HCLSIG/Meetings/2009-08-20 Conference Call
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- Date of Call: Thursday August 20, 2009
- Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
- Dial-In #: +1.617.761.6200 (Cambridge, MA)
- Dial-In #: +33.4.89.06.34.99 (Nice, France)
- Dial-In #: +44.117.370.6152 (Bristol, UK)
- Participant Access Code: 4257 ("HCLS").
- IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC)
- Duration: ~1h
- Convener: Scott, Susie
- Scribe: TBD
- Semantic Enrichment of Systems Biology Models - Camille Laibe (EBI)
- News Updates by BioRDF, COI, LODD, Pharma Ontology, Scientific Discourse, Terminology - All
- SWASD Scientific Discourse Workshop at ISWC - Susie
- Semantic Enrichment of Systems Biology Models [Camille Laibe (EBI)]
- task updates
- Summary of Action Items
<mmarshal> Welcome Camille!
<Camille> Hello Scott and everybody
<Camille> I've just tried to call and apparently the channel is currently closed. Is this normal?
<Camille> Today's slides: http://www.ebi.ac.uk/systems-srv/mp/file-exchange/Model_Semantics_LaibeC_HCLSIG-20090820.pdf?fno=2672
<scribe> scribe: ericP Semantic Enrichment of Systems Biology Models [Camille Laibe (EBI)]
-> http://esw.w3.org/topic/HCLSIG/Meetings/2009-08-20_Conference_Call?action=AttachFile&do=get&target=Model_Semantics_LaibeC_HCLSIG-20090820.pdf Semantic Enrichment of Systems Biology Models
Camille: models store operations and their parameters ... is that enough?
Camille: each model element MUST be uniquely identified
Camille: annotations allow the human to understand the model
Camille: another antipattern: ambiguous strings
Camille: why not use the URL where something is represented? ... [presents list of 5 low-confidence URLs for the same thing]
Camille: we came up with a URI scheme
Camille: qualification from a controlled vocabulary
-> http://biomodels.net/qualifiers/ said vocabulary
Camille: Species(mataid_00000006 bqbiol:hasPart <urn:miriam:uniprot:P07522> , ...
Camille: dual access: programatic, and secondarily human interaction
Camille: small list of requires to add a datatype to MIRIAM ... access is free, no requirements for branchability ... access to entire data corpus
Olivier: if Uniprot has some non-free data, is the free part still compliant?
Camille: haven't address that, probably yes ... if someone submits a datatype which is interesting and used, we'll accept it ... e.g. P12345 would be such an Identifier
Olivier: reactome addresses [protein?] portions, do they qualify?
Camille: we *prefer* a single datatype ... counter examples in KEGG
regular expression indicates some validation
Camille: most resources are available at multiple locations ... the indirection between the model element and the info locations shields the consumer ... once you are satisfied with your model, you'll store it in a database ... if it's done, we need an identifier which will be valid forever ... changes to the resource will not change the annotation ... we provide a resolution service ... if you have a model full of annotations, a miriam URI is not of immediate value to the user ... instead, you ask miriam to resolve the miriam URI
Camille: we have QA scripts validating the resolution and the returned information ... curator will look for data migrations ... will remove dead resources ... we tolerate an e.g. one-day down time
ericP: could you do this with e.g. PURLs?
Camille: we have a 1:n mapping
Camille: size of impl list implies that this service is needed by the community
Camille: someone did a heat map of MIRIAM resources
Camille: contains MathML expressions addressing SBO terms
Camille: we were able to accurately model BioPAX ... there is an online ontology browser ... ontology contributions welcome
Camille: MIASE is the minimum info needed to describe a simulation experiment ... allows users to exchange and reporoduce simulations ... KiSAO: lists widely used simulation algorythms and methods
[slide 49 - life cycle of a model]
[slide 50 - kudos]
Camille: thanks to all contributors, as well as funding bodies task updates
kei: [BioRDF] BCM BioInformatics paper final submission -- expect pub in Oct ... microarray use case: integrates data from different microarray experiments ... working with helen parkinson (EBI) ... she's working on gene expression atlas ... connected her with maryanne martone (NIF), who's working on a lexicon for neuroscience
susie: [LODD] initial databses were clinicaltrials.gov...diseasone
<mscottm> ericP: [COI] Helen looking to involve AGFA colleagues in Canada, excited about query projection, continuing work on access control.
susie: added chinese medical dataset ... have datasource notifications kicking off data refreshes ... poster at DILS, paper at @@@
colin: [[[TrandMed]]] ... presented same poster at @@1 and @@2 ... working on paper for special issue BioInformatics ... focusing on a few dozen classes for the transmed ontology
susie: [scientific discourse] ... three papers: ... .. SWAN ... .. SIOC ... .. SWAN-SIOC integration ... expect to review IG notes in next month ... also working on details for ISWC workshop
mscottm: [Term] ... andrew gibson recently converted GO to SKOS ... looking to link result with SNOMED AOB
mscottm: EBI is talking to ericP and mscottm about a tutorial an RDF tutorial at EBI ... Barend Mons thinks he can get an NSF grant -- wants to work with W3C
mscottm: [question] Noticed interaction with Nicolas Novere about identifiers from Alan Ruttenberg HCLS mailing list posting in 2006 and the suggestion at the time from both sides to work together. Maybe we should do that (get communication going betw SharedNames and MIRIAM).
camille: I was just starting in 2006 but we recently had e-mail contact from Alan R. Would welcome more discussion.