15:57:27 <RRSAgent> RRSAgent has joined #BioRDF
15:57:27 <RRSAgent> logging to http://www.w3.org/2008/12/15-BioRDF-irc
15:57:37 <kei> Zakim, this will be BioRDF
15:57:37 <Zakim> ok, kei; I see SW_HCLS()11:00AM scheduled to start in 3 minutes
15:57:53 <kei> agenda+ introduction [Kei]
15:58:18 <kei> agenda HCLS KB update [Matthias, Adrian]
15:58:34 <kei> agenda+ HCLS KB update [Matthias, Adrian]
15:58:53 <kei> agenda+ Query Federation [Eric, Adrian, Rob]
15:59:07 <kei> agenda+ SMW telconf Summary [Kei]
15:59:16 <Jun> Jun has joined #biordf
15:59:30 <kei> Zakim, take up next agendum
15:59:30 <Zakim> agendum 1. "introduction" taken up [from Kei]
15:59:32 <mscottm> mscottm has joined #biordf
16:00:31 <Zakim> SW_HCLS()11:00AM has now started
16:00:38 <Zakim> +Kei_Cheung
16:00:57 <Zakim> +??P11
16:01:26 <mscottm> Zakim, ??P11 is mscottm
16:01:26 <Zakim> +mscottm; got it
16:01:45 <rfrost> rfrost has joined #BioRDF
16:02:31 <Zakim> +??P15
16:04:06 <Zakim> + +0186528aaaa
16:04:24 <kei> scribenick Rob
16:04:25 <AdrianP> AdrianP has joined #BioRDF
16:05:35 <Zakim> +??P19
16:05:37 <kei> Zakim, who is here
16:05:37 <Zakim> kei, you need to end that query with '?'
16:05:51 <AdrianP> Zakim, P19 is me
16:05:51 <Zakim> sorry, AdrianP, I do not recognize a party named 'P19'
16:05:53 <kei> Zakim, who is here?
16:05:55 <Zakim> On the phone I see Kei_Cheung, mscottm, ??P15, +0186528aaaa, ??P19
16:05:58 <Zakim> On IRC I see AdrianP, rfrost, mscottm, Jun, RRSAgent, Zakim, kei, ericP
16:06:04 <AdrianP> Zakim, ??P19 is me
16:06:05 <Zakim> +AdrianP; got it
16:06:12 <rfrost> Rob is on the phone as well
16:06:53 <rfrost> I may be ??P15
16:07:11 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/HCLS_KB_Thoughts
16:07:27 <mscottm> Zakim, ??P15 is rfrost
16:07:27 <Zakim> +rfrost; got it
16:08:22 <rfrost> kei: URL contains set of potential set of hcls kb thoughts to discuss, distilled from email thread over past week
16:08:47 <mscottm> Zakim, +0186528aaaa is Jun
16:08:47 <Zakim> +Jun; got it
16:10:01 <matthiassamwald> matthiassamwald has joined #biordf
16:10:36 <rfrost> kei:Agenda:first a short intro, then hcls kb review, then query federation discussion, then summary of last ontolog semantic media wiki telcon, finally Q&A/discussion
16:10:55 <Zakim> + +1.416.511.aabb
16:11:36 <matthiassamwald> Zakim, +1.416.511.aabb is matthiassamwald
16:11:36 <Zakim> +matthiassamwald; got it
16:12:19 <rfrost> mattias: looking into optimizing performance of triple store; having trouble with certain queries
16:12:40 <rfrost> ..problems with denial of service attacks
16:13:00 <mscottm> ..especially queries that don't include the named graph in the query
16:13:02 <rfrost> kei: would like URL of kb site
16:13:47 <rfrost> kei: not exactly clear on kb content - would like to see list of datasets that have been loaded
16:14:06 <rfrost> ..would be nice to see list in order to write SPARQL queries
16:14:32 <rfrost> matthais: has neurocommons content, no additional contents
16:14:43 <mscottm> q+
16:15:16 <matthiassamwald> DERI HCLS KB SPARQL endpoint: http://hcls.deri.org:8080/sparql
16:15:42 <matthiassamwald> test
16:16:10 <AdrianP> http://neuroweb.med.yale.edu/senselab/
16:16:20 <matthiassamwald> DERI HCLS KB web page: http://hcls.deri.org (down momentarily)
16:16:30 <rfrost> adrian: AllegroGraph installed, has loaded some data, need to open a port so that it is accessible via SPARQL Protocol externally, not yet accessible
16:16:56 <AdrianP> http://agraph.franz.com/allegrograph/
16:16:59 <Zakim> +EricP
16:17:28 <matthiassamwald> Description of the datasets in the Neurocommons KB (which is at the moment all we have on the DERI endpoint): http://neurocommons.org/page/Bundles
16:17:42 <rfrost> kei: interesting to compare the different triple store technologies as part of HCLS KB effort
16:18:04 <rfrost> ..this comparison will be helpful to the community
16:18:39 <rfrost> ..what are the unique features of each? (Virtuoso & AllegroGraph)
16:19:14 <rfrost> ..support for graph operations - e.g. finding protein in a graph with high connectivity
16:19:36 <AdrianP> AllegroGraph supports Named Graphs for Weights
16:19:42 <rfrost> eric: Oracle may help for that
16:20:05 <mscottm> q+
16:20:15 <AdrianP> and social network analysis, e.g. http://agraph.franz.com/support/documentation/current/reference-guide.html#header3-68
16:21:12 <ericP> Oracle's engine was designed initially for graphs (e.g. maps queries). likely the best topology analysis suppport
16:21:16 <rfrost> scott: federation may be an issue when you add multiple types of triple stores
16:21:48 <rfrost> DARQ or SimWEB
16:21:58 <AdrianP> AllegroGraph has a Sesame SPARQL interface
16:22:40 <rfrost> support federation over any set of SPARQL accessible triple stores
16:23:08 <AdrianP> q+
16:23:09 <rfrost> eric: virtuoso already has federation to some degree - expensive, makes local caches
16:24:28 <matthiassamwald> q+
16:24:32 <rfrost> ..two problems: user directs federations (indicates location of data, not as difficult), user does not direct federation (does not provide location of graphs, more difficult)
16:25:04 <mscottm> 1+
16:25:07 <rfrost> rob: DARQ and SimWEB are in the later category (support arbitrary queries and automatically decompose)
16:25:12 <AdrianP> q-
16:25:29 <AdrianP> federation support by AllegroGraph
16:25:30 <rfrost> +1 on supporting user directed federation to start
16:25:30 <AdrianP> http://agraph.franz.com/support/documentation/current/federation-tutorial.html
16:25:51 <ericP> -> http://www.w3.org/2004/10/04-pharmaFederate/ an experiment in making the user separate the federated sources
16:28:14 <rfrost> adrian/kei: will use a rule layer on top of the triple stores to handle the federation of the queries
16:28:35 <rfrost> the rule layer is executed within a middleware framework
16:29:41 <rfrost> kei: will any triple store technologies allow people to publish RDF data as linked data?
16:29:45 <ericP> q+ to say that the two objectives, automatically federationg vs. directed federation, are steps in the same pipeline
16:30:27 <rfrost> matthais: Univ. of Berlin has a service that will publish RDF as linked data
16:31:03 <matthiassamwald> Pubby: http://www4.wiwiss.fu-berlin.de/pubby/ (exposes resources in a SPARQL endpoint as "linked data")
16:32:17 <rfrost> scott: try federated query using just Virtuoso before executing over multiple distributed SPARQL endpoints
16:33:02 <rfrost> eric: worked with Virtuoso for Banff demo on queries over SQL repos
16:34:15 <ericP> yeah, one of the sources was something that i'd stuck in a nearby MySQL db
16:34:33 <rfrost> kei: how soon will the AllegroGraph repo be externally accessible?
16:35:23 <rfrost> adrian: they need to open externally accessible port; will be delayed by holidays - so, likely beginning of Jan
16:36:20 <rfrost> kei: need to identify which data sets we want to store in which repos and how the federated queries will be executed over those data sets
16:36:33 <rfrost> ..start with the Banff demo data sets?
16:37:16 <rfrost> eric: start with relational data and expose as RDF
16:37:51 <rfrost> jun: what is the goal of the HCLS KB? Public service?
16:38:56 <rfrost> kei: good questions; what can be done depends on interest and resources of group; demo is the short term goal
16:39:13 <rfrost> ..can look to incorporate datasets from drug group
16:39:50 <rfrost> ..providing a stable public service is different level of effort; can consider that after we get past the demo stage; will depend on level of resources
16:40:02 <rfrost> ..don't know that we have enough resources to do both
16:40:34 <matthiassamwald> PDSP Ki
16:41:21 <rfrost> scott: issue when creating queries on PDSP: trying to find substances with high affinities; encountered naming differences on key property in the query
16:41:53 <rfrost> ..PDSP was one of the databases that Matthais integrated last year; this issue was never fully resolved
16:42:36 <kei> kei has joined #BioRDF
16:42:39 <rfrost> ..would be a good idea to go back and make certain that this naming issue is understood/resolve and that a similar issues are not encountered integrating other dbs
16:42:56 <rfrost> kei: believes the issues has been resolved
16:43:24 <rfrost> ..does not know the technical details but they have done work to query across multiple datasets including PDSP
16:44:00 <rfrost> ..how much do we want to try and standardize URIs/naming across datasets when we look at the query federation issue
16:44:15 <rfrost> scott: sounds like good news
16:45:39 <rfrost> kei: going to summarize the ontolog telcon on the SMW that was held last Thurs
16:45:43 <AdrianP> Zakim, mute me
16:45:43 <Zakim> AdrianP should now be muted
16:46:00 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-12-15?action=AttachFile&do=get&target=smw_telconf_summary.pdf
16:46:01 <rfrost> http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2008_12_11
16:47:12 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-12-15?action=AttachFile&do=get&target=smw_telconf_summary.pdf
16:47:43 <ericP> [slide 2]
16:50:28 <rfrost> kei: first talk was on SMW by lead engineer
16:50:37 <rfrost> .. was a high-level overview of SMW
16:51:45 <rfrost> ..second talk covered a variety of SMW extensions developed by Yaron Koren: Semantic Forms, Semantic Drilldown, Semantic Results Forms, Semantic Google Maps, compound queries/data transfer
16:51:59 <ericP> my impression is that most folks who use SMW use Halo
16:52:16 <rfrost> ..third talk was on the Halo extension (funded by Vulcan, implemented by Ontoprise)
16:52:56 <rfrost> ..Ontoprise delivers the Halo extension as SMW+ which includes the Halo extensions and some others (e.g. semantic forms)
16:53:27 <rfrost> ..forth talk was on a rules prototype in SMW
16:53:49 <rfrost> ..fifth was on a SMW extension to support purple numbers
16:54:33 <rfrost> ..last main talk was on concept modeling in SMW via templates
16:54:52 <rfrost> ..one lightning talk on "Ask the Wiki"
16:55:46 <rfrost> There will be another talk on 1/22/2009: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_01_22
16:56:00 <ericP> note, as far as i know, there are no stand-alone paths for ont development in SMW; all require stepping through protogé for the actual modeling
16:56:03 <rfrost> Semantic Wiki Applications & Use Cases (1): vertical applications
16:56:15 <ericP> the wiki is mostly used for posting change requests
16:57:05 <AdrianP> Zakim, unmute me
16:57:05 <Zakim> AdrianP should no longer be muted
16:57:35 <matthiassamwald> (I cannot participate via audio anymore, noise office environment...)
17:00:42 <Zakim> -Jun
17:00:47 <Jun> (sorry, have to go)
17:02:42 <rfrost> kei: how might semantic wikis intersect with hcls kb scenario?
17:03:10 <rfrost> rob: could have a use case where a semantic wiki is use to extend/customize the content of the hcls kb
17:03:20 <rfrost> kei: can explore that scenario more offline
17:03:52 <rfrost> ..interesting to look at using wikis for query construction/execution
17:04:55 <AdrianP> bye
17:05:05 <Zakim> -AdrianP
17:05:07 <Zakim> -Kei_Cheung
17:05:48 <Zakim> -matthiassamwald
17:05:50 <rfrost> rfrost has left #BioRDF
17:06:12 <Zakim> -rfrost
17:08:24 <kei> RRSAgent, please draft minutes
17:08:24 <RRSAgent> I have made the request to generate http://www.w3.org/2008/12/15-BioRDF-minutes.html kei
17:08:36 <kei> RRSAgent, please make long world-visible
17:08:36 <RRSAgent> I'm logging. I don't understand 'please make long world-visible', kei.  Try /msg RRSAgent help
17:08:51 <kei> RRSAgent, please make log world-visible
17:45:40 <Zakim> -mscottm
17:45:45 <Zakim> -EricP
17:45:46 <Zakim> SW_HCLS()11:00AM has ended
17:45:47 <Zakim> Attendees were Kei_Cheung, mscottm, AdrianP, rfrost, Jun, matthiassamwald, EricP