Links to GO terms for types of cilia and villi

[dosumis]

Background: I would like a general push on improving links to cell component terms in GO. I'd like to start with a focus on cleaning up terms for ciliated cell types.

Issues:

1. The current structure includes cells that are not ciliated, but instead have microvilli. These are the brush border epithelial cells. GO has a term for microvillus that we can link these to (unfortunately it does not have a term for brush border, but we could request.
2. Ideally we would distinguish motile from immotile cilia & link to the appropriate term in GO. I think all of the multiciliated epithelial cells have motile cilia. Also I believe ependymal cells are well known examples of multicilliated cells
3. 'single cilliated cell' is a slightly odd term in that I believe most cells have one immotile cilium, which sometimes has a specialised function. Sperm has one motile cilium so strictly should be under ciliated (classification will be automated by adding has_part 'sperm flagellum'
4. We lack textual definitions for a number of cells including brush border cell and have rather minimal defs for others.

Tasks

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1. Revise endometrial ciliated epithelial cells classification and add links to GO terms #2440
   +0
   
2. Addresses #2384 Brush Border cell Classifications and Assertions #2384
   +0
   
3. Fixes#2395- Revise Epithelial Cell of Proximal Tubule and Subclasses #2401
   CL-classhierarchy logical definition text definition +3
   
4. Revise textual definition of ciliated columnar cell of tracheobronchial tree and links to GO terms #2456
   cellxgene text definition +2
   
5. Lung ciliated cell - Add a textual definition and revise logical definition #2458
   cellxgene logical definition text definition +3
   
6. Revise def multiciliated epithelial cell #2460
   logical definition text definition +2
   

[dosumis]

Hi @Caroline-99 & @aleixpuigb - I'm co-assigning this one as perhaps not an ideal early ticket. However, it is a good example of how I would like to clean up links to GO - which will be one of the themes of Caroline's work.

[Caroline-99]

I have started working on this ticket. There is no need to request the term brush border as I believe there is a GO term for brush border https://www.ebi.ac.uk/QuickGO/term/GO:0005903

[dosumis]

IIRC there is no relationship to villi and the term is defined for epithelia not epithelial cells. We could request that GO fix, but will need a work around if this takes time.

…

On Tue, 28 May 2024, 15:32 CEastwood, ***@***.***> wrote: I have started working on this ticket. There is no need to request the term brush border as I believe there is a GO term for brush border https://www.ebi.ac.uk/QuickGO/term/GO:0005903 — Reply to this email directly, view it on GitHub <#2305 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAA3RR3EHKTGZKLCF3ZEGELZESBQXAVCNFSM6AAAAABEFGLRHWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZVGIZTAMZRG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[dosumis]

Sorry - ignore last comment. GO term looks good https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0005903