HCLSIG/Meetings/2009-08-20 Conference Call

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Conference Details

  • 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 #: + (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



  • Topics
    1. Semantic Enrichment of Systems Biology Models [Camille Laibe (EBI)]
    2. task updates
    3. AOB
  • 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?

<mib_9wztcc8p> test

<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)]

<mmarshal> tx

-> 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

[slide 3]

Camille: models store operations and their parameters ... is that enough?

[slide 6]

[slide 8]

[slide 9]

[slide 10]

Camille: each model element MUST be uniquely identified

[slide 11]

Camille: annotations allow the human to understand the model

[slide 12]

[slide 15]

[slide 16]

Camille: another antipattern: ambiguous strings

[slide 17]

Camille: why not use the URL where something is represented? ... [presents list of 5 low-confidence URLs for the same thing]

[slide 18]

[slide 19]

Camille: we came up with a URI scheme

[slide 20]

[slide 21]

[slide 22]

Camille: qualification from a controlled vocabulary

[slide 24]

-> http://biomodels.net/qualifiers/ said vocabulary

[slide 26]

Camille: Species(mataid_00000006 bqbiol:hasPart <urn:miriam:uniprot:P07522> , ...

[slide 28]

Camille: dual access: programatic, and secondarily human interaction

[slide 29]

[slide 31]

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

[slide 32]

regular expression indicates some validation

[slide 33]

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

[slide 34]

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

[slide 35]

Camille: size of impl list implies that this service is needed by the community

[slide 37]

Camille: someone did a heat map of MIRIAM resources

[slide 40]

[slide 42]

Camille: contains MathML expressions addressing SBO terms

[slide 45]

Camille: we were able to accurately model BioPAX ... there is an online ontology browser ... ontology contributions welcome

[slide 48]

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]

[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

ericP: @@

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.