Finished Work

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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/.


neural rod

neural rod cavitation (sensu Teleost)
neural rod formation (sensu Teleost)


People:

Doug
David

Questions:

How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?

Comments:

Neurulation in teleosts is a bit different than it is in other verts. For example, many verts have a clear distinction b/t primary neurulation (epithelial folding etc..) vs. secondary neurulation (mesenchymal cavitation process). In the case of teleosts, they form a 'neural rod' which has an epithelial origin, so is primary neurulation like, but the cell movements are slightly different. Epithelial cells form a solid dorsal structure (the neural keel) which then morphs into a tube (the neural rod) which then cavitates to form the neural tube. It's like primary neurulation in that it has epithelial origins, but is sort of like secondary neurulation in that it is a cavitation process rather than a folding process to form the tube. From what I can find in the literature, the 'neural rod' refers to the developing teleost neural tube structure of epidermal origin. Other verts that use the more conventional primary and secondary neurulation mechanism won't have this structure. Long story short: I think we might be able to simply drop (sensu Telost) from both of these terms.

-Doug

We might be more correct to move 'neural keel formation' to the same level as 'neural rod formation' rather than them having a 'part of' relation to each other. The neural keel develops into the neural rod through a morphogenetic change, but perhaps they are to be considered distinct anatomical structures.

-Doug


NOTE 10/17/07: Changes to the 'neural rod....sensu teleost' terms are waiting for pending discussion between Melissa H. and myself. Plan:

Written to Doug to ask if he has thought further about this 13/12/07.Jen

12/13/07 We believe the 'neural rod' is a teleost specific structure. Therefore it should be fine to drop the 'sensu telost' from the term names. The defs are fairly clear on the term meanings. -Doug




plasmid partitioning (sensu Bacteria)

People:

Eurie
Michelle
Midori


Questions:
It seems to me that plasmid partitioning's definition applies generally to partitioning, whether it is in yeast (2 micron), mammalian cells (for dormant forms of various DNA viruses IIRC) or bacteria. But it leads to questions

  • whether the kind of host cell where the process happens is a defining property of the process.
  • how granular should GO be? There is a child term just for 2 micron - should there be whole branches for every specific plasmid?

My inclination is to fold sensu Bacteria into the parent term. --JimHu 14:21, 22 November 2007 (PST)

Plan:

Eurie: I know nothing about this! =)

We folded the sensu term into the parent.


gastrulation

gastrulation (sensu Vertebrata)
gastrulation (sensu Mammalia)


People:

David
Doug
Victoria

Questions:

What distinguishes mammalian gastrulation from other organisms?

Plan:

Find distinguishing feature or merge terms.


I am tempted to merge the vertebrate term and the mammalian term into the parent and then just make part-of children that are found in gastrulation of different beasts. It turns out that all the beasts use different members of the child set, but they all use different ones. The children are:

  1. invagination involved in gastrulation with mouth forming second is_a morphogenesis of an epithelial sheet
  2. involution involved in gastrulation with mouth forming second is_a morphogenesis of an epithelial sheet
  3. ingression involved in gastrulation with mouth forming second is_a cell migration involved in gastrulation
  4. delamination involved in gastrulation with mouth forming second is_a negative regulation of cell-cell adhesion (we should probably have a generic delamination term)
  5. epiboly involved in gastrulation with mouth forming second is_a morphogenesis of an epithelial sheet

I'd get the defs straight from Gilbert.

David

We merged the terms.

new terms added:

id: GO:0055109 name: invagination involved in gastrulation with mouth forming second

id: GO:0055110 name: involution involved in gastrulation with mouth forming second

id: GO:0055111 name: ingression involved in gastrulation with mouth forming second

id: GO:0055112 name: delamination involved in gastrulation with mouth forming second

id: GO:0055113 name: epiboly involved in gastrulation with mouth forming second

spores and cell walls

spore wall assembly (sensu Bacteria)
spore wall assembly (sensu Fungi)
spore wall (sensu Fungi)

People:

Val
Maria Costanzo
Michelle
Midori
Pascale
Jen
Jim Hu
Tanya

Questions:

What are the distinguishing features of the walls?
or What are the distinguishing features of the assembly of the walls?
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls.
Also relevant to cell walls. [Jen]


Plan:

Michelle speaking - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.

Eurie: The introduction in this publication - PMID:15590821 - has a nice description of what is unique about S. cerevisiae spores.


Notes/action items from Skype Webex meeting/ Midori/Val & Maria Fi 2nd Nov

1. chitin and beta glucan containing cell wall We needed to get rid of chitin and beta-glucan containing cell wall as that does not work for pombe. (pombe cell walls don't have chitin , although spores do).

Propose solution: Change term name to "fungal-type cell wall".

This needs to be defined based on features which distinguish the fungal cell wall, but the def can be refined/clarified to include remarks on features that this type of cell wall does not have (cellulose/pectin) to distinguish from non-fungal cell walls.

Maria: Here's a proposed definition for "fungal-type cell wall", based on the current one for 'chitin and beta-glucan containing cell wall' but hopefully broadened to include all fungi:

A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure.

Current dbxrefs:[source: GOC:mtg_sensu_feb07, ISBN:3540601864, PMID:11283274, PMID:3319422] and we should add PMID:16927300.

2. Spore wall

Similarly change term 'spore wall (sensu fungi)' to 'fungal spore wall' (fungal-type spore wall?)

Val to write new def which distinguishes fungal spores from bacterial spores (i.e. include something about being a product of meiosis)

(N.B. There currently is not a term for plant spores. if it turns out that this term is not appropriate for plant spores they can raise a new term later, if required)

3. invasive growth (sensu fungi) (see below)

4. yeast-form cell wall

Maria to refine def to include 'budding'

Maria: Here's a draft: The wall surrounding a cell of a dimorphic fungus growing in the single-cell budding yeast form, in contrast to the filamentous or hyphal form.

Midori (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)

invasive growth (sensu Saccharomyces)

People:

Maria Costanzo
Val


Questions:

https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1583546&group_id=36855
Also consider pseudohyphal growth and filamentous growth.

Plan (from Nov. 2 meeting): rename to 'fungal-type invasive growth'; make sure mention of budding pattern in def is worded so it's not too restrictive (i.e. so pombe can also use the term); otherwise, the def is good as is.

  • On looking at this again, I have a couple thoughts:
    • this term, as well as 'pseudohyphal growth', have parentage under both 'cell growth' and 'growth'. I would argue that the 'cell growth' parentage should be removed since these are multicellular phenomena.
    • I don't think the 'fungal-type invasive growth' term name is very clear, since severl different kinds of filamentous growth can result in invasion of the medium. How about renaming it 'filamentous growth in response to glucose limitation'? Would pombe be able to use the 'hyphal growth' term?

Midori (Jan. 4, 2008): Both done.