14:56:26 <RRSAgent> RRSAgent has joined #hcls
14:56:26 <RRSAgent> logging to http://www.w3.org/2009/07/23-hcls-irc
14:56:33 <ericP> Zakim, this is hcls
14:56:33 <Zakim> ericP, I see SW_HCLS()11:00AM in the schedule but not yet started.  Perhaps you mean "this will be hcls".
14:56:39 <ericP> Zakim, this will be hcls
14:56:39 <Zakim> ok, ericP; I see SW_HCLS()11:00AM scheduled to start in 4 minutes
14:56:44 <ericP> Zakim, please dial ericP-office
14:56:44 <Zakim> ok, ericP; the call is being made
14:56:45 <Zakim> SW_HCLS()11:00AM has now started
14:56:46 <Zakim> +EricP
14:56:58 <ericP> agenda?
14:57:22 <ericP> agenda+ SBML & the Semantic Web - Mike Hucka 
14:57:34 <ericP> agenda+ ISWC Workshop Update - Susie 
14:57:45 <ericP> agenda+ Next F2F, Nov. 2-6, Santa Clara, CA - Susie 
14:57:50 <ericP> agenda+ AOB
15:00:30 <Zakim> + +1.732.354.aaaa
15:00:46 <KevinDoyle> KevinDoyle has joined #HCLS
15:00:57 <ericP> Zakim, +1.732.354.aaaa is SusieS
15:00:57 <Zakim> +SusieS; got it
15:01:29 <Zakim> + +1.781.839.aabb
15:01:41 <ericP> Zakim, +1.781.839.aabb is Julia
15:01:41 <Zakim> +Julia; got it
15:01:50 <Zakim> + +1.860.255.aacc
15:01:53 <Zakim> + +1.617.395.aadd
15:02:06 <ericP> Zakim, +1.860.255.aacc is Oliver
15:02:06 <Zakim> +Oliver; got it
15:02:19 <ericP> Zakim, +1.617.395.aadd is KevinD
15:02:19 <Zakim> +KevinD; got it
15:03:12 <ericP> Zakim, who is speaking?
15:03:22 <Zakim> ericP, listening for 10 seconds I heard sound from the following: Oliver (42%)
15:04:15 <ericP> topic: administrivia
15:04:42 <Zakim> +[IPcaller]
15:04:44 <Jim> Jim has joined #hcls
15:05:00 <ericP> Zakim, [IPcaller] is MikeHucka
15:05:00 <Zakim> +MikeHucka; got it
15:05:14 <Jim> we're here at Uchc
15:05:57 <mhucka> mhucka has joined #HCLS
15:06:08 <ericP> Zakim, who is here?
15:06:11 <Zakim> On the phone I see MikeHucka, EricP, SusieS, Julia, Oliver, KevinD
15:06:13 <mhucka> MIke Hucka
15:06:14 <Zakim> On IRC I see mhucka, Jim, KevinDoyle, RRSAgent, Zakim, curoli, AlexPassant, Cloud_, ericP
15:07:17 <ericP> scribenick: ericP
15:07:52 <ericP> ericP has changed the topic to: http://drop.io/mhucka_hcls_2009_09_23/asset/mhucka-sbml-2009-07-23-pdf
15:08:16 <ericP> remiss on task updates
15:08:16 <ericP> please remember to send mail to public-semweb-lifesci
15:08:16 <ericP> can prefix with [BioRDF] or whatever so folks can filter (on or off) if they want
15:09:12 <ericP> Zakim, take up agendum 1
15:09:12 <Zakim> agendum 1. "SBML & the Semantic Web - Mike Hucka" taken up [from ericP]
15:09:45 <Julia_Kozlovsky> Julia_Kozlovsky has joined #HCLS
15:11:34 <ericP> [slide 2]
15:11:36 <ericP> [slide 3]
15:12:04 <ericP> [slide 4]
15:13:04 <ericP> [slide 5]
15:14:03 <ericP> mhucka: SBML focuses on modelable/simulatable processes
15:14:57 <ericP> ... before 2000 there was no common model for exchange between software
15:16:50 <ericP> mhucka: no limitation on the expressibility
15:17:19 <ericP> s/expressibility/expressivity/
15:17:57 <ericP> mhucka: not procedural, so doesn't tell you e.g. how long to run
15:20:11 <ericP> mhucka: people encode abstract models which are (intentionally) not bilogically feasible
15:21:13 <ericP> ... the MathML does not support integrals
15:21:51 <ericP> ... right hand side is a diff eq and left hand side is the rate of change of the species
15:23:43 <ericP> ... events model things like a cell reaching a certain size and undergoing mitosis
15:25:46 <ericP> mhucka: "validation" not all captured in XSD or UML, includes some SBML-specific pragmas
15:27:50 <ericP> mhucka: evolved some process, e.g. editors elected for 3 years
15:29:09 <ericP> mhucka: still adding formalism to SBML
15:30:34 <ericP> mhucka: level2 added constructs like initial assignment
15:31:36 <ericP> ... level3 components for things like shape
15:35:07 <ericP> mhucka: SBML vars correspond to e.g. vars in papers
15:37:43 <ericP> mhucka: Miriam provides (amoung other things) a minimal provenance model
15:38:33 <ericP> mhucka: Miriam is not SBML-specific, but requires an SBML binding
15:42:03 <ericP> Oliver: do you have to select the resources from the miriam list?
15:42:36 <ericP> mhucka: for longevity, you want to have confidence in the URL
15:42:46 <ericP> ... had some troubles with LSIDs
15:43:47 <ericP> ... added a redirection
15:43:55 <ericP> ... e.g. GO has changed over the years
15:45:03 <ericP> Oliver: would i use a Uniprot ID or a Miriam ID?
15:46:08 <ericP> mhucka: encourage urn:miriam:... to abstract location
15:49:11 <ericP> mhucka: bqbiol = AKA
15:50:21 <ericP> JimS: we have RDF beyond basic Miram -- e.g. tying to BioPAX
15:50:30 <ericP> ... can we add what we want?
15:51:15 <ericP> mhucka: Miriam-SBML is minimal
15:51:28 <ericP> ... at dev time, many langs didn't have RDF parsers
15:51:46 <ericP> ... you can add whatever, but there's no guarantee that tools will understand it
15:52:56 <ericP> ... put your additional RDF after the SBML-controlled bits
15:54:39 <ericP> [BioModels advanced search page]
15:55:18 <ericP> [slide 31 is a screenshot of the BioModels advanced search page]
15:58:00 <ericP> Zakim, take up next agendum
15:58:00 <Zakim> agendum 2. "ISWC Workshop Update - Susie" taken up [from ericP]
15:58:17 <ericP> susie: wrote a blog and email nagging folks to submit papers
15:58:29 <ericP> ... deadline in 10 days
15:59:05 <ericP> Zakim, take up agendum 1
15:59:05 <Zakim> agendum 1. "SBML & the Semantic Web - Mike Hucka" taken up [from ericP]
15:59:28 <ericP> [slide 32: bleeding edge]
15:59:41 <Zakim> -SusieS
15:59:50 <ericP> mhucka: should also include sybil (SP?) - integrating BioPAX and SBML
16:00:27 <Zakim> -Julia
16:00:30 <ericP> mhucka: first bullet: rich anntations enhance identy and enable model merging
16:01:16 <ericP> ... second bullet: MFO accesses Systems Biology Ontology
16:01:58 <ericP> ... third bullet: paper at last ISMB
16:02:46 <ericP> [slide 35: kudos and upcoming meeting]
16:03:30 <ericP> Oliver: re: extra RDF, is the parser generic RDF?
16:03:49 <ericP> mhucka: some folks would like to change that
16:04:07 <holger_stenzhorn> holger_stenzhorn has joined #hcls
16:04:11 <ericP> ... may have been a design flaw, but goal was to make it easy for tools
16:04:37 <holger_stenzhorn> holger_stenzhorn has left #hcls
16:05:54 <ericP> ericP: i think it was a good engineering soln. will want to lift constraint when folks want to use generic serializer
16:08:16 <mhucka> SBML Level 2 Version 4 specification document: http://precedings.nature.com/documents/2715/version/1
16:08:36 <mhucka> Section 6 describes the RDF bits, see especially p. 93
16:10:06 <ericP> ericP: do you have RDF-like extensibility in the rest of SBML?
16:10:16 <ericP> mhucka: extensibility point is in the annotations
16:11:27 <ericP> ... the packages that layer on the core, add elements and attributes to add representational power
16:11:38 <KevinDoyle> I have to split.  Thanks for all of the info.
16:11:44 <KevinDoyle> KevinDoyle has left #HCLS
16:11:48 <Zakim> -KevinD
16:12:14 <ericP> ericP: if you use these modules, should a naieve tool still interpret core?
16:12:33 <ericP> mhucka: there's a mustUnderstand flag in the packages
16:13:42 <ericP> ... mayUnderstand e.g. auxilliary picture
16:14:22 <ericP> ... a tool interpreting the multi-@@@ package needs the package for complete understanding
16:17:04 <ericP> mhucka: a level3 hierarchical model could be flattened into level2
16:20:24 <ericP> ericP: @@@ interop ideas
16:20:29 <ericP> mhucka: what sort of data?
16:20:45 <ericP> ericP: pathways, receptors, GO
16:20:58 <ericP> ... do you include the relationships between GO terms?
16:21:13 <ericP> mhucka: not the relationships
16:21:32 <ericP> ... an integrating query would have to make sense to some consumer
16:21:56 <ericP> ... many SBML users are interesting in time/@@@3 simulation
16:22:18 <ericP> ... maybe model creators who want to draw from other data sources
16:22:58 <ericP> ... pathway expression use case would be interesting -- happening in Sibil (Oliver)
16:23:25 <ericP> ... RDF-heads are trying to merge and verify models (U Newcastle)
16:23:45 <ericP> ... the models are getting more complex and prohibitive to construct from scratch
16:23:59 <ericP> ... composition will get more useful as models grow
16:26:54 <ericP> ericP: @@@4 could it all be RDF? drug discovery scenario
16:27:29 <ericP> mhucka: prolly could be all RDF. could then model more of the constraints
16:28:10 <ericP> ... Allison Worcester (SP? gender?) MFO was doing that
16:28:40 <ericP> Oliver: we're mirroring the core of SBML to RDF
16:28:40 <mhucka> Allyson Lister
16:28:49 <ericP> ... project: SBPAX
16:29:30 <ericP> ericP
16:29:35 <ericP> ericP: PURLs?
16:30:00 <ericP> mhucka: some detail made it easier to create our own resolution service
16:30:58 <ericP> mhucka: long questions about what would be good to persue
16:33:53 <Zakim> -EricP
16:34:00 <ericP> chair: ericP
16:34:03 <Zakim> -MikeHucka
16:34:06 <ericP> RRSAgent, please draft minutes
16:34:06 <RRSAgent> I have made the request to generate http://www.w3.org/2009/07/23-hcls-minutes.html ericP
16:34:14 <ericP> RRSAgent, please make log world-visible
16:39:03 <Zakim> disconnecting the lone participant, Oliver, in SW_HCLS()11:00AM
16:39:05 <Zakim> SW_HCLS()11:00AM has ended
16:39:06 <Zakim> Attendees were EricP, SusieS, Julia, Oliver, KevinD, MikeHucka