Next Meeting?

[Oliver Ruebenacker]

Hello, All,

How about having a meeting on Tuesday, June 16 (next week)?

Suggested topic:

The Deep Blue Interaction Store (DBIS) lists two reaction R1:
Reactantin -> Intermediarin and R2: Intermediarin -> Productin

The Great Green Pathbase (GGP) lists a reaction R3: Reactantin -> Productin

How do we know whether DBIS and GGP are talking about the same thing?

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

[Andrea Splendiani]

Hi, for me it's fine.
Can you circulate a couple of links or prepare a minimum of background ?
What time ?

ciao,
Andrea

[Alan Ruttenberg]

On Fri, Jun 12, 2009 at 3:01 AM, Oliver Ruebenacker<cur...@gmail.com> wrote:
>
>     Hello, All,
>
>  How about having a meeting on Tuesday, June 16 (next week)?
>
>  Suggested topic:
>
>  The Deep Blue Interaction Store (DBIS) lists two reaction R1:
> Reactantin -> Intermediarin and R2: Intermediarin -> Productin
>
>  The Great Green Pathbase (GGP) lists a reaction R3: Reactantin -> Productin
>
>  How do we know whether DBIS and GGP are talking about the same thing?

Do they provide citations for their reactions?
The first tact would be to read the papers and evaluate it that way.
-Alan

[Oliver Ruebenacker]

Hello, All,

First, I would like to know whether, if we have a meeting on
Tuesday, any one besides Andrea and me would attend.

I don't have any references for the suggested topic. Sorry if the
topic was not defined more clearly: The question is: How can we encode
that one reaction is equivalent to the combination (e.g. chaining) of
two or more others?

A more elaborate example:

(Reaction 1) A + B -> C + D
(Reaction 2) C + E -> F + G

(Reaction 3) A + B + E -> D + F + G

Here reaction 3 may be a combination of 1 and 2. How can it be
asserted that it indeed is in BioPAX-OBO?

But that's just my suggestion for a topic. Feel free to suggest another topic.

Take care
Oliver

[Alan Ruttenberg]

I am out of town until thursday.

On Saturday, June 13, 2009, Oliver Ruebenacker <cur...@gmail.com> wrote:
>
>     Hello, All,
>

>  First, I would like to know whether, if we have a meeting on
> Tuesday, any one besides Andrea and me would attend.
>
>  I don't have any references for the suggested topic. Sorry if the
> topic was not defined more clearly: The question is: How can we encode
> that one reaction is equivalent to the combination (e.g. chaining) of
> two or more others?
>
>  A more elaborate example:
>
>  (Reaction 1)   A + B -> C + D
>  (Reaction 2)  C + E -> F + G
>
>  (Reaction 3)  A + B + E -> D + F + G

You would say (at the instance level) a parrticular reaction 1 and a
particular reaction 2 are part-of a particular reaction 3. A reaction
is a process, so the part-of here related processes.
Note that has-part is inverse of part-of, so one would also get reaction

If it was true that also *every* reaction 3 had two such parts then
you would code that as a class axiom on reaction 3 using the has-part
relation: Every reaction 3 has-part a reaction 1 and has-part a
reaction 2.

You can get more precise, rulng out other part, for example, but
that's the basic idea.

-Alan

[Andrea Splendiani]

Ops... I'm also busy, it seems, this tuesday (at the usual times...)
What about changing the day and tying thursday or friday this week ?

ciao,
Andrea

[Oliver Ruebenacker]

Hello, All,

OK, so no meeting on Tuesday, June 16 (this week).

How about Tuesday, June 23 (next week)?

I can't make Thursday or Friday this week. In general, Wednesday,
Thursday and Friday are not good for me, Monday or Tuesday would be
better.

Take care
Oliver

[andrea splendiani (RRes-Roth)]

Tuesday I'll be on a plane... maybe I can recover one hour in the evening... Monday would be ok.
Next I'll be here and there during July. So to have a meeting next week would be nice.

Ciao,
Andrea

[Andrea Splendiani]

Hi,

Did last planned meeting take place ?
It seems it's hard to fix a meeting these days, I suspect all july
will be the same, as there are a set of meetings around.

A few questions:

who of you will be at ISMB ?
who of you will be at ICBO ?

I'm going to co-organize a workshop on Semantic Web in Life Sciences
on Nov. 20 in Amsterdam... (the second edition of one that went pretty
well). If someone is interested... that would add another possible
common venue (for which I would iterate the above question).

Apart from logistics... why don't we change way of operation, set a
"rewarding" target and work on this ? For instance, we have been
chatting a lot about pathway representation in OWL. Why not going for
a paper like "Integrating biological pathways through the semantic
web" and start the work backward ?

I think perhaps a clear simple achievable and rewarding goal may work...

ciao,
Andrea

[Michel Dumontier]

i'll be at both.

-=Michel=-

--
Michel Dumontier
Assistant Professor of Bioinformatics
http://dumontierlab.com

[JSL913]

I will be at both also.

Joanne

[Andrea Splendiani]

Where are you staying ?

Any particular event you plan to attend ? (talking about ismb)

ciao,

Andrea

Il giorno 21/giu/09, alle ore 22:45, Michel Dumontier ha scritto:

-----------

Andrea Splendiani

post-doc, bootstrep project (www.bootstrep.eu)

UPRES-EA 3888 - Laboratoire d'Informatique Médicale

CHU de Pontchaillou

2, rue Henri Le Guilloux

35033 Rennes - France

Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.)

Fax : +33 2 99 28 41 60

48° 07.275N

1° 41.643W

[Alan Ruttenberg]

I'll be at both.

At ISMB I'll be at the BOSC keynote ;-)

I'm not registered for ISMB, though I'll be around monday and tuesday.

-Alan

[JSL913]

I need a place to stay Fri Night and Saturday night - 

I have something in the works for Sun-when I leave ...

[Oliver Ruebenacker]

Hello Andrea, All,

Last planned meeting was months ago ;)

This week: got no replies except for Andrea, so no meeting this week.

How about next week?

Paper sounds great, but need to be more specific.

Take care
Oliver

On Sun, Jun 21, 2009 at 5:30 PM, Andrea Splendiani
<andrea.s...@univ-rennes1.fr> wrote:
>

[JSL913]

Oliver,

I'm at ISMB next week... as a bunch of us are, maybe it makes sense to
meet there.

Joanne

[Oliver Ruebenacker]

Hello, All,

I agree it makes sense. I am not there though.

Take care
Oliver