Growth and development

J Clark jclark at ebi.ac.uk
Fri Jun 3 04:01:34 PDT 2005 

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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