Growth and development

J Clark jclark at ebi.ac.uk
Fri Jun 3 05:32:49 PDT 2005 

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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