Growth and development

[J Clark]

Hi Pascale,

We'd only need two sensu terms, since there are only two 
possible views. I think it would probably be better to have 
the sensu strings though. Shall we wait and see what others 
on the list say?

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/