From: Chris M. <CJM...@lb...> - 2010-10-28 02:18:44
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On Oct 27, 2010, at 7:02 PM, Chris Mungall wrote: > > On Oct 27, 2010, at 12:40 PM, Arlin Stoltzfus wrote: > >> On 27 October 2010 01:16, Alan Ruttenberg >> <ala...@gm...> wrote: >>> On Fri, Oct 22, 2010 at 10:52 AM, Adam M. Goldstein <z_c...@sh... >>> > wrote: >>>> We discussed this a while back on the list in connection with >>>> phylogenesis. >>>> >>>> I suggested "ramifies" or something similar. >>>> >>>> The problem is that the RO relationships don't have something for >>>> splitting off---a new entity comes from an old one, but both >>>> coexist. >>> >>> Derives from is consistent with this. See http://genomebiology.com/2005/6/5/R46/figure/F3 >>> (c). >>> In BFO 2 draft we have relations 'begins to exist during' and >>> 'ceases to exist during' which would let you further differentiate >>> the cases. >> >> I'm not so sure about that. The text says that one entity >> "succeeds the other across a temporal divide". And it makes a >> distinction with transformation_of, which is a relationship of >> identity over time, in spite of some change in form. In >> tranformation, a thing undergoes a change but retains the relation >> of identity to its previous self at an earlier time. The >> implication is that derives_from doesn't have this property. > > You're absolutely right. > >> Presumably this is why Adam thinks that derives_from does not apply >> to other relationships. >> >> Its true that the BFO paper claims that derives_from is applicable >> to cases such as budding in yeast, in which the parent clearly >> persists after the child (bud) emerges, but how is this not a >> contradiction? > > It *almost* claims this: > > "We can also represent more complex cases where transformation and > an ***analog of*** derivation are combined, for example in the case > of budding in yeast [27] , where one continuant continues to exist > identically through a process wherein a second continuant floats > free from its host" The other option here is to combine derives_from as defined in the paper with part_of. the child derives from part of the parent, that part ceases to exist after the derivation, but the parent as a whole continues to exist. The combined relation could be named derives_from_part_of. > The "analog of" part is easy to miss - in fact I missed it myself > earlier today, which lead me to mis-recall the actual definition of > derives_from as being inclusive of the parent-surviving scenario. > > So I think the correct reading of the paper is that we need a new > relation for the analog of derivation to cover budding, biopsies > etc. The paper is incomplete w.r.t exhaustively partitioning the > type of temporal continuation, and is best viewed as an exercise in > how this should be done. > > In fact this is mostly of theoretical interest, as to my knowledge > none of the anatomical ontologies ever adopted "derives_from" - as > Pankaj points out, the label is misleading (evo folks are > particularly unhappy), and distinguishing transformation_of from > derives_from was considered too difficult. In addition, very many > existing develops_from relationships are neither transformations nor > derivations, because the parent tissue continues to exist. Instead > everyone opted to keep the fuzzy but familiar "develops_from", and > the RO definition of derives_from was relegated to the ivory tower > and never applied. > > I think the way forward as far as most bio-ontologies are concerned > is to focus on biological definitions. > > Melissa summarizing David's talk from the cell meeting: > >> At the cell meeting we discussed the idea that cells can >> derive_from one another as defined in RO, where a derivation would >> involve some kind of cell division and a transformation would not. >> A neuroblast which does not undergo a cell division an becomes a >> neuron would be a transformation. A neuroblast that buds off to >> give rise to a neuron would be a derivation. >> >> Where this breaks down is on the gross anatomical level, where the >> level granularity is arbitrary. When developmental biologists say >> one gross structure develops from another, they mean that there is >> continuity of cell lineage. > > I'm confident from this we have develops_from between cells covered > - though we have to think a bit about the relation between the cels > in a cell line and the in vivo progenitor. > > As Melissa says the gross level is harder. We can define a chain: > > A has_part cell C > C1 develops_from cell C2 > C2 part_of B > ==> > A develops_from B > > But this is almost certainly too permissive. We might need to fudge > it with something hard to formalize like "X% of cells", or perhaps > it can be done using the definition of tissue. > > It would be good for some of the dev bio folks to come up with some > edge cases we can explore. > >> Arlin >> ------- >> Arlin Stoltzfus (ar...@um...) >> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST >> IBBR, 9600 Gudelsky Drive, Rockville, MD >> tel: 240 314 6208; web: www.molevol.org >> >> ------------------------------------------------------------------------------ >> Nokia and AT&T present the 2010 Calling All Innovators-North >> America contest >> Create new apps & games for the Nokia N8 for consumers in U.S. and >> Canada >> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >> marketing >> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi >> Store >> http://p.sf.net/sfu/nokia-dev2dev_______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > |