Growth and development
J Clark
jclark at ebi.ac.uk
Fri Jun 3 05:51:29 PDT 2005
This is quite shocking to have such agreement on a mailing
list! Must be a sign of good teamwork. :-)
I'll update the proposal to include these new terms and the
move of growth out from under development, and then I'll
post it for comment.
Thanks,
Jen
Pascale Gaudet wrote:
> 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/
>
>
>
--
EMBL - European Bioinformatics Institute,
Gene Ontology Consortium,
and Wolfson College, Cambridge.
http://www.ebi.ac.uk/~jclark/
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