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From: Suzanna L. <su...@be...> - 2007-07-02 00:24:01
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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 >>> >>> --------------------------------------------------------------------=20= >>> - >>> - >>> --- >>> This SF.net email is sponsored by DB2 Express >>> Download DB2 Express C - the FREE version of DB2 express and take >>> control of your XML. No limits. Just data. Click to get it now. >>> http://sourceforge.net/powerbar/db2/ >>> _______________________________________________ >>> SOng-devel mailing list >>> SOn...@li... >>> https://lists.sourceforge.net/lists/listinfo/song-devel >> >> >> ---------------------------------------------------------------------=20= >> - >> --- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> SOng-devel mailing list >> SOn...@li... >> https://lists.sourceforge.net/lists/listinfo/song-devel >> > > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. 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