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15:04:02 <mscottm> Zakim, who is here?
15:04:02 <Zakim> sorry, mscottm, I don't know what conference this is
15:04:03 <Zakim> On IRC I see ram, matthias_samwald, Jun, amrapali, RRSAgent, Zakim, Janos, egombocz, rkiefer, bbalsa, achille_zappa, mscottm, ericP
15:04:11 <mscottm> Zakim, this is hcls
15:04:11 <Zakim> ok, mscottm; that matches SW_HCLS(BioRDF)11:00AM
15:04:15 <mscottm> Zakim, who is here?
15:04:15 <Zakim> On the phone I see Tony, +1.510.705.aaaa, tlebo, +1.631.444.aabb, ??P9, Scott_Marshall, ??P1, +46.7.08.13.aadd, ??P13, Chimezie
15:04:17 <Zakim> On IRC I see ram, matthias_samwald, Jun, amrapali, RRSAgent, Zakim, Janos, egombocz, rkiefer, bbalsa, achille_zappa, mscottm, ericP
15:04:18 <matthias_samwald1> matthias_samwald1 has joined #hcls
15:04:43 <Janos> http://dl.dropbox.com/u/21690634/Quantifying%20RDF%20data%20sets.pdf
15:04:44 <Zakim> +??P15
15:05:27 <Zakim> + +1.412.623.aaee
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15:06:03 <chimezie> Zakim, who is on the phone?
15:06:03 <Zakim> On the phone I see Tony, +1.510.705.aaaa, tlebo, +1.631.444.aabb, ??P9, Scott_Marshall, ??P1, +46.7.08.13.aadd, ??P13, Chimezie, ??P15, +1.412.623.aaee
15:07:00 <HarryH> 412 623  is me - Harry Hochheiser Pittsburgh
15:07:01 <mscottm> Brian Lowe: Developer on VIVO project, Susan Mitchell also works as developer / ontology on VIVO
15:07:36 <mscottm> Harry Hochheiser - University of Pittsburgh, interested in HCLS
15:09:03 <mscottm> Brian Lowe: Developer on VIVO project, Stella Mitchell also works as developer / ontology on VIVO
15:09:06 <Stella> Stella has joined #hcls
15:09:09 <ram> Ram from Metaome - We have a life science search engine called DistilBio (distilbio.com)
15:10:01 <Jun> scribe: Jun
15:10:27 <michael> michael has joined #hcls
15:10:34 <Jun> s/Susan/Stella/
15:11:08 <Zakim> + +1.206.732.aaff
15:11:52 <mscottm> Chimezie Ogbuji - Cleveland Clinic, Case Western, Recently started a startup
15:12:34 <Janos> http://dl.dropbox.com/u/21690634/Quantifying%20RDF%20data%20sets.pdf
15:12:55 <Zakim> + +1.857.250.aagg
15:13:31 <chimezie> Zakim, mute me
15:13:31 <Zakim> Chimezie should now be muted
15:13:53 <Jun> Scott: introduce Janos' talk: it's important to differentiate RDF datasets apart from by their content, licenses, etc 
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15:15:49 <mscottm> VIVO - scientific research network ontology
15:15:57 <Jun> Janos: one of the members of CTSA Connect graduate programme, to connect two major ontologies, VIVO and ***, to connect clinical sciences data
15:16:23 <chimezie> yes, I do
15:16:34 <Zakim> +Tony.a
15:16:38 <Janos> http://dl.dropbox.com/u/21690634/Quantifying%20RDF%20data%20sets.pdf
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15:17:09 <Jun> Slide 1: a lot of further work. this just presents a start
15:17:26 <Jun> slide 2
15:17:47 <Jun> Janos: Semantic Web is based on RDF, a graph-based data model
15:18:12 <mscottm> CTSA Connect: http://www.ctsaconnect.org/about-us
15:19:15 <Jun> ... more flexible than relational DBs by allowing parallel edges
15:19:18 <Jun> slide 3
15:19:41 <Jun> Janos: a paper submitted to the Triple Challenge 2010
15:19:59 <Jun> ... they did some quantification of datasets, looking into the internal structure of the data
15:20:08 <Jun> .... drew some of the approaches of this paper
15:20:32 <Jun> ... took a look of the datasets of the challenge, and did some structural analysis and others
15:20:48 <Jun> slide 4
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15:21:51 <Jun> Janos: a basic python library to parse n-triples. it's a memory based approach, and do some processing. based on PyPy
15:22:26 <Jun> .... PyPy for just-in-time compiling. speed up the processing
15:22:26 <Amit> Amit has joined #hcls
15:22:41 <Amit> conference is full! cannot join by voice
15:23:02 <Jun> .... just some basic statistical analysis, then started to do some pattern matching analysis. not by using SPARQL endpoint
15:23:25 <Jun> ... each file is treated as its own graph. didn't use Named Graphs
15:23:51 <Jun> Q: on scalability
15:24:08 <Jun> Janos: largest one is LinkedCT
15:24:38 <Jun> ... 28 millions triples. took 30% of a 64G memory
15:25:20 <Jun> ... SPARQL1.1 might provide better performance promises
15:25:28 <Jun> slide 5
15:26:00 <Jun> ... started with some basic counts
15:27:46 <Jun> slide 6
15:28:21 <Jun> Janos: do some simple fractions calculations
15:28:33 <Jun> ... e.g, how many literals in your triples
15:28:40 <Jun> ... how many literals are unique?
15:28:48 <Jun> ... how many objects are unique?
15:29:43 <Jun> ... structure measurement, by taking out the typing sort of information and literals
15:30:06 <egonw_> egonw_ has joined #HCLS
15:30:24 <Jun> ... subject/object coverage, more pointing or more pointed?
15:30:39 <Jun> ... more concrete examples to follow
15:30:45 <Jun> slide 7
15:31:47 <mscottm> scribenick: Jun
15:31:53 <Jun> Janos: computed it against a couple of LOD datasets, 4 of the LODD, DailyMed, LinkedCT, DrugbankRDF, RxNorm
15:32:55 <Jun> ... BioGrid database: an open access DB on Protein and Genetic Interactions
15:33:09 <Jun> ... BioPAX: pathways in BioPAX format
15:33:21 <Jun> ... bioGrid can be downloaded via OWL format
15:33:42 <Jun> ... VIVO: NIH funded project for scientific networking
15:34:03 <Jun> .... got n-triples for VIVO dataset
15:34:30 <Jun> ... go through by the number of triples desc
15:34:38 <Jun> slide 8
15:35:13 <Jun> Janos: top subjects, top classes, predicates, etc
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15:35:24 <Jun> ... give you a good idea of how people use ontologies
15:36:15 <Jun> ... LinkCT: 40% are literals, objects have 80% repetition
15:36:31 <Jun> ... three dominant classes
15:36:54 <Jun> Michael: have you done this analysis on the GO ontology?
15:37:00 <Jun> Janos: not yet
15:37:09 <Jun> Michael: expecting more diverse coverage
15:37:21 <Jun> Janos: would be interesting to look at
15:37:24 <Jun> slide 9
15:37:38 <Jun> Janos: BioGrid in BioPAX
15:37:58 <Jun> ... 50MB in owl but 40 millions triples in n-triple format
15:38:29 <Jun> ... again, subject, object coverage, and top classes. they are not LOD yet
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15:38:53 <Jun> ... get a good sense of what's actually in the content
15:38:54 <Jun> slide 10
15:39:00 <Jun> Janos: RxNorm
15:39:13 <Jun> ... only 6 classes. pretty small
15:39:36 <Jun> ... quite a bit of literals. structure data is higher than other datasets
15:41:35 <Jun> Q: do you see a big structure differences from these datasets?
15:41:38 <Jun> Janos: TBD
15:41:49 <Jun> slide 11
15:42:04 <Jun> Janos: 1.2 million triples
15:42:37 <Jun> ... data about publications, such as Authorship, Person ...
15:42:44 <Zakim> -??P15
15:42:59 <Jun> ... publication is dominant data source there. pretty good subject/object coverage
15:44:11 <Jun> slide 12
15:44:59 <Jun> Janos: it has a lot of links to outside datasets, have a much higher object coverage
15:45:11 <Jun> slide 13
15:45:33 <Jun> Janos: top predicate: owl:sameAs. again has a lot of links to outside datasets
15:48:50 <Jun> Scott: any idea about how one type of matrix could be more useful than another, or searching for others?
15:49:04 <Jun> s/Scott/mscottm/
15:49:12 <Jun> slide 14
15:49:28 <mscottm> s/matrix/metric/
15:49:32 <Jun> Janos: there are a lot of tools for graph vis and analysis, but not so good with RDF data
15:50:41 <Zakim> +EricP
15:51:22 <Jun> slide 15
15:52:38 <Jun> Janos: the twist is to allow multiple paths between 2 nodes
15:52:40 <Jun> slide 16
15:53:45 <Jun> Janos: there are ways to collapse the parallel edges, or put RDF into XML, in order to use some graph analysis tools
15:54:06 <Jun> slide 17
15:54:13 <Jun> Janos: show some examples
15:54:38 <Jun> ... get co-authors that are only members of a site, to get a smaller co-author network
15:54:46 <Jun> slide 18
15:55:05 <Jun> Janos: do some basic graph analysis using Mathematica
15:56:26 <Jun> ... basic in-degrees, out-degrees, histograms, one/two degree separation etc
15:56:39 <mscottm> Nice!
15:56:47 <Jun> slide 19
15:57:07 <Jun> Janos: Gephi doesn't support parallel edges. you have to do some pre-processing
15:57:24 <Zakim> -tlebo
15:57:49 <Jun> slide 20
15:58:02 <Jun> Janos:some links
15:58:35 <Jun> q+ have you thought about encoding some of the statistics using VoID?
15:58:57 <michael> thanks, janos, i need to drop off
15:59:02 <Zakim> - +1.206.732.aaff
15:59:40 <Zakim> -Tony
16:00:18 <Jun> Eric: any further analysis on some of the results, like the social network?
16:00:33 <Jun> <mscottm, I have to leave for another meeting>
16:01:42 <mattgamble> First how do you work out which metrics are useful? 
16:01:54 <Zakim> -EricP
16:03:26 <Zakim> - +46.7.08.13.aadd
16:05:23 <egombocz> Our Knowledge Explorer also provides metrics for weighing of connections in several ways
16:05:57 <Zakim> -??P1
16:06:10 <chimezie> Zakim, unmute me
16:06:10 <Zakim> Chimezie should no longer be muted
16:08:12 <mscottm> Chime - would you please jot your comment/question into IRC? I received an urgent call exactly when you started.. :(
16:08:28 <Zakim> -Tony.a
16:09:08 <chimezie> My question was whether he had considered using rdflib (https://github.com/RDFLib)
16:10:54 <Zakim> - +1.510.705.aaaa
16:11:50 <michael> michael has left #hcls
16:12:59 <Zakim> - +1.857.250.aagg
16:17:53 <Zakim> -Chimezie
16:18:49 <mscottm> CTSA Connect - ISF - Integrated Semantic Framework: core is combining VIVO ontology and eagle-i ontology
16:19:28 <HarryH> Thanks , Janos - very interesting!
16:19:49 <ram> Thanks Janos
16:20:02 <Stella> thanks all, bye
16:20:04 <Zakim> - +1.412.623.aaee
16:20:08 <Zakim> -Scott_Marshall
16:20:10 <Zakim> -??P13
16:20:10 <Zakim> - +1.631.444.aabb
16:20:12 <mscottm> bye all
16:20:12 <Zakim> -??P9
16:20:12 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:20:12 <Zakim> Attendees were Tony, +1.510.705.aaaa, tlebo, +1.631.444.aabb, +46.7.08.13.aacc, Scott_Marshall, +46.7.08.13.aadd, Chimezie, +1.412.623.aaee, +1.206.732.aaff, +1.857.250.aagg, EricP
16:20:24 <mscottm> Zakim, please draft minutes
16:20:24 <Zakim> I don't understand 'please draft minutes', mscottm
16:21:02 <mscottm> RRSagent, draft minutes
16:21:02 <RRSAgent> I have made the request to generate http://www.w3.org/2012/05/21-HCLS-minutes.html mscottm
16:21:04 <mscottm>  rrsagent, make log world-visible
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