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is_a complete biological process ontology
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.
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
> (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
>> 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.
Department of Information and Computer Science (IDI)
Norwegian University of Science and Technology (NTNU)
Sem Sælandsv. 7
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fax 0047 73594466
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