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is_a complete biological process ontology

Wacek Kusnierczyk waku at idi.ntnu.no
Fri Jan 5 14:03:05 PST 2007


one more comment to 'multi-organismal process'.

if we consider viruses as organisms, then a multi-organismal process 
must necessarily be either a multi-cellular process (if more than one 
cell is involved) or a single-cellular process (in the case a cell 
interacts with one or more viruses);  let's agree for the moment that 
non-cellular organismal processes do not exist.

then a multi-organismal process does not have to be a multi-cellular 
process, but it cannot be a non-multi-cellular, non-single-cellular 
process anyway.  the three categories you claim to be disjoint cannot be 
disjoint on any reasonable interpretation of the terms.

vQ

Wacek Kusnierczyk wrote:
> an interesting initiative.
> i made some inline comments.
> 
> 
> Jennifer Clark wrote:
>> Dear GO-Friends,
>>
>> Areas worked on:
>> 1. Processes are now organized under the major categories of 
>> multicellular organismal processes, cellular processes (including 
>> single-celled organisms), and multi-organism processes (formerly 
>> 'interaction between organisms'; there has been no change in meaning 
>> of this term, only the name has changed). These categories are 
>> disjoint; that is, no terms can have more than one of these terms as 
>> an is_a parent.
> 
> it is not clear what a multicellular organismal process is.  is it a
> process that may take place only in multicellular organisms? (i.e., one
> that cannot take place in a unicellular organism)
> 
> if yes, then why the definition of the term 'multicellular organismal
> process' is 'The biological processes, occurring at the level of the
> organism, pertinent to the function of the organism', which covers many
> processes taking place in unicellular organisms?
> 
> if no, and if the term means a process that _may_ take place not only in
> unicellular organisms, what is then the difference between this term and
> the term 'cellular process' which 'includes single-celled organisms'
> (rather than 'only single-celled organisms')?
> 
> the latter is defined as 'Processes that are carried out at the cellular
> level, but are not necessarily restricted to a single cell. For example,
> cell communication occurs among more than one cell, but occurs at the
> cellular level.'  why cannot such a process be a multi-organismal
> process? (there can be communication between unicellular organisms;
> would this not be covered by your definition?)
> 
> there does not seem to be a clear ground for the claim that the three
> (categories represented by the) terms you mention are disjoint.  perhaps
>  the intention is that they are, but the definitions are hardly an
> evidence for such an intention.
> 
> in fact, if there were a clear cut ditinction between the terms
> 'multicellular process' (only those processes that necessarily involve
> more than one cell) and 'cellular process' (only those processes that
> involve single cells, though may concurrently take place in many cells
> as distinct processes), then a multi-organism process would necessarily
> be a multicellular process.  i am not sure why communication that occurs
>  among more than one cell is a (uni)cellular process, while cytokine
> production is a multicellular process, although a (particular molecule
> of a) cytokine is produced completely by one single cell.  if you decide
> that the cell's being stimulated to the production is a good basis for
> classifying the process as a multicellular process, why is not
> communication (which is nothing else than sending and receiving stimuli)
>  a multicellular process?
> 
> (btw. i think you should avoid defining terms such as 'X process' as
> 'the processes...'.  be consistent.)
> 
>> 2. The major processes 'development' and 'metabolism' have been 
>> changed to 'developmental process' and 'metabolic process' 
>> respectively. Most of the child terms of 'metabolism' have also been 
>> changed to 'metabolic process', likewise for biosynthesis and 
>> catabolism terms. This is because these terms are groups of processes 
>> related by is_a, rather than a set of processes that comprises e.g. 
>> the whole of development related by part_of.
> 
> this sounds correct, though perhaps it would be desirable to have both 
> 'development' and 'developmental process', the latter being part of the 
> former, if you mean that 'part of' is the right relation here.  a quick 
> check at google reveals that the former term is used 3 orders of 
> magnitude (1000x) more often than the latter.  i guess many would still 
> like to be able to refer to development rather than to developmental 
> processes.  it should not be incorrect to say that a gene (product) 
> participates in development, even if it participates only in a specific 
> process.
> 
> (i guess it would not be obvious how to define development: if a 
> developmental process is part of development, then development must also 
> be a process, so what's the difference between development and a 
> developmental process?  or perhaps is 'part of' not the right relation 
> to use?)
> 
>> 3. The term 'physiological process' has been merged into its parent 
>> term, 'biological process', and all terms that included 
>> 'physiological' have either had their names changed to remove this 
>> word, or have been merged into their parent term. This is because we 
>> could find no satisfactory way of defining 'physiological' that 
>> distinguished it from simply 'biological'.
> 
> but is it because you really think that there are not other biological 
> processes than physiological processes, or because go by definition 
> should deal with physiological entities, thus every biological process 
> represented in go is necessarily a physiological process?  if this is 
> the case, then you somewhat contradict barry's intention to name things 
> with the right names:  the plant ontology replaced the term 'cell' by 
> the term 'plant cell', though all cells it speaks of are plant cells.
> 
> are pathological processes not biological processes?  will your 
> modification not lead to difficulties when go is to be combined (merged, 
> mapped, linked, whatever) with ontologies that speak of pathological 
> processes?
> 
>> 4. Homeostasis has been reworked to reflect that it covers the 
>> homeostasis of chemicals and homeostasis of cells, tissues, etc.
> 
> you define 'homeostasis' as 'any of the processes involved in the 
> maintenance of an internal equilibrium within an organism or cell.'
> 
> why can't you define 'development' as 'any of the processes ...', but 
> you can do it with 'homeostasis'?  why is 'cell redox homeostasis' a (is 
> a) 'cell homeostasis' rather than a part of it?  why is there no 
> 'homeostatic process' that would be part of 'homeostasis', analogically 
> to the case with 'development'?  these questions are perhaps silly, but 
> it seems to me a bit incoherent and ad hoc.
> 
>> 5. Pattern specification has been reworked.
>> 6. Protein biosynthesis and translation have been merged into one term.
> 
> i won't be popular if i say that 'protein translation' is an ill-formed 
> term (it is indeed in use, though less frequent that 'protein 
> biosynthesis', as seen at google).  but the case is this:  in ribosomes, 
> mRNA is read, aminoacids are collected (by tRNA) and glued together, and 
> thus a polypeptide (possibly a protein, another problematic 
> terminological issue) is formed.  what is (bio)synthesized is the 
> protein.  what is translated, is the mRNA!  when you translate a book 
> from english to german, it is the english version that you translate, 
> not the german.  (actually, this is a bit more complicated:  when you 
> translate a book, it is still the same book, only in different 
> languages.  what you translate in the case of mRNA and protein is 
> neither mRNA nor protein, but rather -- imperfectly -- the information 
> encoded.)  similar misuse takes place in the case of 'transcription'.
> 
> 
>> Areas that will be revised later:
>> 1. Locomotion, movement and transport
> 
> yes, with 'locomotion during locomotory behavior' as the first in the 
> queue?  you see, 'locomotory behaviour' has 'locomotion in response to 
> stimulus' (thus locomotion) as its _exact_ synonym, and so locomotion 
> during locomotory behavior is locomotion during locomotion in response 
> to a stimulus.
> 
>> 2. Synaptic processes
>>
>> If we do not hear any violent objections, we will commit the changes 
>> (merged with the current GO) on 2nd January 2007. Please let us know 
>> if this will cause any problems for you. We do not anticipate any 
>> problems being caused.
> 
> i guess my comments are not violent objections.
> 
> vQ
> 

-- 
Wacek Kusnierczyk

------------------------------------------------------
Department of Information and Computer Science (IDI)
Norwegian University of Science and Technology (NTNU)
Sem Sælandsv. 7
N-7491 Trondheim

tel.  0047 73591875
fax   0047 73594466

email waku(at)idi.ntnu.no
web   http://www.idi.ntnu.no/~waku
------------------------------------------------------


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