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HCLS meeting minutes 2009-07-23

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 23 Jul 2009 15:32:25 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20090723193225.GH636@w3.org>


                              HCLS Teleconference

23 Jul 2009

   See also: [2]IRC log


          AlexPassant IPcaller JimS Julia Julia_Kozlovsky KevinDoyle
          MikeHucka Oliver SusieS curoli ericP




     * [3]Topics
         1. [4]administrivia
         2. [5]SBML & the Semantic Web - Mike Hucka
         3. [6]ISWC Workshop Update - Susie
         4. [7]SBML & the Semantic Web - Mike Hucka
     * [8]Summary of Action Items


   ericP: we've been remiss on task updates -- aim to fix that in the near
   ... please remember to send mail to public-semweb-lifesci instead of
   long lists of individuals.
   ... helps others keep track of what's going on and potentially provide
   ... helps us motivate others to work with us.
   ... can prefix with [BioRDF] or whatever so folks can filter (on or
   off) if they want.

SBML & the Semantic Web - Mike Hucka

   mhucka: SBML focuses on modelable/simulatable processes
   ... before 2000 there was no common model for exchange between software
   ... no limitation on the expressivity
   ... not procedural, so doesn't tell you e.g. how long to run
   ... people encode abstract models which are (intentionally) not
   bilogically feasible
   ... the MathML does not support integrals
   ... right hand side is a diff eq and left hand side is the rate of
   change of the species
   ... events model things like a cell reaching a certain size and
   undergoing mitosis
   ... "validation" not all captured in XSD or UML, includes some
   SBML-specific pragmas
   ... evolved some process, e.g. editors elected for 3 years
   ... still adding formalism to SBML
   ... level2 added constructs like initial assignment
   ... level3 components for things like shape
   ... SBML vars correspond to e.g. vars in papers
   ... Miriam provides (amoung other things) a minimal provenance model
   ... Miriam is not SBML-specific, but requires an SBML binding

   Oliver: do you have to select the resources from the miriam list?

   mhucka: for longevity, you want to have confidence in the URL
   ... had some troubles with LSIDs
   ... added a redirection
   ... e.g. GO has changed over the years

   Oliver: would i use a Uniprot ID or a Miriam ID?

   mhucka: encourage urn:miriam:... to abstract location
   ... bqbiol = AKA

   JimS: we have RDF beyond basic Miram -- e.g. tying to BioPAX
   ... can we add what we want?

   mhucka: Miriam-SBML is minimal
   ... at dev time, many langs didn't have RDF parsers
   ... you can add whatever, but there's no guarantee that tools will
   understand it
   ... put your additional RDF after the SBML-controlled bits

   [BioModels advanced search page]

   [slide 31 is a screenshot of the BioModels advanced search page]

ISWC Workshop Update - Susie

   susie: wrote a blog and email nagging folks to submit papers
   ... deadline in 10 days

SBML & the Semantic Web - Mike Hucka

   [slide 32: bleeding edge]

   mhucka: should also include sybil (SP?) - integrating BioPAX and SBML
   ... first bullet: rich anntations enhance identy and enable model
   ... second bullet: MFO accesses Systems Biology Ontology
   ... third bullet: paper at last ISMB

   [slide 35: kudos and upcoming meeting]

   Oliver: re: extra RDF, is the parser generic RDF?

   mhucka: some folks would like to change that
   ... may have been a design flaw, but goal was to make it easy for tools

   ericP: i think it was a good engineering soln. will want to lift
   constraint when folks want to use generic serializer

   <mhucka> SBML Level 2 Version 4 specification document:

   <mhucka> Section 6 describes the RDF bits, see especially p. 93

   ericP: do you have RDF-like extensibility in the rest of SBML?

   mhucka: extensibility point is in the annotations
   ... the packages that layer on the core, add elements and attributes to
   add representational power

   <KevinDoyle> I have to split. Thanks for all of the info.

   ericP: if you use these modules, should a naieve tool still interpret

   mhucka: there's a mustUnderstand flag in the packages
   ... mayUnderstand e.g. auxilliary picture
   ... a tool interpreting the multi-package needs the package for
   complete understanding
   ... a level3 hierarchical model could be flattened into level2

   ericP: interop seems like it could happen two ways:
   ... .. SBML->RDF via GRDDL
   ... .. RDF->SBML via SPARQL Query + XSLT
   ... this would be motivated by us wanting to take advantage of your
   data or you wanting to use our data

   mhucka: what sort of data?

   ericP: pathways, receptors, GO
   ... do you include the relationships between GO terms?

   mhucka: not the relationships
   ... an integrating query would have to make sense to some consumer
   ... many SBML users are interesting in time/[missed] simulation
   ... maybe model creators who want to draw from other data sources
   ... pathway expression use case would be interesting -- happening in
   Sibil (Oliver)
   ... RDF-heads are trying to merge and verify models (U Newcastle)
   ... the models are getting more complex and prohibitive to construct
   from scratch
   ... composition will get more useful as models grow

   ericP: can you envision SMBL being completely in RDF? [brief MathML in
   RDF discussion] a motivating drug discovery scenario would be a
   researcher leveraging SBML pathway models when testing if drug X could
   do Y

   mhucka: prolly could be all RDF. could then model more of the
   ... Allyson Lister MFO was doing that

   Oliver: we're mirroring the core of SBML to RDF
   ... project: SBPAX

   ericP: noting that you provide urn resoultion, did you consider PURLs?

   mhucka: some detail made it easier to create our own resolution service
   ... long questions about what would be good to persue

Summary of Action Items

   [End of minutes]

    Minutes formatted by David Booth's [10]scribe.perl version 1.135 (
    [11]CVS log)
    $Date: 2009/07/23 19:31:41 $


   1. http://www.w3.org/
   2. http://www.w3.org/2009/07/23-hcls-irc
   3. http://www.w3.org/2009/07/23-hcls-minutes#agenda
   4. http://www.w3.org/2009/07/23-hcls-minutes#item01
   5. http://www.w3.org/2009/07/23-hcls-minutes#item02
   6. http://www.w3.org/2009/07/23-hcls-minutes#item03
   7. http://www.w3.org/2009/07/23-hcls-minutes#item04
   8. http://www.w3.org/2009/07/23-hcls-minutes#ActionSummary
   9. http://precedings.nature.com/documents/2715/version/1
  10. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  11. http://dev.w3.org/cvsweb/2002/scribe/


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