Alan,
that is a superb message, very well-articulated I will ponder it. And as I said I don't really want to keep doing this theoretical dance and look forward to more substantive conversations. Jeremy On Mar 21, 2013, at 9:38 PM, Alan Ruttenberg <alanruttenb...@gmail.com> wrote: > > > On Thu, Mar 21, 2013 at 7:56 PM, Peter Ansell <ansell.pe...@gmail.com> wrote: > On 22 March 2013 12:05, Alan Ruttenberg <alanruttenb...@gmail.com> wrote: > > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll <j...@syapse.com> wrote: > >> > >> To me, that seems to lead us back to the earlier discussion (rathole?) > >> about owl:sameAs > >> I tend to a view that there are diminishing returns in terms of levels of > >> indirection here! > > > > As the number of levels of indirection increases, perhaps. But here we are > > talking about 1 level - separating claims from truth. > > The question that scientists spend their lives trying to establish is > the one that you seem to think is clearly defined in this statement, > ie, "seperating claims from 'truth'". In some domains, such as > logic/mathematics, "truth" is easy to define, and that seems to be the > basis that the RDF specifications use to justify their semantics. > However, in others, such as life sciences (ie, the domain of > public-semweb-lifesci), at least some of the best information we have > is approximate idealist information that may not exactly match > anything at all in reality (ie, large genome reference assemblies that > are statistically modelled from multiple samples but may not actually > match base for base with any actual DNA strands in the real world). > These approximations are referenced directly by scientists in their > publications without them having to qualify every statement as > referencing a "claim". > > When they need to say it is a claim they do so, either referring to the > matter in that way or by language signals in their text. In the other cases > they are different consequences for getting things wrong. If they assert > something directly and their result depends on it then their result will be > called into question. > > I am not saying that science presented as fact is infallible. Of course it > is. But when we talk about things as fact we tend to back it up by implicit > agreement to revise if the thing presented as fact is determined to be false. > I (and Foundry) take this situation as one where the ontological commitment > is one in which, should we make such statements and find them to be wrong, we > will fix them. There's lots of cases where that isn't the commitment, > Jeremy's case being one of them, I suspect. And there are plenty of true > things (things that no one would object to) despite this. That the > information is about a dna sequence, that it is about differences between > humans, that it is about an amino acid change at one place in the molecule, > etc. > > Associated with each of the three kinds of logical commitment in those slides > I wrote what inconsistency means. IMO, if you have some system and there's no > way for you to be wrong in your usage then it's not worth using. Please tell > me, given your assessment of scientific use of RDF, if there is any such use > that can be wrong or inconsistent? If you can't then I'm guessing we are > going to have a continued 'failure to communicate'.(attempt at humor, culture > specific reference: > http://en.wikipedia.org/wiki/What_we've_got_here_is_(a)_failure_to_communicate) > > I am not sure why you say that there is only one layer of wrapping > needed. I can think of many different situations where someone could > have more than one layer of alternative interpretations that they may > need to accommodate other scientists now and in the future. The 4 or > so layers that the provenance ontology has just for published > documents are worrying enough, and they may not be enough to map the > complexities of genome reference assemblies, as genomics researchers > may have a different "publication" workflow to book publishers. > > Since I am not familiar with the PROV model (I tried to read it through but > got frustrated), please say a little more, and justify why you think these > "layers" need be represented as levels of indirection rather than assertions > on a first or second level such as I have described. > > > 2) I think there's a big difference between what one publishes on the web, > > and what one uses in the privacy of one's home, so to speak. If one is > > publishing on the web, it is good citizenship to respect specifications, and > > to consider the impact of one's assertions on the broader data consumer > > community. That consideration, IMO, is justification enough for the 1 extra > > indirection necessary to not make statements that are too strong. > > The specifications seem to be based on premises that the practicing > scientists may not ever accept. Ie, the idea that there is static > scientific "truth" that can be unamgiuously and continuously > communicated, and not "challengable current theories" that can be > either alternatively stated, or gradually or suddenly revoked and > replaced with new best theories. Scientists need to be able to > interpret, contrast, and concurrently utilise, past information > directly without having to suddenly wrap up past "truths" inside of > "claims" because they may be out of date with something someone else > has now put into the RDF-sphere. The whole idea that statements could > be "too strong" takes its basis from "static truth" and I cannot > personally accept that we need to represent everything for life > sciences inside of "claims" (or alternatively have everyone create new > URIs for everything they want to talk about) just incase it changes in > future or someone would find it difficult to deal with the statement > if their application relies on a different structure for their queries > to work. > > No. The specification is based on the premise that if you are going to share > information there have to at least be some rules. The rules were developed by > a skilled working group, the semantics were written by an expert, and the > whole survived what can be a rather brutal W3C approval process. There is > room in those semantics to express what you want. People seem to be annoyed > that it takes an extra link, some extra thinking, to do that. Tough. > > If someone else has a completely different problem domain that would > find it difficult to deal with direct, "un-framed"/"un-claim-wrapped" > statements from third-parties using a URI because they clash with some > of their statements or assumptions, how would the claim wrapping > practically help them? > > I think you have this backward. Naive engineers (meaning those that haven't > hung around with the people on this list) will read the spec and have > expectations about how things work, such as that one URI represents one > resource, independent of "context". The idea that its ok to break the rules > because they are inconvenient is the equivalent of thinking it's ok to be a > vandal. It's your responsibility as an educated engineer to understand and > use the spec you are using in the documented way, or to write a different > one. If you want to talk about specific problems you have with indirection, > let's talk about that. But it is clear that the onus is on you to figure out > a way to use the technology as specified, rather than me to solve your (at > the moment vague and unspecified) usage problems. > > Life scientists attempting to use RDF to model their heterogeneous > information aren't trying to make ambiguous statements or reject the > wisdom of the logic/maths backgrounds of the specifications authors, > they are just trying to get work done, and it seems that we are being > told that we are bad citizens for having a complex, "un-truthy" > domain. > > If I see a biologist doing mathematics, I'm going to look at whether they get > it right. If they do representation I'm going to expect they do it right. I > look to see that I they do the biology right too (best I can). The labs hire > professionals to do their mass spec. Should we expect less for data? > > Take care, > Alan > > > Cheers, > > Peter >
