Finished Work

Finished Work

Tail tip morphogenesis

Comments:

The tail tip morphogenesis term appears to refer to morphogenesis of the nematode tail tip resulting in development of reproductive structures. Such a process does not occur in fish or vertebrates that I can think of. Fish won't need this term, so I think the resolution of this term can be left to Kimberly's discretion.
-Doug

Plan

For the tail tip morphogenesis term, I think that we can remove the sensu Nematoda suffix without any problems.

--Kimberly

Chromosome

chromosome organization and biogenesis (sensu Bacteria)
chromosome organization and biogenesis (sensu Eukaryota)

People:

Michelle
Jim Hu
Eurie

Questions:

What are the distinguishing features?
Do we lump mitochondrial and plastid with bacterial?

Plan:

Michelle speaking - It seems to me that these processes are really the same - yes different genes and proteins are involved in the different types of organism, but I don't see why there needs to be separate terms. Can these just be merged into their parent? I think you would want to keep mitochondrial and plastid terms separate as they are "auxillary" chromosomes, not the primary genome of the organism (not that they aren't important).

Eurie: I think these might be able to be merged. I think there is evidence for nucleosome-like particles in bacteria now. You guys can correct me if I'm wrong but bacterial chromosomes attaches to the cell wall? Eukaryotic chromosomes attach to the nuclear lamina at various points during the cell cycle. So as long as there wasn't any cell wall vs. nuclear lamina type terms that are children, should be ok.

cell polarity - DONE

establishment and/or maintenance of cell polarity (sensu Fungi)
establishment of cell polarity (sensu Fungi)
maintenance of cell polarity (sensu Fungi)

People:

David
Midori
Rex

Questions:

Plan:

Merge these terms with their non-sensu parents. Fungal cell polarity is the model system for everything on polarity.

Val confirms that merges also work for pombe; see SF 1796071.

Merge done 2007-09-18. [mah]

pigment

pigment cell differentiation (sensu Nematoda and Protostomia)
pigment cell differentiation (sensu Vertebrata)

People:

Kimberly
David
Doug
Victora
Susan Tweedie
Becky Foulger

Questions:

Should we have a sensu designation or should we just enumerate the types of pigment cells underneath the parent pigment term.
Look to the cell ontology for guidance.

Comments:

I vote for a single pigment cell differentiation parent term with individual cell type-specific differentiation terms as children. Merge the sensu Vertebrata (GO:0043358) and sensu Nematoda and Protostomia (GO:0043357) terms with 'pigment cell differentiation' (GO:0050931).

-Doug

A single, merged term should be okay with us, too. C. elegans doesn't really have pigment cells, so we will probably not annotate to this term anyway.

--Kimberly

I'm happy for a single term too. We haven't used this sensu term - our only current annotation is to the generic term.

-Susan

Plan:

Nematode development

negative regulation of vulval development (sensu Nematoda)
positive regulation of vulval development (sensu Nematoda)
regulation of vulval development (sensu Nematoda)
vulval development (sensu Nematoda)

People:
Kimberly
David

Questions:

What is the distinguishing feature of the anatomical structure vulva between species?
Do we want a term just called vulval development?
Can we handle this by making cross references to anatomical dictionaries?

Vulval Development Terms

For these terms, I'm not sure what we should do. I can rewrite the definition of vulval development (and its children, too) to be something like this:

The process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.

However, I'm not sure what to do with the term name. Any suggestions?

--Kimberly

There was some email discussion about this in October. I've pasted the discussion below. I think that removing the sensu Nematoda and just having the vulval terms with the definition above would be okay. If other organisms need a vulva development term, then we could change the term, as David suggested, to nematode-type vulval development.

From Doug:

The new def provided by Kimberly will be more specific than the current one. Though it seems unlikely that many other groups have used that term for annotation, would it be necessary to obsolete and recreate the term with the new def? Also, with Kimberly's new def, why not just call the term 'vulva development'? That is how the work community think of it, and it seems unlikely that other communities would be annotating to that term with a different meaning...plus, the new def is crystal clear in terms what the term means.

my 2c. -Doug

David Hill wrote:

> Kimberly, > > I think the consensus at the meeting was that we could use taxon info in the terms if they became too strange when we tried to come up with another term. So if we need to have 'nematode-type vulval development' for example, I think it is o.k. I still don't want to use this as a crutch, but if it the best way, then I think that is the way we should go. We still need very good defs. > > David

genderization

hermaphrodite germ-line sex determination (sensu Nematoda)
feminization of hermaphroditic germ-line (sensu Nematoda)
masculinization of hermaphroditic germ-line (sensu Nematoda)
hermaphrodite somatic sex determination (sensu Nematoda)
feminization of hermaphrodite soma (sensu Nematoda)
masculinization of hermaphrodite soma (sensu Nematoda)

People:

Kimberly

Questions:

Is there any other type or can we just merge into the generic parent?

Plan:

At this point, I can't see any reason why we shouldn't merge these terms into the generic parents.

--Kimberly