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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

1. Some Axioms Suggested by Kei-Cheung

   1. EquivalentClass(CerebellarPurkinjeCell intersectionOf(PurkinjeNeuron, Restriction(locatedInBrainRegion allValuesFrom(Cerebellum)))

      1. BB[2007-02-13]:I'm not certain I understand how the allValuesFrom restriction on this axiom would work. Kei - could you explain?

      2. Need to add the classes CerebellarPurkinjeCell, PurkinjeNeuron and the property locatedInBrainRegion to the ontology

   2. Alternatively, one can add a general property is_located_in: Neuron is_located_in BrainRegion

      1. 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)

   3. DopaminergicNeuron contains TyrosineHydroxylase

2. Reduced ubiquitin C-terminal hydrolase-1 expression levels in dementia with Lewy bodies. M. Barrachina et al., 2006.

   1. subClassOf(CTerminalHydrolase1 Protein)

   2. subClassOf(Dementia Disease)

   3. Class(Patient)

   4. subClassOf( intersectionOf(Patient Restriction(has-disease someValuesFrom(Dementia)))
      

      • intersectionOf(Patient Restriction(has-sample someValuesFrom(intersectionOf(Protein Restriction(has-expression-level hasValue(reduced))))))

   5. The above is incomplete. Need to model classes for Sample and properties has_sample, contains, has-expression-level

   6. Alan Ruttenberg suggested that the subclassOf precisely identify a subset relationship between subclasses of patients
3. Some axioms suggested by Nigam Shah

   1. AllelicVariant is_present_in Gene

   2. Class(AllelicVariant Restriction(is_present_in someValuesFrom(Gene)))

   3. Protein transcribed_from Gene

   4. Class(Protein Restriction(transcribed_from someValuesFrom(Gene)))

4. Aggresome-related biogenesis of Lewy bodies.

   1. Aggresome is some class in the subtree of Anatomical Entity

   2. Biogenesis subclass-of Pathway? or do we need to define a class called Biological Process?

   3. Introduce Axiom: equivalentClass(AggresomeRelatedBiogenesisLewyBody,
      

• intersectionOf(Biogenesis, Restriction(involves, allValuesFrom(LewyBody)), Restriction(relatedTo, someValuesFrom(Aggresome))))

  1. Aggresomes formed by alpha-synuclein and synphilin-1 are cytoprotective.

     1. Create a new relation called formedBy

     2. domain(formedBy) = Aggresome
     3. range(formedBy) = Protein

     4. subClassOf(intersectionOf(Aggresome, Restriction(formedBy, someValuesFrom(intersectionOf(alpha-synuclein, synphilin-1)))),
        

Restriction(hasFunction, hasValue(cytoprotective)))

1. Alpha-synuclein-enhanced green fluorescent protein fusion proteins form proteasome sensitive inclusions in primary neurons.

2. Clinicogenetic study of mutations in LRRK2 exon 41 in Parkinson's disease patients from 18 countries.

3. The LRRK2 I2012T, G2019S and I2020T mutations are not common in patients with essential tremor.

4. Glucocerebrosidase mutations are not found in association with LRRK2 G2019S in subjects with parkinsonism.