HCLSIG BioRDF Subgroup/Meetings/2010/10-25 Conference Call

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Conference Details

  • Date of Call: Monday, October 25, 2010
  • Time of Call: 11:00 am Eastern Time (5 pm CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.203.318.0479 (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), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
  • Duration: ~1 hour
  • Convener: M. Scott Marshall
  • Scribe: Lena Deus


Scott Marshall, Kei Cheung, Lena Deus, Rob Frost, Michael Miller, Eric Prud'hommeaux, Matthias Samwald,


  • Introduction
  • Next phase of BioRDF


<Lena> mscottm: fuuture bioRDF focus is on use cases in the neurosciences domains,  federation and provenance
<Lena> mscottm: by working with people in the community (EBI, etc), we can setup standard services for microarray data
<Lena> Linked open data mailing list is discussing best practices, about, among other things, provenance metadata
<Lena> role of bioRDF in LOD is to provide federation use cases
<Lena> (ex: what are the requirements for provenance?)
* michael has joined #hcls
<Lena> pharmGKB lexicon in RDF dataset with NCBO SPARQL endpoint
<Zakim> + +1.206.605.aabb
<Lena> can we integrate that data with what we already have in bioRDF?
<Lena> cooperate with consumers of EBI microarray data
<Lena> see if there is something that EBI has that we can learn from 
<Lena> can we increase federability of our knowledge resources (i.e. HCLS Kb)?
<Lena> if a URI is used to refer to a repository, things can be said about the graph itself
<Lena> reflective statements - added to the graph; if there is provenance metadata, it should be using the graph URI
<Lena> the idea is to use graph URI as they are used by EBI
<Lena> things like rdfs:label can be used to refer to the graph URI
<Lena> void can be used to talk about each of the grpahs in the Kb
<Lena> such as the ones we have used in the example queries
<Lena> kei: how to use rdfs:label to refer, for example, to a pathway graph?
<Lena> mscottm: when NCBO provides a lengthy, complete, URI; to display it in the interface, the label can be used 
<Lena> that way, the labels can be queried
<Lena> string matching through labels as part of the search
<Lena> what if that was a type instead?
<Lena> ericP: that way, hierarquies can be added
<ericP> { <...g218> a hcls:PathwayData . hcls:PathwayData rdfs:label "Pathway Data" . } <...g218> { ... pathway stuff ... }
<Lena> mscottm: the idea is to enable developers to stay in SPARQL to build the datasets
<Lena> mscottm: in the case of disease ontology, by creating this sets of provenance, we can 1) query the sets directly (use the information in the provenance to build the query itself)
<Lena> the hardest work is deciding on the predicates to use
<rfrost> Got to drop off early - talk to everyone next call
<Lena> create a description using widely used rdf terms to create a vocabulariy
<Zakim> -rfrost
<Lena> ericP: discoverability and composability 
<Lena> mscottm: a lot in common with SADI 
<Lena> mscottm: SADI - given an rdf graph describing the input and some rdf neighbourhood
<Lena> ericP: SADI unit of charatecterizarion of services is al at the predicate level
<Lena> ericP: this makes SADI look much more like voiD
<Lena> ericP: at NCI, some work in this space also
<Lena> ericP: integrating web services using SPARQL (code wrote a while ago)
<Lena> ericP: may be able to make a better use of stuff at NCBO
<Lena> (correction - no NCBI, but NCBO above)
<Lena> ericP: encourage NCBO to do SPARQL such that it is more like a service than a function 
<Lena> ericP: plan is to integrate with stuff at NCBO, TMO and bioRDF (next 3 months)
<Lena> ericP: in a function, inputs can be left blank whereas in service they cannot
<Lena> ericP: execution path affects the outcome
<Lena> mscottm: microarray / NCBO link
<Lena> kei: NCBO implemented SPARQL endpoint; 
<Lena> ericP: service constrains in SPARQL do not allow to specify default named graph
<Lena> ericP: we needed to add a default graph parameter
<Lena> ericP: are there going to be a lot of endpoints where we need to specify the named graphs?
<Lena> kei: e.g. in database systems querying, we can specify the db name as part of the query
<Lena> kei: that is often quite useful; along the same lines, that parallel in SPARQL would be useful
<Lena> ericP: the parallel is informative, does not tell us if that funcionality if fully required 
<Lena> ericP: a SQL command can do that in a database; the required databases would have to be loaded first
<kei> lena: use the same disease id to link diseome dataset with other other sets
<kei> sorry, I have to go to another meeting now...
<Zakim> -Kei_Cheung
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<mscottm> I have to go to..
<mscottm> I have to go too..
<Zakim> -matthias_samwald
<Zakim> -mscottm
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* michael has left #hcls
* jodi has joined #HCLS
* jodi has left #HCLS
<ericP> SPDL
* matthias_samwald has quit IRC (Quit: Leaving.)
<ericP> http://www.w3.org/2007/Talks/0511-egp-spdl/#%281%29
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<Zakim> - +1.832.386.aaaa
<Lena> my connection fell.. :(
<Lena> but I can't call back
<Lena> that's ok, I have to go in a few minutes
* ericP sorry Lena!
<Zakim> -EricP
<Zakim> - +1.206.605.aabb
<Zakim> SW_HCLS(BioRDF)11:00AM has ended
<Zakim> Attendees were mscottm, Kei_Cheung, EricP, +1.832.386.aaaa, rfrost, matthias_samwald, +1.206.605.aabb
* ericP also sorry that i didn't notice before