HCLSIG BioRDF Subgroup/Meetings/2009-01-26 Conference Call

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Conference Details

  • Date of Call: Monday January 26, 2009
  • Time of Call: 11:00am Eastern Time
  • 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: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Kei Cheung

Attendees

  • Eric Prud'hommeaux, Scott Marshall, Kei Cheung, Matthias Samwald, Jesse Erdmann, Rob Frost, Adrian Paschke

Agenda

  • Roll call and introduction (Kei Cheung)
  • BioSIOC presentation (Matthias Samwald)
  • Query Federation -- progress and next steps (All)

Minutes

  • <kei> matthias: present biosioc/atag
  • <kei> manuscript for matthias talk: http://docs.google.com/Doc?id=dggh6vwh_46ckk2kdf4
  • <ericP> +1 to better than ppt
  • HelenC (c0be4b14@128.30.52.43) has joined #hcls
  • <kei> matthias: section -- intro/background of Matthias
  • <kei> matthias: postdoc research at DERI and Konrad Lorenz Institute -- working in both industry and academia
  • <kei> matthias: multidisciplinary experiences
  • <kei> matthias: practical work
  • HelenC (c0be4b14@128.30.52.43) Quit (Quit: CGI:IRC (EOF) )
  • <kei> matthias: physically located at Konrad Lorenz Institute
  • <kei> matthias: section 2 -- speed up R&D
  • <kei> matthias: integration is important
  • <kei> matthias: improved decision making and enable discovery
  • <kei> matthias: create a structure for easy integration and support integrated queries
  • <kei> matthias: data integration should be meaningful in some scientific context
  • <kei> matthias: technologies should be friendly to computer implementation
  • <kei> matthias: this allow large-scale uptake of technologies
  • <kei> matthias: section -- RDF is not enough
  • <kei> matthias: RDF is not a panecea
  • <ericP> ETL is perhaps easier if the data isn't already nicely linked RDF
  • <kei> matthias: data should be interlinked in a meaningful way
  • <ericP> -2:s/easier/easier in csvs
  • <kei> matthias: e.g., senselab ontology linked with obo ontologies
  • <kei> matthias: heterogenous structures (even they are synactically in RDF) hinder data integration
  • <mscottm> Zakim, who is making noise?
  • <kei> matthias: syntactic representation using rdf is not enough
  • <Zakim> mscottm, listening for 10 seconds I heard sound from the following: EricP (15%), matthias_samwald (63%)
  • <mscottm> Zakim, mute EricP
  • <Zakim> EricP should now be muted
  • ericP promises to stop breathing
  • ericP impressed with mscottm's proficiency with zakim
  • <kei> matthias: section 4: atag and biosioc
  • <kei> matthias: some of the guiding prinicples include: simplicity, intuitive user interface, practicality, etc
  • <kei> matthias: embedding tags in document -- e.g., rdfa
  • <kei> matthias: grddl and rdfa relationship
  • ericP Zakim, please unmute me
  • Zakim EricP should no longer be muted
  • <kei> matthias: grddl uses xslt and xml -- rdfa can be implemented using grddl
  • <kei> matthias: use of obo foundry ontologies
  • <kei> matthias: social net -- web 2.0
  • <kei> matthias: growing use of social networking (e.g., sioc) in scientific work
  • <kei> matthias: sioc uses rdf to represent social network
  • <kei> matthias: section 5 - structure of atag
  • <kei> matthias: atag means associative tag -- mark up small pieces of text
  • <kei> matthias: atags come from sioc items
  • <kei> matthias: atags relate to linked data
  • <kei> matthias: the advantage of atags is simple
  • <kei> matthias: e.g., protein 1 interacts with protein 2
  • <kei> e.g., overexpression of protein 1 in tissue 2 is the cause of disease 3
  • <kei> matthias: human friendly tags
  • <ericP> can also provide interesting specificity in e.g. a firefox plugin
  • <kei> matthias: simple use of atags can also facilitate integration
  • <kei> matthias: molecule bindings -- data source protein interactions -- contexts are the same
  • <kei> matthias: hiding some of the complexities
  • <kei> matthias: small sets of semantics sometimes are enough in many cases
  • <kei> matthias: attempt to reduce complexity while increasing the usefulness of datasets
  • <kei> matthias: explore how to strike the right balance
  • <kei> matthias: integration of atags with advanced features such as reasoning, inferencing, etc
  • <matthias_samwald> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags
  • <kei> matthias: there is wiki page at biordf describing the biosioc/atag project
  • <kei> matthias: section 8 -- development of lightweight applications
  • <kei> matthias: bookmarking is one example
  • <kei> matthias: support searching and querying
  • <kei> matthias: write end-user directed applications
  • <kei> matthias: pubmed abstracts bookmarked with atags
  • <kei> matthias: demonstrate in federated queries
  • matthias_samwald, i'd be keen to geek with you about this
  • <ericP> n.b. i owe rob calls as well
  • <kei> matthias: sindice and virtuoso
  • <kei> matthias: section 9 interoperation with other task forces (e.g., swan/sioc)
  • <kei> matthias: at Konrad Lorenz -- evolutionary biology domain
  • <kei> matthias: it might be complementary to the neuroscience
  • <kei> matthias: add to hcls kb
  • <mscottm> q+
  • Zakim sees mscottm on the speaker queue
  • <matthias_samwald> eric --- i am looking forward go geek with you.
  • <kei> scott: question: can you give more concrete example(s)?
  • <kei> scott: interface? -- how do you see that working?
  • <kei> scott: uri's for atags
  • <kei> scott: any thoughts on creating uri's linking to commonly shared names (uri's)
  • <kei> matthias: yes, reusing obo ontology entries as much as possible
  • <kei> matthias: sharing of identifiers and semantics between datasets are currently lacking in many datasets
  • <kei> matthias: try to address this issue by reuse
  • <kei> scott: libraries/api's can be used?
  • <kei> matthias: ebi provides some api's, for example.
  • <ericP> q+
  • Zakim sees mscottm, ericP on the speaker queue
  • <mscottm> q-
  • Zakim sees ericP on the speaker queue
  • <mscottm> eric?
  • <kei> eric: using this information for query federation
  • <apaschke> btw, we did a lot of work on extracting relevant entities from Pubmed
  • <apaschke> abstracts
  • <kei> eric: information about resources
  • <matthias_samwald> adrian -- if you have the results available in structured format we might look into converting them to aTags.
  • <kei> scott: look for information need to know which sources have the relevant information answering the queries
  • <kei> eric: provenence information
  • <kei> scott: annotation on the statements
  • <kei> kei: named graph?
  • <ericP> matthias_samwald, sahree, didn't mean to distract so much
  • <kei> scott: open linked data uri?
  • <kei> kei: I think we need to move on..
  • <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation
  • <Zakim> -JesseErdmann
  • ericP is very late responding to Rob's email -- got me started working on a C++ version of FeDeRate
  • <apaschke> what is the deadline for CHals?
  • <apaschke> chals -> C-Shals
  • <mscottm> same here
  • <ericP> apaschke, deadline is passed, but we already have a slot to talk about the state of the art
  • <Kei> reviewed progress on the query federation demo
  • <Adrian> Adrian tested the receptor query on the HCLS KB at Free Univ. It seemed to work
  • <Kei> need to compare the receptor query results with HCLS KB at DERI
  • <Rob> reported progress on the dbpedia receptor query (worked with Kingsley's team to resolve the missing data issue in dbpedia)
  • <Rob> Merged receptors returned from dbpedia with receptors returned from HCLS KB at DERI.
  • <Rob> Working with Eric to incorporate FeDeRate.
  • <Kei> To help expedite demo implementation, let's plan on having biordf call on a weekly basis until the C-SHALS meeting.
  • <Kei> Next biordf call will be on Feb 2 @ 11 am EDT.