1 ade logical #5
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Fixes obophenotype#1933 logical definition club cell
Add a definition for 'flight muscle cell'. Also rename to 'insect flight muscle cell', to avoid any possible confusion with muscles involved in flight for other flying animals.
Add a definition for 'pole cell'. Also remove the explicit classification as an 'animal cell', which is already inherited from 'primordial germ cell'.
Add definitions for the '(sensu Nematoda and Protostomia)' versions of 'neuroblast', 'neuroglioblast', and 'glioblast'.
Addresses obophenotype#1910 Build eye slim
Add a definition to 'imaginal disc cell' and 'adepithelial cell'. Also add a taxon restriction to the insect class.
Add a definition to 'Kenyon cell', as well as a part_of relationship with UBERON's 'mushroom body'.
Add a definition to 'histoblast'. Re-classify as a 'progenitor cell' rather than as a 'simple columnar epithelial cell' (there is no indication that those cells are columnar epithelial cells; there are located within the larval epidermis, which is a type of epithelium, but may not be epithelial cells themselves). Also add a taxon restriction to insects.
Add a definition to 'scolopale cell' and make it part_of a 'chordotonal organ' (imported from Uberon).
'scolopidial sheath cell' and 'scolopale cell' refer to the same cell type, so we obsolete the former.
Add a definition for 'scolopidial ligament cell'. Re-classify as a 'supporting cell' instead of a 'ligament cell' -- the scolopidial ligament cell is *not* a ligament cell, despite its name. Also make it part_of the chordotonal organ.
Add a definition and a taxon restriction to 'cardioblast (sensu Arthropoda)'.
Add a definition to 'compound eye cone cell'. Make it part_of Uberon's 'ommatidium' rather than 'compound eye', since ommatidia themselves are part_of the compound eye.
Add FBbt-based definitions to 'border follicle cell', 'centripetally migrating follicle cell', and 'interfollicle cell'. Also re-classify 'interfollicle cell' correctly as a 'follicle cell of egg chamber'.
This term was added to FBbt even though it is seemingly never used in the literature. It may remain in FBbt (FlyBase has at least one curation records referring to it), but CL has no need for it.
Podocytes are merely a transient state of plasmatocytes rather than a distinct cell type.
What was called 'polygonal cells' turned out to be 'prohemocytes', so the former term can be obsoleted and merged with the latter.
There is no need for a 'macrophage' subclass to 'plasmatocyte', since plasmatocytes ARE the macrophages of Diptera.
Clarify the hierarchy of hemocytes subclass so that we ultimately have: * embryonic hemocyte (all hemocytes derived from embryonic mesoderm) * embryonic crystal cell * embryonic plasmatocyte * lymph gland hemocyte (all hemocytes derived from the lymph gland) * lymph gland crystal cell * lymph gland plasmatocyte Add proper definitions where needed.
Add a proper definition to 'crystal cell'. Also remove the cross-reference to FMA's 'cell crystal', which has nothing to do with this cell type.
Add a proper definition of 'plasmatocyte'. Move the `capable_of some 'encapsulation of foreign target'` from the parental 'hemocyte' term to this class, as plasmatocytes are the real phagocytic hemocytes.
Add a definition to 'lamellocyte' and re-classify as a 'hemocyte' rather than as a 'plasmatocyte', as those cells are considered to be a distinct type of hemocytes rather than a subtype of plasmatocytes.
Remove compound eye retinal cell. Add vertebrate lens cell, ciliary muscle cell, pigmented ciliary epithelial cell, non-pigmented ciliary epithelial cell, retinal melanocyte, retinal pigment epithelial cell, keratocyte
Addresses obophenotype#1910 Build eye slim
Do not classify 'CNS interneuron' as a 'CNS neuron (sensu Vertebrata)', as this makes the term specific to vertebrates even though its logical definition applies across all species. Also do not classify it as an 'interneuron', since it is already in the logical definition.
Add a text definition to 'CNS interneuron' -- basically a direct text rendering of the logical definition. Also add a comment to explain why we have such a term in addition to 'interneuron'.
Do not classify 'taste receptor cell' as part_of some 'stratum basale of epidermis', as the latter term is chordate-specific while the former has a logical definition that applies across a wider range of species.
Amend the text definition of 'taste receptor cell' to align it with the
neighbouring 'auditory epithelial cell' and 'olfactory epithelial cell'
("a specialized cell involved in X sensory perception"), and to move the
details about the typical location in the tongue to a second sentence
that makes it clear this only applies to vertebrates.
The definition was specific for the CD103-positive subset. Now is general, and a NTR for the subset should be added.
…eptor-cell-taxon-neutral Make 'taste receptor cell' taxon-neutral
IAO:0000233 is supposedly the annotation property to use for linking to a bug tracker issue, so it should not be flagged as an "illegal" annotation.
Add IAO:0000233 to the list of allowed annotation properties.
…neuron-taxon-neutral 1960-Make 'CNS interneuron' taxon-neutral
…_lung_TRM Addresses obophenotype#1956 NTR lung TRM
…_receptor_tongue Fixes obophenotype#1964 NTR taste receptor cell of tongue and taste cell definition
Fixes obophenotype#1976 chemoreceptors
…cell Fixes obophenotype#1976 chemoreceptors
…merular_mesangial_cell Addresses obophenotype#515 Update 'glomerular mesangial cell'
* Fixes obophenotype#1389 * update template --------- Co-authored-by: Anita Caron <[email protected]>
Addresses #1 logical definition epithelial cells
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Closes #1