Ontology meeting 2022-12-05

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  • Group members: Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
  • Present: Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, Chris, Paul
  • Regrets: David

Announcements

This is the last call of the year. Next call will be on Jan 9th - the no GO calls week was swapped from the week of Jan 9th to the week of January 2nd to give a longer holidays break).

Discussion arising from DP work: Differentiation

  • Pascale & David have proposed new definitions for 'cell differentiation' and main children (cell development, cell fate specification, cell fate determination, etc), see https://github.com/geneontology/go-ontology/issues/24390
  • We'd like to discuss these and get feedback from groups annotating development papers in various species
  • Comments and suggestions:
    • Alex Diehl: I am concerned that both the original definition and the proposed definition of 'cell differentiation' fail to consider the differentiation of the highly specialized cells of the immune system, such as when a 'naive T cell' (already considered a mature cell type) differentiates into an 'effector T cell' or a 'memory T cell', when a 'memory T cell' differentiates into an effector memory T cell upon reencounter with an antigen, or when a 'class-switched B memory cell' differentiates into a 'plasma cell'.
    • Feedback from FB
    • Feedback from XenBase
    • Val and Pascale propose to make cell differentiation a multicellular organism-specific process, see https://github.com/geneontology/go-ontology/issues/24411; however there are 'differentiation' processes in unicellular organisms, such as sporulation, spore germination, and dimorphic switch. These are also 'conceptually' different because these processes are *meant* to be reversible, while differentiation in multicellular organisms is most irreversible, except for Alex's example where a differentiated cell can 'transdifferentiate', or cell dedifferentiation. Maybe these processes are not developmental processes, ie could we consider the 'naive T cell' as differentiated, and put 'effector T cell' and 'memory T cell' in a different branch ?

Summary of the discussion

We didn’t make any decisions yesterday. We discussed the comments in the ticket, including yours about the differentiation of already mature cells. Cell fate determination, cell fate specification and cell fate commitment were pretty clear, with potential improvements suggested by Helen (she will make ‘clean’ proposals for new definitions’).

We were much less clear as to how cell development and cell maturation were supposed to be used.

Did you see Nick’s comment about cell maturation? “For GO:0048469 cell maturation Nick commented that he regards"cell maturation [..] to the case where a fully differentiated cell, then shifts to another "more mature" state. The only place I have come across it is in the immune system." - which is what how wanted for cell differentiation; if instead we extend the definition of differentiation I think we will need to change how terms are organized.


Editors discussion items

Jim

Tickets by ontology editors

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