Growth and development

David Hill dph at informatics.jax.org
Fri Jun 3 05:29:08 PDT 2005 

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/
>>
>>
>>
>>
>


-- 
David P. Hill, Ph.D.
Senior Scientific Curator
Gene Expression Database
Gene Ontology Consortium
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
tel:207-288-6430
htpp://www.informatics.jax.org

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