Growth and development

Pascale Gaudet pgaudet at northwestern.edu
Fri Jun 3 05:37:31 PDT 2005 

Yes, I like it!

Pascale


At 01:32 PM 6/3/2005 +0100, J Clark wrote:
>Yes, I like that. What do you think Pascale?
>
>Jen
>
>David Hill wrote:
>
>>How about 2 terms:
>>Term:developmental growth of a unicellular organism
>>def: The growth of single celled organisms prior to division, that is 
>>aimed at the progression of the organisms over time from an initial 
>>condition to a later condition.
>>PART_OF cell development?
>>term: non-developmental growth of  a unicellular organism
>>def: The growth of single celled organisms prior to division, that is not 
>>for the purpose of change in the organism over time, from an initial 
>>condition to a later condition.
>>IS_A cell growth
>>
>>
>>
>>J Clark wrote:
>>
>>>Hi,
>>>
>>>This thread has gone a bit quiet. Since we now know why Chris is not 
>>>replying shall we try to make term names and then just talk to him about 
>>>the plan when he gets back?
>>>
>>>David and Tanya: Do you have any views on term name strings and sensu 
>>>endings that Pascale and I have discussed below?
>>>
>>>Thanks,
>>>
>>>Jen
>>>
>>>
>>>
>>>Pascale Gaudet wrote:
>>>
>>>>Sorry I missed that.
>>>>
>>>>What about swapping the term and synonym for 'unicellular organism 
>>>>developmental growth'? So that you would have two different terms? Can 
>>>>a term name be a synonym of another term?
>>>>
>>>>I am just worried that you will create sensu terms for every 
>>>>unicellular organisms? That sounds like many terms.
>>>>
>>>>Pascale
>>>>
>>>>
>>>>At 03:29 PM 5/25/2005 +0100, J Clark wrote:
>>>>
>>>>>Hi Pascale,
>>>>>
>>>>>The thing is that without the sensu string the two terms will have the 
>>>>>same name. We have to add the sensu strings to differentiate between them.
>>>>>
>>>>>For the sensu string:
>>>>>Even with 'sensu Dictyosteliida' the other organism groups will still 
>>>>>be able to use the term because 'sensu Dictyosteliida' just means 'in 
>>>>>the sense of Dictyosteliida' and so is not restricted to annotation to 
>>>>>Dictyosteliida gene products.
>>>>>
>>>>>Jen
>>>>>
>>>>>Pascale Gaudet wrote:
>>>>>
>>>>>>I thought since the definition included " for organisms whose 
>>>>>>research community considers that that kind of growth _is_ part (or 
>>>>>>is_not_part) of development.", we didn't need sensu terms. I would be 
>>>>>>happy to share this term with other organisms!
>>>>>>Maybe in the comments you can add the different species that consider 
>>>>>>unicellular organism growth part of/not part of development, and not 
>>>>>>add sensu terms?
>>>>>>Pascale
>>>>>>
>>>>>>At 03:18 PM 5/25/2005 +0100, J Clark wrote:
>>>>>>
>>>>>>>Cool. What d'y think about the defs? Also I guess we use sensu 
>>>>>>>Dictyosteliida for one but I'm not really sure about the other.
>>>>>>>
>>>>>>>How about sensu Schizosaccharomyces? Val said that as a pombe person 
>>>>>>>she was happy to consider this kind of growth as part of development.
>>>>>>>
>>>>>>>Thanks,
>>>>>>>
>>>>>>>Jen
>>>>>>>
>>>>>>>Pascale Gaudet wrote:
>>>>>>>
>>>>>>>>Sounds good to me!
>>>>>>>>At 02:51 PM 5/25/2005 +0100, J Clark wrote:
>>>>>>>>
>>>>>>>>>Hi Pascale,
>>>>>>>>>
>>>>>>>>>>I am not sure why we need the 'prior to division' bit??
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>True. :-)
>>>>>>>>>
>>>>>>>>>'unicellular organism growth' then?
>>>>>>>>>
>>>>>>>>>as a child of 'cell growth'?
>>>>>>>>>
>>>>>>>>>Jen
>>>>>>>>>
>>>>>>>>>>At 02:20 PM 5/25/2005 +0100, J Clark wrote:
>>>>>>>>>>
>>>>>>>>>>>Hi Pascale,
>>>>>>>>>>>
>>>>>>>>>>>Yes that seems like a good plan. I could add that parentage.
>>>>>>>>>>>
>>>>>>>>>>>Do you think the term string is okay as it is or could we have a 
>>>>>>>>>>>less clunky version?
>>>>>>>>>>>
>>>>>>>>>>>Jen
>>>>>>>>>>>
>>>>>>>>>>>Pascale Gaudet wrote:
>>>>>>>>>>>
>>>>>>>>>>>>Jennifer,
>>>>>>>>>>>>This may be a bit off topic, but how does this term relates to 
>>>>>>>>>>>>'cell proliferation'? In the case of Dictyostelium, unicellular 
>>>>>>>>>>>>organism growth should probably be a child of cell 
>>>>>>>>>>>>proliferation (if the definition of cell proliferation gets 
>>>>>>>>>>>>fixed to remove the "rapid expansion" bit).
>>>>>>>>>>>>Pascale
>>>>>>>>>>>>
>>>>>>>>>>>>At 03:05 PM 5/24/2005 +0100, J Clark wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>>Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>>I've written to Chris several times over the last few weeks to 
>>>>>>>>>>>>>ask if he agrees with this proposal and I think he must just 
>>>>>>>>>>>>>be too busy to get back to us. In order not to hold things up 
>>>>>>>>>>>>>any longer I propose now to implement the proposal below 
>>>>>>>>>>>>>(previous e-mail) in some form.
>>>>>>>>>>>>>
>>>>>>>>>>>>>Does anybody have any ideas for the term strings and sensu 
>>>>>>>>>>>>>taxa for these terms?
>>>>>>>>>>>>>
>>>>>>>>>>>>>Term: unicellular organism growth prior to division
>>>>>>>>>>>>>(sensu x)
>>>>>>>>>>>>>exact_synonym: unicellular organism developmental growth
>>>>>>>>>>>>>prior to division
>>>>>>>>>>>>>def: The growth of single celled organisms, prior to division, 
>>>>>>>>>>>>>for organisms whose research community considers that that 
>>>>>>>>>>>>>kind of growth _is_ part of development.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>Term: unicellular organism growth prior to division
>>>>>>>>>>>>>(sensu y)
>>>>>>>>>>>>>def: The growth of single celled organisms, prior to division, 
>>>>>>>>>>>>>for organisms whose research community considers that that 
>>>>>>>>>>>>>kind of growth _is_not_ part of development.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>>Jen
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>J Clark wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>>Hi,
>>>>>>>>>>>>>>I have rewritten the proposal clarifying the two terms of 
>>>>>>>>>>>>>>interest.
>>>>>>>>>>>>>>Does this seem like a better representation?
>>>>>>>>>>>>>>If it does then would Chris be happy with the use of a sensu 
>>>>>>>>>>>>>>designation so high up in the DAG?
>>>>>>>>>>>>>>Thanks,
>>>>>>>>>>>>>>Jen
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>Proposal:
>>>>>>>>>>>>>>Currently we are saying that some species research groups 
>>>>>>>>>>>>>>that study single celled organisms
>>>>>>>>>>>>>>define the relationship between growth and development
>>>>>>>>>>>>>>differently from other species research groups.
>>>>>>>>>>>>>>e.g. one group may say that the growth that occurs prior to
>>>>>>>>>>>>>>  division of the single celled organsim is developmental 
>>>>>>>>>>>>>> growth (e.g. pombe),
>>>>>>>>>>>>>>whilst other research groups say that that kind of growth is
>>>>>>>>>>>>>>not developmental growth (e.g. dicty).
>>>>>>>>>>>>>>The way we're suggesting we'll deal with this is to represent
>>>>>>>>>>>>>>individual instances of growth according to the view of the
>>>>>>>>>>>>>>relevant research community and that we'll clarify things by
>>>>>>>>>>>>>>adding synonyms. If a term 'x growth' needs to have a
>>>>>>>>>>>>>>development parent as well as a growth parent then I add an
>>>>>>>>>>>>>>exact synonym 'x developmental growth'. If a term 'x growth'
>>>>>>>>>>>>>>does not need a development parent then it does not get the
>>>>>>>>>>>>>>synonym. It seems to me that we might also need a sensu term
>>>>>>>>>>>>>>as follows:
>>>>>>>>>>>>>>[i]development
>>>>>>>>>>>>>>---[p]developmental growth
>>>>>>>>>>>>>>------[i]unicellular organism growth prior to division
>>>>>>>>>>>>>>          (sensu x)
>>>>>>>>>>>>>>[i]growth
>>>>>>>>>>>>>>---[i]unicellular organism growth prior to division
>>>>>>>>>>>>>>       (sensu y)
>>>>>>>>>>>>>>---[i]developmental growth
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>Term: unicellular organism growth prior to division
>>>>>>>>>>>>>>       (sensu x)
>>>>>>>>>>>>>>exact_synonym: unicellular organism developmental growth
>>>>>>>>>>>>>>              prior to division
>>>>>>>>>>>>>>def: The growth of single celled organisms, prior to 
>>>>>>>>>>>>>>division, for organisms whose research community considers 
>>>>>>>>>>>>>>that that kind of growth _is_ part of development.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>Term: unicellular organism growth prior to division
>>>>>>>>>>>>>>       (sensu y)
>>>>>>>>>>>>>>def: The growth of single celled organisms, prior to 
>>>>>>>>>>>>>>division, for organisms whose research community considers 
>>>>>>>>>>>>>>that that kind of growth _is_not_ part of development.
>>>>>>>>>>>>>
>>>>>>>>>>>>>--
>>>>>>>>>>>>>EMBL - European Bioinformatics Institute,
>>>>>>>>>>>>>Gene Ontology Consortium,
>>>>>>>>>>>>>and Wolfson College, Cambridge.
>>>>>>>>>>>>>http://www.ebi.ac.uk/~jclark/
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>--
>>>>>>>>>>>EMBL - European Bioinformatics Institute,
>>>>>>>>>>>Gene Ontology Consortium,
>>>>>>>>>>>and Wolfson College, Cambridge.
>>>>>>>>>>>http://www.ebi.ac.uk/~jclark/
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>--
>>>>>>>>>EMBL - European Bioinformatics Institute,
>>>>>>>>>Gene Ontology Consortium,
>>>>>>>>>and Wolfson College, Cambridge.
>>>>>>>>>http://www.ebi.ac.uk/~jclark/
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>--
>>>>>>>EMBL - European Bioinformatics Institute,
>>>>>>>Gene Ontology Consortium,
>>>>>>>and Wolfson College, Cambridge.
>>>>>>>http://www.ebi.ac.uk/~jclark/
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>--
>>>>>EMBL - European Bioinformatics Institute,
>>>>>Gene Ontology Consortium,
>>>>>and Wolfson College, Cambridge.
>>>>>http://www.ebi.ac.uk/~jclark/
>>>>
>>>>
>>>>
>>>>
>
>--
>EMBL - European Bioinformatics Institute,
>Gene Ontology Consortium,
>and Wolfson College, Cambridge.
>http://www.ebi.ac.uk/~jclark/

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