Meeting Notes 2

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Trichome Meeting - 4th April

Present: Jen, Becky, Tanya, Donghui and Susan (with comments from Harold and David over the phone)

Resolving terms containing trichome.

It was generally agreed that the term 'trichome' is used less frequently in insects than plants. In insects, 'hair' is synonomous with 'trichome' and 'hair' is used more often - both words refer to non-sensory cell projections from larval and adult epidermal cells. On this basis...

The insect term 'trichome organization and biogenesis (sensu Insecta)' was changed to 'non-sensory hair organization and biogenesis'; the definition was changed to match.

However, there could be a problems with this in future if there are non-sensory mammalian hairs that are also cell projections. Mouse people (Harold or David?) were emailed to check.

'Trichome' is retained in the following plant term names and (sensu Magnoliophyta) removed.

trichome differentiation (sensu Magnoliophyta)
trichome morphogenesis (sensu Magnoliophyta)
trichome branching (sensu Magnoliophyta)
trichome initiation (sensu Magnoliophyta)
positive regulation of trichome initiation (sensu Magnoliophyta)
trichome patterning (sensu Magnoliophyta)

Oogenesis Meeting - 18th April

Present: David, John Eppig (oogenesis expert from Jackson Lab)

I met this morning with John Eppig to discuss the oogenesis terms in the GO. I basically had 2 questions for him:
Q1) Should we split oogenesis into types based on differences in how the process occurs, for example flies and mammals?
Q2) Absolutely not. People in the field would not like to see oogenesis split this way. There are subtle differences in oogenesis even among different species of mammals, and yet all forms of oogenesis accomplish the same goal. Based on the way the part_of relationship is set up in GO (necessarily is part) it makes more sense to have one oogenesis term and then all the parts below it.

Q2) Does mammalian oogenesis look o.k.?
A2) Although oogeneis looks ok, the stages that we have listed under oogenesis are actually stages that the follicle goes through and would probably be more appropriate under ovarian follicle development. Technically oogenesis only refers to making the oocyte. The discussion was very similar to the issues we faced with neurogenesis. Oogenesis is often referred to in the same context with the stages we have listed because oogenesis and folliculogenesis go hand in hand. You can't have one without the other. He will send me a review and we will see if we can address this issue.


Things we need to discuss

Jane/Jen/David

This vacuole sourceforge item:
https://sourceforge.net/tracker/index.php?func=detail&aid=1700649&group_id=36855&atid=440764

Jane/Jen/David/Chris

remaining true sensus
do we group processes on outcome or similarity of route to outcome? In oogenesis apparently we are grouping on outcome. Is this a general rule?


Between meeting progress - 8th May

Added two new terms:

[Term]
id: GO:0055051
name: ATP-binding cassette (ABC) transporter complex, integrated substrate binding
namespace: cellular_component
def: "A complex for the transport of metabolites out of the cell, consisting of 4 domains: 
two ATP-binding domains and two membrane spanning domains. In some cases, all 4 domains are 
contained on 1  polypeptide, while in others one ATP-binding domain and one membrane spanning
domain are together on one polypeptide in what is called a \"half transporter\". Two 
\"half-transporters\" come together to form a functional transporter. Transport of the 
substrate across the membrane is driven by the hydrolysis of ATP." [GOC:mlg, GOC:mtg_sensu]
is_a: GO:0043190 ! ATP-binding cassette (ABC) transporter complex

[Term]
id: GO:0055052
name: ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
namespace: cellular_component
def: "A complex for the transport of metabolites into the cell, consisting of 5 subunits:
two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit.
In organisms with two membranes, the substrate-binding protein moves freely in the 
periplasmic space and joins the other subunits only when bound with substrate. In organisms
with only one membrane the substrate-binding protein is tethered to the cytoplasmic 
membrane and associated with the other subunits. Transport of the substrate across the 
membrane is driven by the hydrolysis of ATP." [GOC:mlg, GOC:mtg_sensu]
is_a: GO:0043190 ! ATP-binding cassette (ABC) transporter complex

Sensu Meeting -12th June

Participants: Jennifer Deegan, Midori Harris, Jane Lomax, Louise Daugherty, Becky Foulger, David Hill.

We worked on terms that were descendents of oogenesis. There were sensu Insecta and sensu Mammalia terms. The oogenesis sensu Mammalia term was merged into the generic parent, and the child terms just had the sensu endings removed. The Insect terms were mainly merged into their generic parents.

We have not yet resolved the follicle terms and the oogenesis sensu Insecta terms has not yet been dealt with.

Sensu Meeting - 7th August

Participans: Jennifer Deegan, David Hill.

We merged a number of glial and neuroblast terms into their generic parents.

Sensu Meeting - 8th August

Participants: Jennifer Deegan, David Hill, Midori Harris.

We fixed the remaining insect terms. Oocyte terms, optic placode terms and ovarian follicle cell terms.

Sensu Meeting - 21st August

Participants: Jennifer Deegan, David Hill, Pascale Gaudet.

We began working on the fruiting body terms. The idea is that we will use the parents of the individual sensu terms to get the distinguishing features about them. Jen also sent around an interesting reference by Nancy Pataky. It may be that the fungal terms can get special names based on the terms used to describe fruiting bodies in those orgnanisms. We did not commit changes. Instead we will make the plan and send it to Michelle Gwinn-Giglio and Maria Costanzo for comments.


Sensu Meeting - 22nd August

Participants: Jennifer Deegan, David Hill, Pascale Gaudet.

Fixed fruiting body terms. The graph is being sent to Michelle Gwinn-Giglio for checking and it currently in the scratch directory.

Sensu Meeting - 23rd August

Participants: Jennifer Deegan, David Hill.

Worked on odontogenesis terms and vascular tissue development terms. Still using the fruiting body file in the scratch directory.


Things to do

Chitin and cell walls

We have to revisit the fungal cell wall terms, because Val has learned that the S. pombe cell wall does not contain chitin.
See SF 1778472:
https://sourceforge.net/tracker/index.php?func=detail&aid=1778472&group_id=36855&atid=440764
Invite Midori and Val to a conference call.

Fruiting bodies

We are waiting to hear back from Michelle on her view of the revamped sensu dicty friting body terms and their position with respect to the response to starvation term that used to be sensu bacteria. The file is in scratch waiting to be committed back. The parent file was checked out on about 21st August. The following e-mail summarizes the plan to implement. For now the file with this rearrangement is in the scratch directory.

Hi Jen,

Thanks for the screen shot.

This all looks fine to me as well as David's suggestion about the cellular terms.

Michelle


Hi Everyone, So for the dicty vs bacterial terms. One solution we could have is to make the current bacterial term fruiting body development involved in cellular response to starvation' . We would make this term a child of a new term called 'fruiting body development in response to starvation' and make the dicty term a child of the new term. The issue here is that the bacteria are cells and dicty is a multicellular orgnanism and we'd like to have the proper parentage.


Jennifer Deegan (nee Clark) wrote: Hi, David, Pascale and I have been doing some work on the sensu terms covering fruiting body development in the process ontology. We wondered if you could take a look at the attached graph and give us comments before we commit the file back to the live GO? The main question is about putting the dicty terms under the term that used to be sense bacteria but is now just a term covering any kind of fruiting body formation in response to stress. Does this seem okay? Thanks, Jen

Vascular tissue

Change the plant vascular tissue development sensu tracheophyta term.
Tanya: I'd like to keep the synonym 'vascular tissue development' because that is what some plant papers use. Can we still have 'and/or' in a term name? If so, we can have 'xylem and/or phloem development' as the primary name. I see that the children are 'xylem histogenesis' and 'phloem histogenesis.'

Alex asked that we should not merge withe the mammal version.

fungal cell polarity and otoliths

Midori has looked into these so can help when we get to them.