSMs
type: Class
subclass of: Dataset statistic
description: Number of PSMs in a dataset

Number of raw data
type: Class
subclass of: Dataset statistic
description: Number of raw data in a dataset

Number of spectra
type: Class
subclass of: Dataset statistic
description: Number of spectra in a dataset

Organ
type: Class
subclass of: Sample
description: organ of sample.

Peptide area
type: Class
subclass of: Quantitative value
description: area of peptide spectrum for quntification

Peptide intensity
type: Class
subclass of: Quantitative value
description: intensity of peptide spectrum for quntification

Peptide
type: Class
subclass of: MS_1000860
subclass of: jPOST entry
description: a jPOST entry describing a peptide.

Peptide evidence
type: Class
subclass of: jPOST entry
description: a jPOST entry describing peptide evidence in mzIndentML.

Peptide spectrum match
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a peptide matched to spectrum.

Plex
type: Class
subclass of: Profile
description: plex information of multi-plex experiment

Profile
type: Class
subclass of: jPOST entry
description: Metadata of a experimental procedure.

jPOST project
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a project.

Protein
type: Class
subclass of: MS_1000882
subclass of: jPOST entry
description: a jPOST entry describing a protein.

Protein isoform
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a protein isoform in a dataset.

Protein group
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a protein group

Quantification platform
type: Class
subclass of: MS instrument mode
description: platform type for quantification.

Quantitative value
type: Class
subclass of: Measurement value

Raw data
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a raw data of mass spectrometer run.

Relative quantitative value
type: Class
subclass of: Quantitative value

Representative isoform
type: Class
subclass of: jPOST entry
description: a jPOST entry describing a representative isoform in a dataset.

Sample
type: Class
subclass of: Profile
description: metadata of a sample.

Sample type
type: Class
subclass of: Sample
description: sample type of sample.

Shared peptide
type: Class
subclass of: MS_1001175
subclass of: Peptide
description: Peptide shared in multiple database sequence

Shared peptide at MS level
type: Class
subclass of: SharedSequence
description: Peptide shared in multiple database sequence at MS level. (not distinguish leucine and isoleucine)

Spectrum
type: Class
subclass of: MS_1000442
subclass of: jPOST entry
description: a jPOST entry describing a spectrum of LC-MS/MS

Tissue
type: Class
subclass of: Sample
description: tissue of sample.

Unique peptide
type: Class
subclass of: MS_1001363
subclass of: Peptide
description: Peptide unique to one database sequence

Unique peptide at MS level
type: Class
subclass of: Unique peptide
description: Peptide unique to one database sequence at MS level. (not distinguish leucine and isoleucine)

Variable modification
type: Class
subclass of: Modification type
description: a possible amino acid mass modification.

Modification type
type: Class
subclass of: Enzyme/Modification
description: Experimental amino acid mass modification type in database search