HCLS/OntologyTaskForce/SeedOntology/SeedOntologyDetailedFollowup
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Entities from the Parkinsonian Syndrome Seed Ontology
NOTE - BB (2007-02-21): The original goal for this page was to experiment with expressing experimental observations from research articles focussed on a microdomain within the HCLS PD and/or AD Use Cases. As this page diverged from this goal, a separate page has not been created just focussed on that originally proposed test - expressing research observations & assertions using the OBO Phenotype Syntax and the OBO Ontology of Phenotypic Qualities.
Real-World entities fitting into subsumptive taxonomic hierarchies
These are relatively straight-forward to use in mapping phenotype via the formal OBO Phenotype Syntax using the OBO Ontology of Phenotypic Qualities.
These are given here solely according to a subsumptive is_a hierarchy. The more complex interactions can then be given both via higher order graphs such as pathways and mereotopological graphs specifying adjacency, contiguity, containment, and long-range connectivity, the latter being particularly important in the mammalian CNS.
Please note, as many have mentioned, Gene is a problematic entity to map in the real-world, but I'm going to leave it in this group for the time being.
VK (2006-9-28): The subsumptive hierarchy above has been incorporated in the latest version of the ontology dated 27th September 2006.
VK (2006-09-14): NN = Neuronames, GO = Gene Ontology, EC = NC-IUBMB Enzyme Classification
Disease is another problematic entity to Map in a subsumptive hierarchy
Research Articles making statements about these PD/PS associated entities
- Some Axioms Suggested by Kei-Cheung
- EquivalentClass(CerebellarPurkinjeCell intersectionOf(PurkinjeNeuron, Restriction(locatedInBrainRegion allValuesFrom(Cerebellum)))
- a) BB[2007-02-13]:I'm not certain I understand how the allValuesFrom restriction on this axiom would work. Kei - could you explain?
- b) Need to add the classes CerebellarPurkinjeCell, PurkinjeNeuron and the property locatedInBrainRegion to the ontology
- EquivalentClass(CerebellarPurkinjeCell intersectionOf(PurkinjeNeuron, Restriction(locatedInBrainRegion allValuesFrom(Cerebellum)))
- Alternatively, one can add a general property is_located_in: Neuron is_located_in BrainRegion
- a) BB[2007-02-13]: This is exactly the strategy adopted by the OBO Foundry community to post-coordinate more fundamental entities into complex, related entities (see below)
- DopaminergicNeuron contains TyrosineHydroxylase
- Reduced ubiquitin C-terminal hydrolase-1 expression levels in dementia with Lewy bodies. M. Barrachina et al., 2006.
- subClassOf(CTerminalHydrolase1 Protein)
- subClassOf(Dementia Disease)
- Class(Patient)
- subClassOf( intersectionOf(Patient Restriction(has-disease someValuesFrom(Dementia)))
intersectionOf(Patient Restriction(has-sample someValuesFrom(intersectionOf(Protein Restriction(has-expression-level hasValue(reduced))))))
- The above is incomplete. Need to model classes for Sample and properties has_sample, contains, has-expression-level
- Alan Ruttenberg suggested that the subclassOf precisely identify a subset relationship between subclasses of patients
- Some axioms suggested by Nigam Shah
- AllelicVariant is_present_in Gene
- Class(AllelicVariant Restriction(is_present_in someValuesFrom(Gene)))
- Protein transcribed_from Gene
- Class(Protein Restriction(transcribed_from someValuesFrom(Gene)))
- Aggresome-related biogenesis of Lewy bodies.
- Aggresome is some class in the subtree of Anatomical Entity
- Biogenesis subclass-of Pathway? or do we need to define a class called Biological Process?
- Introduce Axiom: equivalentClass(AggresomeRelatedBiogenesisLewyBody,
intersectionOf(Biogenesis, Restriction(involves, allValuesFrom(LewyBody)), Restriction(relatedTo, someValuesFrom(Aggresome))))
- Aggresomes formed by alpha-synuclein and synphilin-1 are cytoprotective.
- Create a new relation called formedBy
- domain(formedBy) = Aggresome
- range(formedBy) = Protein
- subClassOf(intersectionOf(Aggresome, Restriction(formedBy, someValuesFrom(intersectionOf(alpha-synuclein, synphilin-1)))),
Restriction(hasFunction, hasValue(cytoprotective)))
- Alpha-synuclein-enhanced green fluorescent protein fusion proteins form proteasome sensitive inclusions in primary neurons.
- Clinicogenetic study of mutations in LRRK2 exon 41 in Parkinson's disease patients from 18 countries.
- The LRRK2 I2012T, G2019S and I2020T mutations are not common in patients with essential tremor.
- Glucocerebrosidase mutations are not found in association with LRRK2 G2019S in subjects with parkinsonism.
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