NRTF mappings
From Program on Ontologies of Neural Structures
UNDER CONSTRUCTION
Warning - the mappings on this page should all be considered experimental - they do not necessarily reflect of the views or approval of NRTF members.
NRTF curation tool and its out put can be found here: http://incfnrci.appspot.com/. This is an attempt to map this work to existing relations and ontologies and to proposed relations for representing neuro-anatomy.
Contents |
Mapping spreasheet entries to OWL2
The following lists spreadsheet column headings and abberviations for them use in the proposed OWL2 formalization (Manchester syntax) that follow:
Each entry in the neuron registry table can be formalized in OWL 2.0 (Manchester syntax) as:
class:NT
SubClassOf: has_part some (NP that REL some V)); Annotations: REF, rdfs:comment; (*)
Where Neuron Type = NT;(Neuron) Part = NP; Relation = REL Value = V; Reference = REF; Note = rdfs:comment.
e.g.:
Class: 'CA1 pyramidal cell'
SubClassOf:
has_part some ('dendritic shaft' that receives_contact_from some 'CA1 trilaminar cells')
SubClassOf:
has_part some '(dendrite apical tuft' that located_in some 'CA1 stratum lacunosum-moleculare')
Annotations: REF:PMID:8576427
(*Note - may not be quite correct syntax for multiple axiom annotations in Manchester Syntax).
SubClassOf denotes a necessary condition for membership of the class. If enough conditions where collected to specify complete necessary and sufficient conditions for membership of a class, all of these conditions would be combined using AND to make a single EquivalentTo expression.
For example, if the above criteria were sufficient for defining a 'CA1 pyramidal cell' (they are almost certainly not) then we would write:
EquivalentTo:
has_part some ('dendritic shaft' that receives_contact_from some 'CA1 trilaminar cells')
and
has_part some '(dendrite apical tuft' that located_in some 'CA1 stratum lacunosum-moleculare')
Annotations: REF:PMID:8576427
Relation mappings
makes_contact_to maps to synapsed_to
receives_contact_from maps to synapsed_by
has_part - Maps to relations ontology has_part
has_quality - Maps to relations ontology has_quality
has_shape Maps to relations ontology has_quality with range restriction PATO:shape
lacks quality Maps to !has_quality (where ! indicates negation)
lacks_part Maps to !has_part
located_in maps to overlaps (Note discussion with Giorgio makes clear that it is not safe to assume part_of)
not_located_in maps to !overlaps
has_molecule maps to has_part with range restriction CHEBI molecule ??
does_not_have_molecule maps to (!(has_part with range restriction CHEBI molecule))
No mappings yet
has_current
has_firing_pattern
has_orientation
Term mappings
Mappings from neuron registry neuron part (see column 2) to GO cell component terms, with hyperlinks to GO term pages on QuickGO can be found here: http://pons.neurocommons.org/page/GO_neuron_component_terms
The following spreadsheet is a draft mapping of all the terms used so far. This is intended to be used in rolling an draft OWL 2 version of the ontology.
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