Re: Reminder: SysBio Wednesday 11AM ET / 4PM GMT / 5PM CET

I think it is a bit generic... the 'semantic' component is missing,
see for instance:

"Semantic Systems Biology is a complementary approach to Systems
Biology which makes use of semantic web technologies to provide
biological insights and hypotheses based on biological knowledge that
has been adequately represented which in turn might be exploited using
reasoners for instance." [1, 2, 3]

or:

"Semantic Systems Biology is the marriage between a need for
integration and standardized access to biological data sources and the
technologies devised to address that problem in a domain independent
fashion." [4]

or:

HCLSIG/SysBio@W3C --> http://www.w3.org/wiki/HCLSIG/SysBio

cheers,
Erick
[1] http://www.biomedcentral.com/1471-2105/10/S10/S11
[2] http://bib.oxfordjournals.org/content/10/4/392.full
[3] http://www.semantic-systems-biology.org/faq/faqs-ssb
[4] http://hcls.deri.ie/semantic-systems-biology/

On 28 May 2012 23:19, Michel Dumontier <michel.dumontier@gmail.com> wrote:
> I guess I do :)
>
> m.
>
>
> On Tue, May 29, 2012 at 12:05 AM, Erick Antezana <erick.antezana@gmail.com>
> wrote:
>>
>> so, do you define 'semantic systems biology' as "an interdisciplinary
>> approach to create a more powerful modelling and validation
>> framework..."?
>>
>> cheers,
>> Erick
>>
>> On 28 May 2012 21:41, Michel Dumontier <michel.dumontier@gmail.com> wrote:
>> > My goal in pursing semantic systems biology is to i) see to what extent
>> > model behaviour can be validated against accrued experimental evidence,
>> > and
>> > ii) that qualitative knowledge can be used to reformulate valid models.
>> > Thus, it is an interdisciplinary approach to create a more powerful
>> > modelling and validation framework.
>> >
>> > Best,
>> >
>> > m.
>> >
>> >
>> >
>> >
>> > On Mon, May 28, 2012 at 8:16 PM, Franco Du Preez
>> > <franco.dupreez@gmail.com>
>> > wrote:
>> >>
>> >> Hi Michel,
>> >>
>> >> Thanks for the questions and references. It would definitely help to
>> >> clarify the perceived 'chasm'. In my experience of systems biology,
>> >> understanding the control of different cellular processes on the
>> >> behaviour
>> >> of the cell/organism has been a central element. Approaches such as
>> >> metabolic control analysis provides researchers with a framework to
>> >> reach
>> >> this goal, but what would be the analogue of this, if approached from
>> >> the
>> >> semantic side? Or is the goal different, to link models to knowledge
>> >> frameworks and to make use of automated reasoning instead?
>> >>
>> >> You also asked wether the approach or application create the chasm. To
>> >> me
>> >> the approach is clearly different. In the absence of quantitative
>> >> models, I
>> >> would say that the application also differs because its hard to imagine
>> >> how
>> >> one would predict the effects of quantitative changes in a system
>> >> without
>> >> such models.
>> >>
>> >> I should also add that the integration of data and models is an
>> >> important
>> >> issue at JWS Online and the SEEK, so I am glad to learn more.
>> >>
>> >> Best regards,
>> >> Franco
>> >>
>> >>
>> >> On 25 May 2012, at 4:50 PM, Michel Dumontier wrote:
>> >>
>> >> Franco,
>> >>
>> >> On Thu, May 24, 2012 at 10:38 PM, Franco Du Preez
>> >> <franco.dupreez@gmail.com> wrote:
>> >>>
>> >>> Hi all,
>> >>>
>> >>> As someone speaking purely from the kinetic modeling side, I have to
>> >>> admit that there seems to be a quite a big chasm between 'traditional
>> >>> systems biology' (if it has existed for a long enough period to be
>> >>> called
>> >>> that ;)) and the semantic approach.
>> >>
>> >>
>> >> in what what do you think there is a "chasm"? is it just in that the
>> >> approaches appear vastly different - one deals with values changing
>> >> with
>> >> time, the other with truth values? Or is it that the applicability
>> >> seems
>> >> unclear? If biomodels database is any indication, one can semantically
>> >> annotate the model entities with ontologies without much problem [1]. I
>> >> and
>> >> others have shown how to use those ontologies to check the consistency
>> >> of
>> >> the models [2]. More recently work [3], shows how we can integrate the
>> >> results of simulations in order to answer questions that spans beyond
>> >> the
>> >> original model annotations.  There are plenty more things that we can
>> >> do
>> >> now, particularly in the context of enrichment analysis, association
>> >> studies, rule mining, etc.
>> >>
>> >> m.
>> >>
>> >> [1] http://www.ncbi.nlm.nih.gov/sites/entrez/16333295
>> >> [2] http://www.biomedcentral.com/1752-0509/5/124
>> >>
>> >>
>> >> [3] http://www.slideshare.net/micheldumontier/formal-representation-of-models-in-systems-biology
>> >>
>> >>
>> >>
>> >>>
>> >>> This being said, I really looked forward to yesterdays session as  it
>> >>> touched on the interesting and practical application of model
>> >>> alignment, but
>> >>> alas, I could not get my audio via the dial in. I guess many must have
>> >>> asked
>> >>> why were not using skype, so I wont, but Mark's mail has prompted me
>> >>> to do
>> >>> more digging and I finally got round to downloading a voip client that
>> >>> can
>> >>> dial sip addresses (holding thumbs for next time).
>> >>>
>> >>> Cheers,
>> >>> Franco du Preez
>> >>>
>> >>> On 24 May 2012, at 5:18 PM, Mark wrote:
>> >>>
>> >>> > Hi all SysBio'ers!
>> >>> >
>> >>> > I know it isn't really my place to be saying anything, but... when
>> >>> > has
>> >>> > that ever stopped me ;-)
>> >>> >
>> >>> > The last conference call was... odd?...  and while Jun's
>> >>> > extraordinary
>> >>> > efforts to keep it moving forward were greatly appreciated (!!  well
>> >>> > done
>> >>> > !!) I think it might be worth having a very open discussion about
>> >>> > what our
>> >>> > expectations are from this group, since it was a fairly small group
>> >>> > and
>> >>> > apparently with a wide range of experience and expertise.
>> >>> >
>> >>> > From what I could hear, there were four "tiers" of expertise in the
>> >>> > group.  Starting from the bottom:
>> >>> >
>> >>> > 1)  People like me, who know nothing at all beyond that the
>> >>> > SysBio/Modeling community have worked hard on putting together
>> >>> > standards and
>> >>> > technologies that are bearing fruit; and that I (as a mere potential
>> >>> > user of
>> >>> > the tech) need to become MUCH more aware of what they're doing in
>> >>> > order to
>> >>> > successfully pursue my own research interests.  So... I'm the
>> >>> > ultimate
>> >>> > lurker on the call.
>> >>> >
>> >>> > 2)  People like Erich, who know *a lot* about what's going on in the
>> >>> > field (because this is their company's business!) but, as a vendor,
>> >>> > isn't
>> >>> > going to be the first one to speak in a call like this because it
>> >>> > might
>> >>> > come-off sounding like a sales-pitch.  He's likely interested in
>> >>> > both how
>> >>> > the technology is evolving (to ensure their products stay current)
>> >>> > as well
>> >>> > as listening to the needs of the community (so that their products
>> >>> > stay
>> >>> > relevant), but I don't expect him to lead the discussion if for no
>> >>> > other
>> >>> > reason than he's simply too polite to "take-over"  :-)
>> >>> >
>> >>> > 3)  People like Jun, who has put in a lot of time learning what's
>> >>> > out
>> >>> > there, has a deep and genuine interest, and wants to discuss the
>> >>> > pro's and
>> >>> > con's of the various pieces at some level of detail with people who
>> >>> > have at
>> >>> > least tried to use it.  (...but there weren't many! ...so she was
>> >>> > speaking
>> >>> > to herself most of the time...)
>> >>> >
>> >>> > 4)  The full experts in the domain, most of whom were not able to
>> >>> > make
>> >>> > the call, unfortunately.  And I don't say that in any way as an
>> >>> > accusation,
>> >>> > but rather, looking forward, I see a potential "boredom problem",
>> >>> > which is
>> >>> > what I think needs to be discussed.  At least one of the domain
>> >>> > experts who
>> >>> > did attend, left the call mid-chat on the basis that it was "too
>> >>> > simplistic"
>> >>> > (exact quote from IRC)... so if we don't find a way to engage you,
>> >>> > the
>> >>> > experts, we might be in for some disappointing meetings!
>> >>> >
>> >>> >
>> >>> > What I'd like to ask the SysBio community - especially category (4),
>> >>> > since it seems to me that they are the critical ones to have on
>> >>> > these calls,
>> >>> > is:  "what can WE (1), (2), (3) do to make these calls as useful to
>> >>> > you as
>> >>> > they will be to us?"  I understand that you're probably already
>> >>> > talking to
>> >>> > each other, since this field is your "baby", and thus these calls
>> >>> > have the
>> >>> > potential to offer you little benefit beyond your existing email
>> >>> > (etc.)
>> >>> > chats!  ...So... what can we do, as the broader-community, to
>> >>> > provide
>> >>> > value/feedback/etc. that would ensure we all - experts and noobs
>> >>> > alike - get
>> >>> > something useful out of this group and enjoy and value the hour that
>> >>> > we
>> >>> > spend together every couple of weeks?
>> >>> >
>> >>> > If I'm speaking out-of-turn, please flame me :-)  I can take it!
>> >>> >  LOL!
>> >>> > I just want to see this group succeed, and I am willing to stick my
>> >>> > neck out
>> >>> > to see if I can help!
>> >>> >
>> >>> > :-)===={
>> >>> >
>> >>> >   ^^^
>> >>> >  my neck
>> >>> >
>> >>> > Best wishes all!
>> >>> >
>> >>> > Mark
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> Michel Dumontier
>> >> Associate Professor of Bioinformatics, Carleton University
>> >> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>> >> Group
>> >> http://dumontierlab.com
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > Michel Dumontier
>> > Associate Professor of Bioinformatics, Carleton University
>> > Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>> > Group
>> > http://dumontierlab.com
>> >
>
>
>
>
> --
> Michel Dumontier
> Associate Professor of Bioinformatics, Carleton University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
> http://dumontierlab.com
>

Received on Monday, 28 May 2012 21:57:01 UTC