Re: [SO-devel] SO immunology Workshop

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Hi Chris,

I thought we'd definitely ruled out (a)

and that there is clean-up work to be done accordingly.

-S

On Jun 21, 2007, at 7:39 PM, Chris Mungall wrote:

>
> On Jun 21, 2007, at 3:27 PM, Alan Ruttenberg wrote:
>
>> Nice to see this summary! Thanks so much!
>>
>> Some questions/comments.
>>
>>> (Barry wants to make it clear that sequences are biological reality
>>> =96 not representations.)
>>
>> Alan would like to have this to. However I would also like to know
>> what they are in biological reality -
>> what are their instances? Are they independent or dependent?
>
> Let me expand on Alan's question then answer:
>
> Do the terms in the SO "located sequence feature" branch, such as
> gene, RNA, exon, chromosome and so on, represent:
>
> (a) Molecules, things made of molecules, and parts of these molecular
> entities
>
> (b) Characteristics of some molecules - specifically their sequence.
>
> Molecules are the bearers of various characteristics such as mass, 3-
> dimensional shape, and in some cases, linear sequence. Sequences, by
> contrast, do not have these kinds of qualities. (bearers of qualities/
> characteristics are sometimes called independent, and the qualities
> themselves dependents - it's a useful distinction)
>
> Making this kind of elementary distinction is crucial for SO to be
> successful outside genomics exchange formats, and also for rational
> structuring of SO.
>
> For most ontologies no conscious choice has to be made - for example
> the GO cellular component hierarchy clearly represents things made of
> molecules. With SO it is a little trickier because of the way people
> overload words in the genomics domain.
>
> I was only there for the first day of the meeting, but I believe the
> commitment was made that the LSF branch has terms that represent
> sequences and pieces of sequences.
>
> This may seem trivial but it has some implications - many SO
> definitions are written as if they are definitions for the
> corresponding molecules, and some terms confusingly overlap with GO
> cellular component; SO:chromosome should really be called
> SO:chromosome_sequence. It also has implications for relations: for
> example, an mRNA may become spatially distant from the transcript-
> encoding genomic region that served as template, similarly with the
> intron and the transcript it is spliced from.
>
> Alan's second question (actually first but I'm going in reverse
> order) is: what are the *instances* of SO terms such as transcript,
> exon etc? In OBO, terms represent general kinds of entities that are
> instantiated in nature. This is quite simple for GO - an instance of
> the GO term "chromosome" would be an actual chromosome, occupying a
> specific region of space at any given time. With sufficiently
> advanced instrumentation you could count the number of chromosomes in
> a room.
>
> If we instead ask what is an instance of a SO:chromosome_sequence,
> there are two possible answers. One is that each individual physical
> chromosome has its own distinct unique chromosome sequence - there is
> a 1-1 correspondence. The other is that chromosome sequences are
> considered to be shared by distinct physical chromosomes, if they are
> indistinguishable with respect to the sequence of base types.
>
> I believe it was decided the latter was chosen. This means that
> instances of SO LSF terms are in fact patterns that are each present
> in multiple locations. I think this decision is correct if we are to
> give a sensible account of alleles as distinct entities from genes.
> It also maps well to conventional usage: you would say the typical
> human has 38 odd HOX genes. You would not say they have 38*10^12 HOX
> genes; and it would awkward to say they had 38 HOX gene types. This
> has big implications for people using SO as an ontology rather than
> terminology.
>
> The obvious parallel is books: as humans we naturally switch between
> talk of copies-of-books and book-patterns
>
>>> A is an allele of B =3D definition there is some C such that A and B
>>> are both mutations of C.
>>
>> Shouldn't the definition allow also for  A being a mutation of B or
>> B  a mutation of A?
>>
>>> 2. Spliced_variant_of
>> If you want to match typical usage it would be
>> "splice_variant_of" (not past tense) As is it reads as if the
>> comparison is between something not spliced and something spliced.
>>
>>> Splice variants are different from allelic variants.
>>> A is a splice product of B means that A is an mRNA and B is a type
>>> of primary transcript.
>>> Every instance of A arises through splicing from some instance of B.
>>
>> primary transcript is_a mRNA, yes?
>>
>>> A is a spliced_variant_of B =3D definition there is some C such that
>>> A is a splice product of C and B is a splice product of C and A and
>>> C are structurally different.
>>
>> "A and B" vs "A and C". Structurally different should be clarified as
>> different with respect to the primary structure - if the same
>> sequence mRNA folds in a different way we wouldn't call them splice
>> variants.
>>
>> -Alan
>>
>> On Jun 21, 2007, at 2:11 PM, Karen Eilbeck wrote:
>>
>>> Hi all,
>>> I just wanted to let you know that SO held a workshop for
>>> immunology terms last week in Salt Lake City.
>>> The workshop was very productive, resulting in several updates to
>>> the ontology, some new collaborations, and even a new relation
>>> being added to the obo relations ontology.
>>> The focus was modelling the MHC/HLA sequence, and also VDJ
>>> recombination.
>>> The webpage for the workshop details the attendees, the talks, the
>>> notes/action items and a list of changes made to SO.
>>>
>>> A couple of highlights being that the definition of gene was
>>> updated, the following terms were added: haplotype, diplotype,
>>> genotype, genome, allele.
>>>
>>> The page can be accessed at:
>>> http://www.sequenceontology.org/immuno_workshop.shtml
>>>
>>> Cheers,
>>> Karen
>>>
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