Alan,
Thanks for that summary.
SWAN is not a software project - it is a project for a technology-
mediated social infrastructure. Those fancy words mean we are trying
to get the working scientists themselves to curate the material for
their own benefit, self-understanding & "karma points". We think it
is the only sustainable & scalableway to represent hypotheses.
Nothing in principle - and I hope we can test this out - should
prevent people who want to link very deep annotation of various kinds
to SWAN hypotheses, from doing so. But that is not our project. We
are "just" providing the framework. An essential criterion is that
whatever we do is doable by working scientists and helps them to work.
Best
Tim
On TuesdayMar 6, 2007, at 9:59 PM, Alan Ruttenberg wrote:
Here's my analysis:
I think Bill wants (1). Bill is trying to convince the SWAN team to
curate to a level deeper than you are going now, by naming and
collecting relationships between the biological entities that are
being talked about in the paper SWAN curates. The page he
references is detailing his own effort to simultaneously learn for
himself and engage us (HCLS) to try to explicitly representing more
of the biological facts/hypotheses at the level of the
participating biological entities. PATO, the ontology he is trying
to learn how to use, is just one of the OBO ontologies - its
domain is phenotypes (or qualities in BFO speak) of organisms and
properties of some sub-organismal biological material. He thinks
that there is a lot a work in the rest of the OBO ontologies and
other community efforts, and that this should be taking advantage
as much as possible in our efforts.
He's also coming from perspective, which I think originates with
Barry Smith, that many of the problems we have had in managing and
making productive use of information related to biology and health
in recent history originate from not trying to represent reality,
and instead representing "concepts" which, because they don't
connect clearly enough to reality, don't land up having enough
shared meaning to make good use of when integrated or scaled.
My understanding from discussions we (Tim and I) have had is that
the SWAN project has, as a matter of setting scope, and addressing
its use cases, decided against doing this, at least for the moment.
This is an understandable choice - it's pretty hard work to learn
and do this kind of representation, as practices and the
ontologies themselves are just developing. I think this is a
reasonable decision, given that what Bill is suggesting is by no
means easy. I'm curious to see what happens with SWAN. I suspect
that Bill is too!
Still, Bill is hopeful that the SWAN team will change its mind,
because he thinks, as some subset of the people on this list, that
his kind of representation will be what leads to the most
substantial payback in what it enables for science and medicine.
Hope this helps,
Alan
On Mar 6, 2007, at 9:10 PM, Tim Clark wrote:
BIll:
(1) or (2) or none of the above is good enough for right now. I
am finding your proposal difficult to follow.
Tim
On TuesdayMar 6, 2007, at 7:43 PM, William Bug wrote:
Sorry, Tim.
Can't really go into more detail right now. I have a lot of
planning still to do on an all day meeting I must lead tomorrow.
I lay it out considerable detail on this proposal on that page I
cite below:
http://esw.w3.org/topic/HCLS/OntologyTaskForce/
OboPhenotypeSyntaxExperiment
It is just a suggestion. As I said a few weeks ago when I put it
out there, I welcome any feedback. Please amend, append, or
correct as you see fit.
As I mentioned to you a few weeks ago, I'd see this as a way of
providing much more structure to back up the "Concepts" and
"Claims" that are represented in SWAN. In fact, the
"Concepts" (as represented in RDF using community shared
ontologies/terminologies) provide a link into this more structure
"bridge" I'm describing and the wealth of detail contained in RDF
converted versions of BioPAX, SenseLab (BioPharm), ABA, MPO-based
annotations from MGI & RDG, etc.
I hope this helps a little.
Cheers,
Bill
On Mar 6, 2007, at 4:33 PM, Tim Clark wrote:
Bill,
I am trying to understand your proposal. Which are you suggesting:
(1) we curate in to SWAN some existing published work
hypothesizing connection of, for example, MPTP/MPP+ mechanism to
some forms of PD; or
(2) we build "our own" hypothesis of MPTP/MPP+ mechanism
relationship etc, not existing in the literature, and curate it
in to SWAN?
or something else?
Tim
On TuesdayMar 6, 2007, at 7:25 PM, William Bug wrote:
Hi All,
Looks like a lot of substantive work was done at the F2F.
Kudos to all who participated!
I'd like to highlight one of the issues EricN mentioned.
On Mar 6, 2007, at 8:29 AM, Eric Neumann wrote:
As part of the scernario using the known aggregate of facts,
add a few *select* hypotheses (triple graphs), that would make
major connections with the rest of the graph that would
function as a "bridge" across the data and models; Show the
new insights from this merged compositeby re-applying queries
that now retireve more connections. One example Karen had was
around the MPTP/MPP+ mechanism for some forms of PD.
This suggestion that came from the off-line discussion amongst
several call-in participants is EXACTLY the point I've been
trying to make since September with the proposal to use the OBO
Foundry PATO + Phenotype assertion syntax.
http://esw.w3.org/topic/HCLS/OntologyTaskForce/
OboPhenotypeSyntaxExperiment
I think this is critical to bringing together the various
resources around complex concepts such as LTP/LTD - which, as
I've mentioned before is a MODEL not a fact per se.
The advantage to using this approach is your assertions are
based on reported evidence from the literature - not on a high-
level encapsulation of an abstraction in the form of a complex
model.
The strategy I'm proposing is only contrived in the sense you
focus in specifically on a collection of articles covering a
particular micro domain within the general use case. I've even
proposed a way in which one could determine a metric to decide
exactly how much of this sort of highly structured curation is
required. The amount will likely be a function of the
complexity and abstraction in the underlying hypothesis and the
extent to which the underlying RDF sources are already inter-
liked via shared semantic frameworks such as MeSH, GO, BioCyc,
etc.
I would note the article I chose as an example was appropriate
given the PD use case as of September 2006. It was mainly put
out there to illustrate how to approach this task. We'd now
want to focus specifically on articles that cover the specific
micro domains in the most recent, narrowed version of the use
case.
I have been working on how to use tools such as SWOOP to
greatly reduce the effort required to construct these phenotype
assertions.
I'm afraid I'm busy for the next week with BIRN meetings - some
of which I need to lead - so I don't expect to be able to
provide much help on this until late next week.
Best of luck!
Cheers,
Bill
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
Please Note: I now have a new email - [EMAIL PROTECTED]
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
Please Note: I now have a new email - [EMAIL PROTECTED]
