View source for HCLS/OntologyTaskForce/SeedOntology

__NOTOC__
'''Seed Ontology for Bench to Bedside Ontology (Cellular and Molecular Biologist View)'''

[[Media:HCLS$$OntologyTaskForce$$SeedOntology$ParkinsonsDisease.owl|OWL Version of Parkinson's Disease Ontology]] <br>
Currently '''LOCK''' with [mailto:vkashyap1@partners.org Vipul Kashyap] <br>
Please request the lock from the current holder '''BEFORE''' making changes to this ontology.

This is the latest version of the ontology dated '''27th September 2006'''

[[BillBug]] (2006-09-05): added a [[/SeedOntologyDetailedFollowup|page]] that includes:
* research article references for each specific entity specified here
* a [http://www.fruitfly.org/~cjm/obd/pheno-syntax.html OBO Phenotype Syntax]-styled formal description of some of the statements made in these articles that make reference to these entities making use of the [http://bioontology.org/wiki/index.php/PATO:About Ontology of Phenotypic Qualities].

The current version of the ontology looks like:

Class [[AllelicVariant]]
         subClassOf: owl:Thing
  Class [[AlphaSynuclein]]
         subClassOf: Gene
  Class [[AnatomicalEntity]]
         subClassOf: owl:Thing
  Class [[BioMarker]]
         subClassOf: owl:Thing
  Class Brain
         subClassOf: Organ
  Class Cell
         subClassOf: [[MaterialAnatomicalEntity]]
  Class [[CellularComponent]]
         subClassOf: [[MaterialAnatomicalEntity]]
  Class [[CellularPathway]]
         subClassOf: Pathway
  Class [[CellularStudy]]
         subClassOf: Study
  Class [[CerebellarCortex]]
         subClassOf: [[GrossAnatomicalCerebellumPart]]
  Class [[CerebellarCortexLobePart]]
         subClassOf: [[RegionalCerebellarCortexPart]]
  Class [[CerebellarCortexLobularPart]]
         subClassOf: [[RegionalCerebellarCortexPart]]
  Class [[CerebellarHemisphere]]
         subClassOf: [[RegionalCerebellarCortexPart]]
  Class [[CerebellarPurkinjeNeuron]]
         subClassOf: [[PurkinjeNeuron]]
  Class [[CerebellarWhiteMatter]]
         subClassOf: [[GrossAnatomicalCerebellumPart]]
  Class Cerebellum
         subClassOf: [[RegionalBrainPart]]
  Class [[CerebralPeduncle]]
         subClassOf: [[RegionalMidBrainPart]]
  Class CTerminalHydrolase-1
         subClassOf: [[MacroMolecule]]
  Class [[CytoarchitecturalCerbellumPart]]
         subClassOf: [[RegionalCerebellumPart]]
  Class [[CytoarchitecturalCerebellarCortexPart]]
         subClassOf: [[CytoarchitecturalCerbellumPart]]
  Class [[CytosolicProteasomeComplex]]
         subClassOf: [[CellularComponent]]
  Class Dardarin
         subClassOf: Protein
  Class [[DeepCerebellarNuclei]]
         subClassOf: [[GrossAnatomicalCerebellumPart]]
  Class Dementia
         subClassOf: Disease
  Class Disease
         subClassOf: owl:Thing
  Class DJ-1
         subClassOf: Protein
  Class [[DopaminergicNeuron]]
         subClassOf: Neuron
  Class [[E3Ligase]]
         subClassOf: Protein
  Class Gene
         subClassOf: owl:Thing
  Class Glucocerebrosidase
         subClassOf: [[MacroMolecule]]
  Class [[GrossAnatomicalCerebellumPart]]
         subClassOf: [[RegionalCerebellumPart]]
  Class [[LewyBody]]
         subClassOf: [[NonCellularStructure]]
  Class LRRK2
         subClassOf: Gene
  Class LRRK2Variant
         subClassOf: [[AllelicVariant]]
  Class [[MacroMolecule]]
         subClassOf: [[MaterialAnatomicalEntity]]
  Class [[MaterialAnatomicalEntity]]
         subClassOf: [[AnatomicalEntity]]
  Class [[MidBrain]]
         subClassOf: [[RegionalBrainPart]]
  Class [[NeuromelaninPigmentedCell]]
         subClassOf: Neuron
  Class Neuron
         subClassOf: Cell
  Class Neuropil
         subClassOf: [[SupraCellularStructure]]
  Class [[NonCellularStructure]]
         subClassOf: [[MaterialAnatomicalEntity]]
  Class Organ
         subClassOf: [[MaterialAnatomicalEntity]]
  Class Parkin
         subClassOf: Protein
  Class [[ParkinGene]]
         subClassOf: Gene
  Class [[ParkinsonsDisease]]
         subClassOf: Disease
  Class [[ParsCompacta]]
         subClassOf: [[RegionalSubstantiaNigraPart]]
  Class [[ParsReticulata]]
         subClassOf: [[RegionalSubstantiaNigraPart]]
  Class Pathway
         subClassOf: owl:Thing
  Class Patient
         subClassOf: owl:Thing
  Class PINK-1
         subClassOf: Protein
  Class Protein
         subClassOf: owl:Thing
  Class [[ProteosomalPathway]]
         subClassOf: Pathway
  Class [[PurkinjeNeuron]]
         subClassOf: Neuron
  Class [[RegionalBrainPart]]
         subClassOf: [[RegionalOrganPart]]
  Class [[RegionalCerebellarCortexPart]]
         subClassOf: [[DeepCerebellarNuclei]]
  Class [[RegionalCerebellumPart]]
         subClassOf: [[RegionalBrainPart]]
  Class [[RegionalCerebralPedunclePart]]
         subClassOf: [[RegionalMidBrainPart]]
  Class [[RegionalMidBrainPart]]
         subClassOf: [[RegionalBrainPart]]
  Class [[RegionalOrganPart]]
         subClassOf: [[MaterialAnatomicalEntity]]
  Class [[RegionalSubstantiaNigraPart]]
         subClassOf: [[RegionalCerebralPedunclePart]]
  Class Sample
         subClassOf: owl:Thing
  Class Study
         subClassOf: owl:Thing
  Class [[SubstantiaNigra]]
         subClassOf: [[RegionalCerebralPedunclePart]]
  Class [[SupraCellularStructure]]
         subClassOf: [[MaterialAnatomicalEntity]]
  Class Synuclein
         subClassOf: Protein
  Class Tau
         subClassOf: Gene
  Class THPlusNeuron
         subClassOf: Neuron
  Class [[Tyrosine3Monooxygenase]]
         subClassOf: [[MacroMolecule]]
  Class [[TyrosineHydroxylase]]
         subClassOf: [[MacroMolecule]]
  Class [[UbiquitinProteinLigase]]
         subClassOf: [[MacroMolecule]]
  Class UCHL-1
         subClassOf: Gene
  Property associated_with
         domain: Pathway
         domain: Protein
         range: Cell
         range: [[BioMarker]]
  Property causes_disease
         domain: LRRK2Variant
         domain: [[AllelicVariant]]
         range: [[ParkinsonsDisease]]
         range: Disease
         inverseOf: disease_caused_by
  Property component_of
         domain: Protein
         range: [[AnatomicalEntity]]
         inverseOf: has_component
  Property contains
         domain: [[DopaminergicNeuron]]
         domain: Sample
         range: [[TyrosineHydroxylase]]
         range: Protein
  Property disease_caused_by
         domain: Disease
         domain: [[ParkinsonsDisease]]
         range: [[AllelicVariant]]
         range: LRRK2Variant
         inverseOf: causes_disease
  Property has_component
         domain: [[AnatomicalEntity]]
         range: Protein
         inverseOf: component_of
  Property has_disease
         domain: Patient
         range: Disease
  Property has_function
         domain: [[ProteosomalPathway]]
         range: xsd:string
  Property has_mutation
         domain: Gene
         range: [[AllelicVariant]]
         inverseOf: is_mutation_of
  Property has_pathological_hallmark
         domain: [[ParkinsonsDisease]]
         range: [[LewyBody]]
         inverseOf: is_pathological_hallmark_of
  Property has_risk_factor
         domain: [[ParkinsonsDisease]]
         range: UCHL-1
         inverseOf: is_risk_factor_of
  Property has_sample
         domain: Patient
         range: Sample
  Property has_variant
         domain: Gene
         range: [[AllelicVariant]]
         inverseOf: is_variant_of
  Property interacts_with
         domain: Protein
         range: Protein
         inverseOf: interacts_with
  Property involved_in
         domain: Protein
         range: Pathway
         inverseOf: involves
  Property involves
         domain: Pathway
         range: Protein
         inverseOf: involved_in
  Property is_located_in
         domain: Neuron
         range: Brain
  Property is_mutation_of
         domain: [[AllelicVariant]]
         range: Gene
         inverseOf: has_mutation
  Property is_pathological_hallmark_of
         domain: [[LewyBody]]
         range: [[ParkinsonsDisease]]
         inverseOf: has_pathological_hallmark
  Property is_risk_factor_of
         domain: UCHL-1
         range: [[ParkinsonsDisease]]
         inverseOf: has_risk_factor
  Property is_variant_of
         domain: [[AllelicVariant]]
         range: Gene
         inverseOf: has_variant
  Property level_of_expression
         domain: Protein
         range: xsd:string
  Property replication
         domain: [[AllelicVariant]]
         range: xsd:int
  Property transcribes_from
         domain: Dardarin
         domain: Protein
         range: Gene
         range: UCHL-1
         inverseOf: transcribes_to
  Property transcribes_to
         domain: UCHL-1
         domain: Gene
         range: Dardarin
         range: Protein
         inverseOf: transcribes_from