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

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.