HCLSIG BioRDF Subgroup/Meetings/2009-03-30 Conference Call
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- Date of Call: Monday March 30, 2009
- Time of Call: 11:00 am 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: Adrian Paschke
- Scott Marshall, Kei Cheung, Jun Zhao, Adrian Paschke, Eric Prud'hommeaux, Matthias Samwald, Michel Dumontier, TN Bhat
- Rob Frost
- HCLS KB update (Matthias, Adrian)
- Face-to-face meeting (All)
- BMC Bioinformatics paper submission (All)
<apaschke> Topic: HCLS KB update (Matthias and Adrian)
<apaschke> Matthias: worked together with Scott to provide access to AIDA
<apaschke> Scott: access W3C HCLS KB (Virtuoso) via AIDA
<apaschke> Scott: web interface - see all the repositories which are available - browse all the repositories and ontologies (hierarchical view of an ontology such as GO)
<apaschke> Scott: visualizes named graphs as possible "repositories"
<apaschke> Scott: search for keywords and add them to the query
<apaschke> Scott: introduces a hierarchy in an ontology - the top level constructs and allows browsing through the hierarchie
<apaschke> Scott: Matthias, do you have plans to fix the second query on the demo page
<apaschke> Matthias: answering the query without named graphs is quite demanding
<apaschke> Matthias: needs optimization
<apaschke> Matthias: needs upgrade to Virtuoso version 6
<apaschke> Matthias: optimization of the memory consumption, etc.
<apaschke> Scott: there seems to be some kind of time limit / time out
<apaschke> Matthias: yes, we introduced it due to too many requests
<apaschke> Eric: shall we wait till the next release of Virtuoso version 6?
<apaschke> Eric: Scott, can you work with the query without named graphs
<apaschke> Matthias: Data is in named graphs - but not used in the current version
<apaschke> Scott: tried to load UMLS into Sesame - required a 64bit machine
<apaschke> Scott: will try with a Amazon cloud
<apaschke> Scott: have to figure out how to split costs, e.g. by using a EC2 could
<apaschke> Yun: we currently run a 64 bit server in our group for FlyBase
<apaschke> Jun: currently funded by our group
<apaschke> Jun: costs proportional to the size of the triple store and the number accesses
<apaschke> AllegroGraph version 3.2 release, query optimizations & more
<apaschke> average, an order of magnitude faster
<apaschke> performance improvements include RDFS++ Reasoning, get-triples, client/server bulk loading, SPARQL, Jena and Sesame
<apaschke> Gruff graph-based browser for AllegroGraph
<kei> scott: contacted a staff member about issusing sparql through endpoint, but there is a security concern ...
<apaschke> Scott: might try to add a new layer of interfaces for AIDA to access the AllegroGraph store
<apaschke> Matthias: the DERI Virtuso store is also accessed via a http SPARQL interface by AIDA
<apaschke> Matthias: should also work for the instance of AllegroGraph
<apaschke> Scott: Will look into that again
<apaschke> AGWebView - A Web Browser Server for AllegroGraph - AGWebView gives you access to your triple store data via from an ordinary Web browser. Available for Windows, Linux, and Mac OSX.
<kei> when these are set up, they can be demo'ed to the group.
<apaschke> Topic: * Face-to-face meeting (All)
<apaschke> kei: F2F meeting end of April in Boston
<apaschke> kei: what will the BioRDF group present?
<ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F F2F home page
<apaschke> kei: breakout sessions for BioRDF; who will attend
<scott> will attend
<michel> i intend to
<matthias> may be depending on funding situation, but a DERI representative will attend
<apaschke> Kei: present dynamic queries, aTag effort, add new activities, collaborations with other task forces (e.g. LODD, Jun's herbal data set ),
<apaschke> ericP: there might be a possibility to dial-in
<ericP> i stuck an anchor on http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F#BioRDF so we can nav there directoy
<apaschke> Kei: ... collaboration with Bio2RDF
<apaschke> Eric: would like to encourage people to add ideas
<apaschke> Scott: federated queries using more bio-informatics data in the demo
<apaschke> Topic: BMC Bionformatics paper submission
<apaschke> Kei: about one week left
<apaschke> Kei: deadline, April 6th
<apaschke> Kei: main part is federation
<apaschke> EricP: built a mapping file and a small database to query it
<apaschke> EricP: little bug in the encoding site, currently crashes parser
<apaschke> EricP: spread sheet or large databases ?
<apaschke> EricP: make the table structure flat or nested / linked?
<apaschke> Kei: biomedical domain data often disseminated in spreadsheet format -> i.e. flat
<apaschke> Kei: could be presented as simple RDF graph
<apaschke> Kei: leightweight ontologies built from flat rel. schemas
<apaschke> Kei: could be interesting to show this mapping
<apaschke> EricP: explain mapping file for both structures (flat and deep database schema)
<apaschke> Scott: seems to be useful for the reader
<apaschke> EricP: gene records with different types; point to other tabels -> is a realistic representation
<apaschke> EricP: could show the two mapping approaches in the paper
<apaschke> Matthias; would only show the first mapping and simply state that we could also do the other approach (without explanation)
<apaschke> Kei: could a compromise - show the simple mapping in details and simply discuss the other approach in the discussion section
<apaschke> Scott: add an example in the discussion section
<apaschke> EricP: there wouldn't be much difference between the two, except some rules which can be explained
<apaschke> EricP: shall we discuss on the public HCLS mailing list?
<apaschke> Scott: in general yes. But 500 subscribers might wonder - since it is a discussion about the contents for a paper
<apaschke> EricP: send some general discussion about technical issues (not details of the paper)
<apaschke> Kei: DBPedia, receptor table "B"
<apaschke> Kei: federate triple formatted sources
<apaschke> Matthias: integrate statements which use rdf-a tags in some of the triples
<mscottm> Zakim, this will be hcls
<Zakim> ok, mscottm, I see SW_HCLS(BioRDF)11:00AM already started
<apaschke> EricP: no parser for RDFa currently
<apaschke> Matthias: XSLT to translate RDFa via GRRDL to RDF/XML
<matthias_samwald> (gives you the RDF/XML version of the aTag RDFa pastebin)
<ericP> Human EG for 2550 9568
<ericP> Rat: 81657 83633
<ericP> Mouse: 54393 242425
<matthias_samwald> http://en.wikipedia.org/wiki/GABAB_receptor mentions "2550"
<ericP> excellent. and the DBpedia query which will retrieve that?
<apaschke> Loom would be certainly interesting in this context too http://www.loomp.org/
<apaschke> Kei: future directions - open query federation
<apaschke> Kei: exploit meta data to open query federation
<apaschke> Kei: link together data
<apaschke> Kei: URI issues in query federation
<matthias_samwald> wow, loomp looks a lot like aTags :)
<apaschke> Scott: how can we proceed in the next days?
<apaschke> Kei: by email
<apaschke> EricP: by IRC?
<apaschke> Scott: use HCSL IRC? might be taken
<apaschke> EricP: hcls is fine
<apaschke> Kei: let's use this IRC to proceed and use emails
<apaschke> Kei: let's have a working BioRDF call next week just on the paper
<apaschke> Kei: our next regular BioRDF call will be in two weeks (April 13)