IRC log of hcls on 2009-07-23

Timestamps are in UTC.

14:56:26 [RRSAgent]
RRSAgent has joined #hcls
14:56:26 [RRSAgent]
logging to
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]
14:56:58 [ericP]
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]
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:
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]
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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]
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]
15:59:50 [ericP]
mhucka: should also include sybil (SP?) - integrating BioPAX and SBML
16:00:27 [Zakim]
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]
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16:04:11 [ericP]
... may have been a design flaw, but goal was to make it easy for tools
16:04:37 [holger_stenzhorn]
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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:
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]
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]
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]
16:34:00 [ericP]
chair: ericP
16:34:03 [Zakim]
16:34:06 [ericP]
RRSAgent, please draft minutes
16:34:06 [RRSAgent]
I have made the request to generate 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