Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM EDT

A great deal of the content of papers is *not* about numbers, but
statements intertwined with propositional attitudes. Good evidence for this
is in the use of hedging.  See,

Hyland, K., Hedging in scientific research articles. Pragmatics &
beyond,1998, Amsterdam ; Philadelphia: John Benjamins Pub. Co. ix, 307 p.


 - Bob Futrelle
   BioNLP.org

On Fri, Feb 24, 2012 at 1:46 PM, Oliver Ruebenacker <curoli@gmail.com>wrote:

>     Hello Anita, All,
>
>  I'm mostly interested in numbers. Presumably, these statements have
> been derived from numbers that can be found in these papers. The
> challenge is to classify numbers and group them into systems and
> states. Could your epistemic model help do that?
>
>     Take care
>      Oliver
>
> On Fri, Feb 24, 2012 at 12:15 PM, Waard, Anita de A (ELS-NYC)
> <A.dewaard@elsevier.com> wrote:
> > All,
> >
> > I was struck by the phrase 'turning biological knowledge into
> mathematical models' and wondering if anyone is interested to model
> 'epistemic information' in biology articles, added to the knowledge of the
> type that Oliver mentioned?
> >
> > In particular I am interested in modelling clauses such as 1 a., 2 a., 3
> a., and 3.b in the sentences below - I have a model to classify these and
> would like to add this 'knowledge attribution' layer to existing
> representations of triples in papers.
> >
> > 1 a. These studies have shown that
> > 1.b. the 5' untranslated region (5'UTR) can be complex
> >
> > vs.
> >
> > 2. a. It has been reported that
> > 2. b. 5' untranslated exons, and sometimes introns, can regulate the
> expression of genes in two different ways.
> >
> > vs.
> >
> > 3. a. Thus, our analysis revealed areas of active chromatin remodeling
> in the vicinity of exon 1
> > 3. b. suggesting that
> > 3. c. this area may be important for CCR3 transcription.
> >
> > Is this part of the remit of this group and/or is anyone interested in
> collaborating on this topic?
> >
> > Thanks,
> > Best,
> >
> > - Anita.
> >
> > Anita de Waard
> > Disruptive Technologies Director, Elsevier Labs
> > http://elsatglabs.com/labs/anita/
> > a.dewaard@elsevier.com
> >
> >
> >
> > -----Original Message-----
> > From: Oliver Ruebenacker [mailto:curoli@gmail.com]
> > Sent: Fri 2/24/2012 11:55
> > To: Helena Deus; public-semweb-lifesci
> > Subject: Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at
> 11AM EDT
> >
> >
> >     Hello Helena, All,
> >
> >  I'm interested in joining the Systems Biology Taskforce. Sorry I
> > could not make the initial call. My interest is turning biological
> > knowledge into mathematical models, automatically. A brief description
> > is below.
> >
> >  Thanks!
> >
> >     Take care
> >     Oliver
> >
> >  Living organisms are so enormously complex that we need computer
> > simulations to understand the consequences of their vast biochemical
> > reaction networks. As we uncover an increasing part of these networks,
> > our established knowledge is increasingly stored in free web databases
> > and available for query and download in machine-readable formats,
> > especially in the RDF/OWL-based community standard Biological Pathways
> > Exchange (BioPAX) [1]. The available data is massive and growing, e.g.
> > Pathway Commons [2] stores 1,700 pathways, 414 organisms, 440,000
> > interactions and 86,000 substances. This data is fully linked with
> > open controlled terminologies such as gene ontology (e.g. anatomical
> > features) [3] and other free online databases such as ChEBI
> > (chemicals) [4], KEGG (genes a.o.) [5], UniProt (proteins) [6] and
> > PubMed (publications) [7].
> >
> >  Automatic use of this knowledge for computer simulations of
> > biological organisms has been an ongoing challenge [8,9,10]. Now,
> > Systems Biology Pathway Exchange (SBPAX) [11], a BioPAX extension,
> > allows the inclusion of quantitative data and systems biology terms,
> > especially the Systems Biology Ontology (SBO) [12]. SBPAX support has
> > been implemented by the Virtual Cell [13], Signaling Gateway Molecule
> > Pages [14] and System for the Analysis of Biochemical Pathways -
> > Reaction Kinetics (SABIO-RK) [15]. For the first time, a mathematical
> > model can be automatically built and fully annotated from a pathway of
> > interest.
> >
> >  Citations:
> >
> >  [1] Biological Pathway Exchange (BioPAX), www.biopax.org
> >  [2] Pathway Commons, www.pathwaycommons.org
> >  [3] Gene Ontology (GO), www.geneontology.org/
> >  [4] Chemical Entities of Biological Interest (ChEBI),
> www.ebi.ac.uk/chebi/
> >  [5] Kyoto Encyclopedia of Genes and Genomes (KEGG),
> wwww.genome.jp/kegg/
> >  [6] UniProt, www.uniprot.org
> >  [7] PubMed, www.ncbi.nlm.nih.gov/pubmed/
> >  [8] Modeling without Borders: Creating and Annotating VCell Models
> > Using the Web, Michael L. Blinov, Oliver Ruebenacker, James C. Schaff
> > and Ion I. Moraru,  Lecture Notes in Computer Science, 2010, Volume
> > 6053 (2010).
> >  [9] Using views of Systems Biology Cloud: application for model
> > building, Oliver Ruebenacker, Michael Blinov, Theory in Biosciences,
> > Volume 130, Number 1, 45-54 (2010).
> >  [10] Integrating BioPAX pathway knowledge with SBML models, Michael
> > L Blinov, Oliver Ruebenacker, Ion I Moraru, IET Syst. Biol., 2009,
> > Vol. 3, Iss. 5, pp. 317-328 (2009).
> >  [11] Systems Biology Pathway Exchange (SBPAX), www.sbpax.org
> >  [12] Systems Biology Ontology, www.ebi.ac.uk/sbo/main/
> >  [13] Virtual Cell, http://vcell.org
> >  [14] Signaling Gateway Molecule Pages,
> www.signaling-gateway.org/molecule/
> >  [15] System for the Analysis of Biological Pathways - Reaction
> > Kinetics (SABIO-RK), http://sabio.villa-bosch.de/
> >
> > On Tue, Feb 21, 2012 at 4:32 PM, Helena Deus <helenadeus@gmail.com>
> wrote:
> >> Dear All,
> >>
> >> Please join me tomorrow for the kick-off telco of the Systems Biology
> Task
> >> Force. Systems Biology is about looking at biological systems from an
> >> integrated perspective and to use that perspective to understand
> disease. We
> >> will be discussing the general goals, strategy and structure of the task
> >> force.
> >>
> >> Please see http://www.w3.org/wiki/HCLSIG/SysBio for an initial
> motivation,
> >> and description, of what this task will be focused on (with due
> flexibility
> >> according to participants input).
> >>
> >>
> >> * Date of Call: Tuesday February 21, 2012
> >> * Time of Call: 11:00am Eastern Daylight Time (EDT)
> >> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> >> * [Note: limited access to European dial in numbers below]
> >> * Dial-In #: +33.4.26.46.79.03 (Nice, France)
> >> * Dial-In #: +44.203.318.0479 (Bristol, UK)
> >> * Participant Access Code: 4257 ("HCLS").
> >> * IRC Channel: irc.w3.org port 6665 channel #HCLS
> >> For instant IRC access:
> >> see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or
> >> see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]), Quick Start:
> Click
> >> on
> >> [http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
>  mibbit]
> >>
> >> * Duration: ~1h
> >> * Convener: Helena
> >> * Scribe: TBD
> >>
> >> Kind regards,
> >> Helena
> >
> >
> >
> > --
> > Oliver Ruebenacker, Computational Cell Biologist
> > Virtual Cell (http://vcell.org)
> > SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
> > http://www.oliver.curiousworld.org
> >
> >
> > Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The
> Netherlands, Registration No. 33156677 (The Netherlands)
> >
>
>
>
> --
> Oliver Ruebenacker, Computational Cell Biologist
> Virtual Cell (http://vcell.org)
> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
> http://www.oliver.curiousworld.org
>
>