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
otolith
otolith mineralization (sensu Actinopterygii)
otolith mineralization (sensu Tetrapoda)
People:
David Fashena
https://sourceforge.net/tracker/index.php?func=detail&aid=1109256&group_id=36855&atid=440764
Midori
David
Emily
Victoria
Doug (I can consult with Dave F. as he is in the next office over)
Questions:
Comments:
I believe the initial introduction of the 'sensu Actinopterygii' term was because fish otoliths continue to grow throughout the life of the fish. It was my understanding that this was not true for tetrapods. If this distinction doesn't hold water, then perhaps a merge could happen.
-Doug
I have written to the GO list to see if anyone knows. 20 Nov 2007.
Plan:
outer membrane biogenesis (sensu ProteoBacteria)
People:
Jim Hu
Michelle
Questions:
Check how we distinguish the outer membrane in the component ontology.
Plan:
It looks like the sensu terms have already been addressed in the component ontology. Shouldn't the biogenesis process term point to the component term? If this is mirrored in the biogenesis term, then it seems to me that the sensu should be removed from the biogenesis term and GO:0043165 outer membrane biogenesis (sensu ProteoBacteria) should be renamed to GO:0043165 cell outer membrane biogenesis and the definition should be
The assembly of a cell outer membrane [GO: 0009279]. As in, but not restricted to, the Gram-negative bacteria
Looking at these raises some other issues that we will put on Sourceforge. --JimHu 14:38, 22 November 2007 (PST)
larval development
larval development (sensu Amphibia)
larval development (sensu Nematoda)
People:
Becky Foulger
Kimberly
Questions:
What are the distinguishing features?
Is it worth having separate terms for each?
Plan:
Yes, I do think we'll need to have separate terms for each. The distinguishing features seem significantly different enough to warrant that. Nematode larvae have essentially the same body plan as adults, but grow larger and develop specific anatomical structures during larval development. Also, the successive molts at larvae stage transitions is a key component of nematode larval development.
--Kimberly
Shall we just make these amphibian larval development and nematode larval development? We can make really clear defs to show the differences.
--Jen
That sounds reasonable. Here is a proposed definition for nematode larval development:
The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (e. g., fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
--Kimberly
From Becky:
amphibian larval development
The process whose specific outcome is the progression of the amphibian larva over time, from its formation to the mature structure. Amphibian larvae, sometimes called pollywogs or tadpoles, hatch from eggs and begin to grow limbs and other adult physical features at various times, depending on the species, before they metamorphose into the adult form.
Mainly taken from http://www.livingunderworld.org/biology/.