Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. Location: Stata G451, MIT.
The Stata Center is the huge Gehry building at the corner of Vassar and Main in Cambridge. G451 is on the 4th floor very close to the east (= Gates = Main St) elevator bank. From the elevators go short distances straight, left, right, right, straight; see floor plan at http://www.csail.mit.edu/resources/maps/4G/G451.gif .
We'll discuss the relations between BioPAX, the semantic web, and OBO (especially OBI and OBO Foundry).
<jonathan.r...@gmail.com> wrote: > The meeting will be:
> Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > Location: Stata G451, MIT.
> The Stata Center is the huge Gehry building at the corner of Vassar > and Main in Cambridge. > G451 is on the 4th floor very close to the east (= Gates = Main St) > elevator bank. From the elevators go short distances straight, left, > right, right, straight; see floor plan athttp://www.csail.mit.edu/resources/maps/4G/G451.gif.
> We'll discuss the relations between BioPAX, the semantic web, and OBO > (especially OBI and OBO Foundry).
I don't think this group has ever had dialin participants before, but we'll set up something for you - at worst a laptop with its microphone & speaker + skype. I will investigate improvements on this, like maybe equipment that will allow you to hear what's being said; I may be able to borrow one of those fancy phones. If a dialin were available would you be able to use it?
Jonathan
On Oct 10, 9:13 am, Michel Dumontier <michel.dumont...@gmail.com> wrote:
> <jonathan.r...@gmail.com> wrote: > > The meeting will be:
> > Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > > Location: Stata G451, MIT.
> > The Stata Center is the huge Gehry building at the corner of Vassar > > and Main in Cambridge. > > G451 is on the 4th floor very close to the east (= Gates = Main St) > > elevator bank. From the elevators go short distances straight, left, > > right, right, straight; see floor plan athttp://www.csail.mit.edu/resources/maps/4G/G451.gif.
> > We'll discuss the relations between BioPAX, the semantic web, and OBO > > (especially OBI and OBO Foundry).
> I don't think this group has ever had dialin participants before, but > we'll set up something for you - at worst a laptop with its microphone > & speaker + skype. I will investigate improvements on this, like maybe > equipment that will allow you to hear what's being said; I may be able > to borrow one of those fancy phones. If a dialin were available would > you be able to use it?
> Jonathan
> On Oct 10, 9:13 am, Michel Dumontier <michel.dumont...@gmail.com> > wrote: > > Hi, > > Will I able able to skype into the meeting?
> > <jonathan.r...@gmail.com> wrote: > > > The meeting will be:
> > > Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > > > Location: Stata G451, MIT.
> > > The Stata Center is the huge Gehry building at the corner of Vassar > > > and Main in Cambridge. > > > G451 is on the 4th floor very close to the east (= Gates = Main St) > > > elevator bank. From the elevators go short distances straight, left, > > > right, right, straight; see floor plan > athttp://www.csail.mit.edu/resources/maps/4G/G451.gif.
> > > We'll discuss the relations between BioPAX, the semantic web, and OBO > > > (especially OBI and OBO Foundry).
The "attitudes" in this paper seem most relevant to our planned discussion, and I believe they point us toward 3 excellent avenues for BioPAX's evolution and growth.
jonathan.r...@gmail.com wrote: > The meeting will be:
> Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > Location: Stata G451, MIT.
> The Stata Center is the huge Gehry building at the corner of Vassar > and Main in Cambridge. > G451 is on the 4th floor very close to the east (= Gates = Main St) > elevator bank. From the elevators go short distances straight, left, > right, right, straight; see floor plan at > http://www.csail.mit.edu/resources/maps/4G/G451.gif .
> We'll discuss the relations between BioPAX, the semantic web, and OBO > (especially OBI and OBO Foundry).
I think [1] clearly identifies several important issues in using BioPAX as it stands now. **Dan, can you elaborate on what 3 avenues for BioPAX evolution and growth comes from [2]? [3] compares with SBML and others and [4] shows an applicaiton in data integration and ontology extensions.
> The "attitudes" in this paper seem most relevant to our planned > discussion, and I believe they point us toward 3 excellent avenues > for BioPAX's evolution and growth.
> I hope all those meeting tomorrow will have read about them.
> Dan
> jonathan.r...@gmail.com wrote: > > The meeting will be:
> > Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > > Location: Stata G451, MIT.
> > The Stata Center is the huge Gehry building at the corner of Vassar > > and Main in Cambridge. > > G451 is on the 4th floor very close to the east (= Gates = Main St) > > elevator bank. From the elevators go short distances straight, left, > > right, right, straight; see floor plan at > > http://www.csail.mit.edu/resources/maps/4G/G451.gif .
> > We'll discuss the relations between BioPAX, the semantic web, and OBO > > (especially OBI and OBO Foundry).
Tensions between "record" and "domain" attitudes in BioPAX.org have slowed the growth of the BioPAX standard. The attitudes compete to influence a single, monolithic, over-controlled "next release", but they are so much at odds that little happens. [2] identifies and names the attitudes, which alone will encourage some resolution.
It may come if BioPAX standards by policy shift into a more open, modular form, in which "attitudes" can be independently expressed and formalized within smaller sub-schema. Authored and released by sub-groups, each could then be selectively re-integrated as BioPAX end-users saw fit, not unlike modules in a programming library.
Modularizing release standards requires "statement" attitudes and concepts. They get ignored in BioPAX 2.0, as they arise (gasp) in NLP work. Yet they can advance interoperability, not merely among competing BioPAX modules, but among open sets of ontologies from many sources - each seen as the competing statement that it is.
A way forward: adopt modular release policies plus the "statement" design patterns, concepts, and support tools they require. An old proposal on this exists, but would benefit from some updating:
> I think [1] clearly identifies several important issues in using BioPAX > as it stands now. **Dan, can you elaborate on what 3 avenues for BioPAX > evolution and growth comes from [2]? [3] compares with SBML and others > and [4] shows an applicaiton in data integration and ontology extensions.
> Cheers,
> -=Michel=-
> On 10/10/07, *Dan Corwin* <d...@lexikos.com <mailto:d...@lexikos.com>> wrote:
> Hi All -
> The "attitudes" in this paper seem most relevant to our planned > discussion, and I believe they point us toward 3 excellent avenues > for BioPAX's evolution and growth.
> I hope all those meeting tomorrow will have read about them.
> Dan
> jonathan.r...@gmail.com <mailto:jonathan.r...@gmail.com> wrote: > > The meeting will be:
> > Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > > Location: Stata G451, MIT.
> > The Stata Center is the huge Gehry building at the corner of Vassar > > and Main in Cambridge. > > G451 is on the 4th floor very close to the east (= Gates = Main St) > > elevator bank. From the elevators go short distances straight, left, > > right, right, straight; see floor plan at > > http://www.csail.mit.edu/resources/maps/4G/G451.gif .
> > We'll discuss the relations between BioPAX, the semantic web, and OBO > > (especially OBI and OBO Foundry).
Great! In that case, you may be interested the owl design pattern [1] that I will present at WOMO07 later this month. In it, I argue the need to separate primitive (non-disjoint) trees from layers of "world view" restrictions, and these separated from assumptions (una/closure, etc). The idea supports multiple "competing" views for reasoning / validation.
> Tensions between "record" and "domain" attitudes in BioPAX.org have > slowed the growth of the BioPAX standard. The attitudes compete to > influence a single, monolithic, over-controlled "next release", but > they are so much at odds that little happens. [2] identifies and > names the attitudes, which alone will encourage some resolution.
> It may come if BioPAX standards by policy shift into a more open, > modular form, in which "attitudes" can be independently expressed > and formalized within smaller sub-schema. Authored and released by > sub-groups, each could then be selectively re-integrated as BioPAX > end-users saw fit, not unlike modules in a programming library.
> Modularizing release standards requires "statement" attitudes and > concepts. They get ignored in BioPAX 2.0, as they arise (gasp) in > NLP work. Yet they can advance interoperability, not merely among > competing BioPAX modules, but among open sets of ontologies from > many sources - each seen as the competing statement that it is.
> A way forward: adopt modular release policies plus the "statement" > design patterns, concepts, and support tools they require. An old > proposal on this exists, but would benefit from some updating:
> > I think [1] clearly identifies several important issues in using BioPAX > > as it stands now. **Dan, can you elaborate on what 3 avenues for BioPAX > > evolution and growth comes from [2]? [3] compares with SBML and others > > and [4] shows an applicaiton in data integration and ontology > extensions.
> > Cheers,
> > -=Michel=-
> > On 10/10/07, *Dan Corwin* <d...@lexikos.com <mailto:d...@lexikos.com>> > wrote:
> > Hi All -
> > The "attitudes" in this paper seem most relevant to our planned > > discussion, and I believe they point us toward 3 excellent avenues > > for BioPAX's evolution and growth.
> > I hope all those meeting tomorrow will have read about them.
> > Dan
> > jonathan.r...@gmail.com <mailto:jonathan.r...@gmail.com> wrote: > > > The meeting will be:
> > > Thursday, 11 October 2007, from 3:00pm to 5:00pm EDT. > > > Location: Stata G451, MIT.
> > > The Stata Center is the huge Gehry building at the corner of > Vassar > > > and Main in Cambridge. > > > G451 is on the 4th floor very close to the east (= Gates = Main > St) > > > elevator bank. From the elevators go short distances straight, > left, > > > right, right, straight; see floor plan at > > > http://www.csail.mit.edu/resources/maps/4G/G451.gif .
> > > We'll discuss the relations between BioPAX, the semantic web, and > OBO > > > (especially OBI and OBO Foundry).
> > -- > > Michel Dumontier > > Assistant Professor of Bioinformatics > > http://dumontierlab.com
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