obophenotype
NTR L2 marginal neuron and Lamp5 Lhx6 neuron
Fixes #2346 #2345
In Lamp5 Lhx6 neuron, I wanted to add in the logical definition and (expresses some 'LIM/homeobox 6') but it does not seem to be available in the database.
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Here's a diff of how these changes impact the classified ontology (on -simple file):
Ontology comparison
Left
- Ontology IRI:
http://purl.obolibrary.org/obo/cl/cl-simple.owl - Version IRI:
http://purl.obolibrary.org/obo/cl/releases/2024-05-08/cl-simple.owl - Loaded from:
file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl
Right
- Ontology IRI:
http://purl.obolibrary.org/obo/cl/cl-simple.owl - Version IRI:
http://purl.obolibrary.org/obo/cl/releases/2024-05-08/cl-simple.owl - Loaded from:
file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl
Ontology imports
Ontology annotations
L2 marginal neuron http://purl.obolibrary.org/obo/CL_4042012
Added
-
L2 marginal neuron has exact synonym "layer 2 marginal neuron"
- database_cross_reference "PMID:32108571"
-
L2 marginal neuron has exact synonym "L2MN"
-
database_cross_reference "PMID:29311847"
-
database_cross_reference "PMID:32108571"
-
L2 marginal neuron date "2024-04-23T09:31:39Z"^^dateTime
-
L2 marginal neuron symbol "L2MN"
-
L2 marginal neuron label "L2 marginal neuron"@en
-
L2 marginal neuron definition "An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1."
-
database_cross_reference "PMID:29311847"
-
database_cross_reference "PMID:32108571"
-
-
Class: L2 marginal neuron
-
L2 marginal neuron SubClassOf L2 intratelencephalic projecting glutamatergic neuron
Lamp5 Lhx6 neuron http://purl.obolibrary.org/obo/CL_4042013
Added
-
Lamp5 Lhx6 neuron definition "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_cluster', Lamp5 Lhx6."
-
database_cross_reference "PMID:37824655"
-
database_cross_reference "PMID:36007006"
-
database_cross_reference "PMID:37824669"
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database_cross_reference "PMID:34004146"
-
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Lamp5 Lhx6 neuron has exact synonym "Ivy cell"
- database_cross_reference "PMID:36007006"
-
Lamp5 Lhx6 neuron has exact synonym "Lamp5-Lhx6 type"
- database_cross_reference "PMID:30382198"
-
Lamp5 Lhx6 neuron date "2024-04-23T09:37:55Z"^^dateTime
-
Lamp5 Lhx6 neuron label "Lamp5 Lhx6 neuron"@en
-
Class: Lamp5 Lhx6 neuron
-
Lamp5 Lhx6 neuron SubClassOf lamp5 GABAergic cortical interneuron
Here's a diff of your edit file (unreasoned)
Ontology comparison
Left
- Ontology IRI:
http://purl.obolibrary.org/obo/cl.owl - Version IRI: None
- Loaded from:
file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl
Right
- Ontology IRI:
http://purl.obolibrary.org/obo/cl.owl - Version IRI: None
- Loaded from:
file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl
Ontology imports
Ontology annotations
L2 marginal neuron http://purl.obolibrary.org/obo/CL_4042012
Added
-
L2 marginal neuron has_exact_synonym "layer 2 marginal neuron"
- database_cross_reference "PMID:32108571"
-
L2 marginal neuron has_exact_synonym "L2MN"
-
database_cross_reference "PMID:29311847"
-
database_cross_reference "PMID:32108571"
-
L2 marginal neuron date "2024-04-23T09:31:39Z"^^dateTime
-
L2 marginal neuron symbol "L2MN"
-
L2 marginal neuron label "L2 marginal neuron"@en
-
L2 marginal neuron definition "An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1."
-
database_cross_reference "PMID:29311847"
-
database_cross_reference "PMID:32108571"
-
-
Class: L2 marginal neuron
-
L2 marginal neuron SubClassOf L2 intratelencephalic projecting glutamatergic neuron
Lamp5 Lhx6 neuron http://purl.obolibrary.org/obo/CL_4042013
Added
-
Lamp5 Lhx6 neuron definition "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_cluster', Lamp5 Lhx6."
-
database_cross_reference "PMID:37824655"
-
database_cross_reference "PMID:36007006"
-
database_cross_reference "PMID:37824669"
-
database_cross_reference "PMID:34004146"
-
-
Lamp5 Lhx6 neuron has_exact_synonym "Ivy cell"
- database_cross_reference "PMID:36007006"
-
Lamp5 Lhx6 neuron has_exact_synonym "Lamp5-Lhx6 type"
- database_cross_reference "PMID:30382198"
-
Lamp5 Lhx6 neuron date "2024-04-23T09:37:55Z"^^dateTime
-
Lamp5 Lhx6 neuron label "Lamp5 Lhx6 neuron"@en
-
Class: Lamp5 Lhx6 neuron
-
Lamp5 Lhx6 neuron SubClassOf lamp5 GABAergic cortical interneuron
Much easier to review with diffs working again.
Couple of concerns:
- This still feels like an uneasy mix of classic def and t-type. It's classified under lamp5 GABAergic cortical interneuron so inherits the assertion about lamp5 expression from there. The text includes Lhx6 expression as a differentium, but this is not reflected in the axioms. It's possible that neither of these is 100% safe for all subtypes. It feels somewhat arbitrary to have axioms asserting expression of one but not the other.
- The reference data used as differentium is human specific, but the class is not.
So - I think needs a bit more discussion.
Some notes based Jorstad as a reference:
Lamp5 & Lamp5 Lhx6 t-types are disjoint:
LAMP5 consistently marks both & all subclusters (crossArea)
Lhx6 consistently is a very clean marker of the Lhx6 cluster - there is only subcluster (i.e. one cell set, 2 annotations)
Based on the above the, marker assertions appear safe (although we don't know about other species - would be good to look at mice). The bigger problem is t-type disjointness vs classical def subsumption.
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