Metazoan cell types are not consistently subclasses of 'animal cell'

[cmungall]

alias cl='runoak -i sqlite:obo:cl'
cl info .desc//p=i cell .not .desc//p=i 'animal cell'

340 cell types non-animal-cl.txt

some are correctly species-general (although the value of some of these groupings is questionable). E.g.

CL:0011026 ! progenitor cell CL:0000064 ! ciliated cell

but many clearly should be animal cells

CL:0010007 ! His-Purkinje system cell CL:0009003 ! larval midgut cell CL:1000147 ! heart valve cell

confirmed by looking at OLS:

discussing solutions with @dosumis

1. change patterns to use animal cell as genus
   • would still need additional assertions?
2. use TC in logical def and auto-classify
3. abandon 'animal cell as grouping'

[dosumis]

I'd like to keep animal cell as a grouping. This might be easy to fix manually by moving grouping classes. If not, I suggest SPARQL to change all using of 'cell' in genus position (subClassOf or EquivalentTo) and curation to switch back the relatively small number that are incorrect. @ubyndr should be able to design Sparql update. @bvarner-ebi could work on curation.

@bvarner-ebi - I think that based on this, we should not use the animal_cell tag in CAP. I think just switch this to cell.

[ubyndr]

Adding this term list, output.csv, upon @bvarner-ebi request. He will curate this list to whether to add them as animal cell or not.

[dosumis]

Tracking sheet here @bvarner-ebi - I see lot of terms here flagged as animal cell. Can all the non-controversial ones just be moved, or if they have already, could you link the relevant PR?

[ghost]

Thanks for adding the link above.

Below are the cell type classes that are probably considered non-controversial to add as subclasses of 'animal cell'. PR to be linked.

As previously discussed, once there is a better understanding of usage of the remaining terms (those that are strictly functional/descriptive and/or not strictly animal cells), they can be added, edited or obsoleted.

Cell type classes to add under 'animal cell'

activated skeletal muscle satellite cell adaxial cell adepithelial cell adult skeletal muscle myoblast alarm substance cell amoeboid cell amoeboid sperm cell anterior cone cell (sensu Endopterygota) anterior lateral line neuromast mantle cell apocrine cell atrioventricular bundle cell cap cell cardiac myoblast cardiac septum cell cardiac valve cell cardioblast (sensu Arthropoda) CD25+ mast cell cell of skeletal muscle choroidal cell of the eye choroidal melanocyte cnidocyte coelomocyte compound eye cone cell compound eye retinal cell corneocyte cyanoblast cyanophore dark melanocyte dental papilla cell dermal melanocyte distal tip cell (sensu Nematoda) egg cell endocrine cell epidermal melanocyte epithelial melanocyte equatorial cone cell (sensu Endopterygota) erythrophore exocrine cell fast muscle myoblast fat body cell fetal hepatobiliary progenitor cell fibro/adipogenic progenitor cell flagellated sperm cell flask cell follicular dendritic cell folliculostellate cell foreskin melanocyte fusion competent myoblast ganglion mother cell germline-derived nurse cell glioblast hair follicle cell hair follicle melanocyte hatching gland cell hepatic oval stem cell His-Purkinje system cell hypothalamus cell invertebrate nurse cell iridoblast iridophore labyrinth supporting cell larval midgut cell leucoblast leucophore Leydig cell ligament cell light melanocyte lung ciliated cell lung secretory cell male gamete Malpighian tubule stellate cell malpighian tubule tip cell melanoblast melanocyte melanocyte of eyelid melanocyte of foreskin melanocyte of skin melanocyte of skin of face mesenchymal cell mesenchyme condensation cell motile sperm cell mural cell muscle founder cell muscle precursor cell myoblast myoendocrine cell neural progenitor cell neuromast mantle cell non-motile sperm cell notochordal cell notochordal sheath cell notochordal vacuole cell oenocyte ooblast oogonial cell pancreatic endocrine cell pancreatic epsilon cell paracrine cell paraganglia type 2 cell Peyer's patch follicular dendritic cell phagocyte phagocyte (sensu Nematoda and Protostomia) pigment cell (sensu Nematoda and Protostomia) pigment erythroblast pituitary gland cell polar body pole cell posterior cone cell (sensu Endopterygota) posterior lateral line neuromast mantle cell posterior lateral line neuromast supporting cell preameloblast precementoblast prechondroblast preodontoblast preosteoblast primary pigment cell primary polar body primary spermatocyte primordial germ cell progenitor cell of endocrine pancreas progenitor cell of mammary luminal epithelium quiescent skeletal muscle satellite cell retinal melanocyte salivary gland cell Schwann cell precursor scleral cell scolopale cell scolopidial ligament cell sebaceous gland cell secondary pigment cell secondary polar body secondary spermatocyte serous cell of epithelium of bronchus serous cell of epithelium of lobular bronchiole serous cell of epithelium of terminal bronchiole serous cell of epithelium of trachea sheath cell (sensu Nematoda) skeletal muscle myoblast skeletal muscle satellite cell skeletal muscle satellite myogenic cell slow muscle myoblast smooth muscle myoblast somatic cell somatic muscle myoblast somatic nurse-like cell sperm spermatid spermatocyte spermatogonium tertiary pigment cell thecogen cell thyroid hormone secreting cell tip cell tracheobronchial serous cell transit amplifying cell of anorectum transit amplifying cell of appendix transit amplifying cell of colon transit amplifying cell of small intestine visual pigment cell visual pigment cell (sensu Nematoda and Protostomia) X chromosome-bearing sperm cell xanthoblast Y chromosome-bearing sperm cell

[dosumis]

@ubyndr to help with ROBOT template.

[ghost]

Classes mentioned above have been added as subclasses under 'animal cell'.