Re: [Linked Life Data] Minutes from May 21 Janos Hajagos presentation

Hi Eric,

Something seems to have gone wrong with the generation of the minutes
again. Could you please take a look at it?
I am pasting the log from my mIRC buffer below for those who want to
take a look in the meantime.

Cheers,
Scott

RRSagent, draft minutes
<RRSAgent> I have made the request to generate
http://www.w3.org/2012/05/21-HCLS-minutes.html mscottm
<mscottm>  rrsagent, make log world-visible
<RRSAgent> I have made the request, mscottm

<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
<Zakim> On IRC I see ram, matthias_samwald, Jun, amrapali, RRSAgent,
Zakim, Janos, egombocz, rkiefer, bbalsa, achille_zappa, mscottm, ericP
* matthias_samwald1 (m@128.131.167.8) has joined #hcls
<Janos> http://dl.dropbox.com/u/21690634/Quantifying%20RDF%20data%20sets.pdf
<Zakim> +??P15
<Zakim> + +1.412.623.aaee
* BrianLowe (8054fe2e@78.129.202.38) has joined #hcls
* HarryH (8231b338@64.62.228.82) has joined #hcls
* chimezie (chimezie@99.59.109.32) has joined #hcls
<chimezie> Zakim, who is on the phone?
<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
* matthias_samwald (m@149.148.241.249) Quit (Ping timeout)
<HarryH> 412 623  is me - Harry Hochheiser Pittsburgh
<mscottm> Brian Lowe: Developer on VIVO project, Susan Mitchell also
works as developer / ontology on VIVO
<mscottm> Harry Hochheiser - University of Pittsburgh, interested in HCLS
<mscottm> Brian Lowe: Developer on VIVO project, Stella Mitchell also
works as developer / ontology on VIVO
* Stella (80fd5743@78.129.202.38) has joined #hcls
<ram> Ram from Metaome - We have a life science search engine called
DistilBio (distilbio.com)
<Jun> scribe: Jun
* michael (d17cbd27@64.62.228.82) has joined #hcls
<Jun> s/Susan/Stella/
<Zakim> + +1.206.732.aaff
<mscottm> Chimezie Ogbuji - Cleveland Clinic, Case Western, Recently
started a startup
<Janos> http://dl.dropbox.com/u/21690634/Quantifying%20RDF%20data%20sets.pdf
<Zakim> + +1.857.250.aagg
<chimezie> Zakim, mute me
<Zakim> Chimezie should now be muted
<Jun> Scott: introduce Janos' talk: it's important to differentiate
RDF datasets apart from by their content, licenses, etc
* mattgamble (801e06c7@64.62.228.82) has joined #hcls
<mscottm> VIVO - scientific research network ontology
<Jun> Janos: one of the members of CTSA Connect graduate programme, to
connect two major ontologies, VIVO and ***, to connect clinical
sciences data
<chimezie> yes, I do
<Zakim> +Tony.a
<Janos> http://dl.dropbox.com/u/21690634/Quantifying%20RDF%20data%20sets.pdf
* BobF (81b0c518@78.129.202.38) has joined #hcls
<Jun> Slide 1: a lot of further work. this just presents a start
<Jun> slide 2
<Jun> Janos: Semantic Web is based on RDF, a graph-based data model
<mscottm> CTSA Connect: http://www.ctsaconnect.org/about-us
<Jun> ... more flexible than relational DBs by allowing parallel edges
<Jun> slide 3
<Jun> Janos: a paper submitted to the Triple Challenge 2010
<Jun> ... they did some quantification of datasets, looking into the
internal structure of the data
<Jun> .... drew some of the approaches of this paper
<Jun> ... took a look of the datasets of the challenge, and did some
structural analysis and others
<Jun> slide 4
* AmitSheth (826c0136@64.62.228.82) has joined #hcls
<Jun> Janos: a basic python library to parse n-triples. it's a memory
based approach, and do some processing. based on PyPy
* AmitSheth (826c0136@64.62.228.82) Quit (Quit: http://www.mibbit.com
ajax IRC Client)
<Jun> .... PyPy for just-in-time compiling. speed up the processing
* Amit (826c0136@109.169.29.95) has joined #hcls
<Amit> conference is full! cannot join by voice
<Jun> .... just some basic statistical analysis, then started to do
some pattern matching analysis. not by using SPARQL endpoint
<Jun> ... each file is treated as its own graph. didn't use Named Graphs
<Jun> Q: on scalability
<Jun> Janos: largest one is LinkedCT
<Jun> ... 28 millions triples. took 30% of a 64G memory
<Jun> ... SPARQL1.1 might provide better performance promises
<Jun> slide 5
<Jun> ... started with some basic counts
<Jun> slide 6
<Jun> Janos: do some simple fractions calculations
<Jun> ... e.g, how many literals in your triples
<Jun> ... how many literals are unique?
<Jun> ... how many objects are unique?
<Jun> ... structure measurement, by taking out the typing sort of
information and literals
* egonw_ (egonw@145.20.139.203) has joined #HCLS
<Jun> ... subject/object coverage, more pointing or more pointed?
<Jun> ... more concrete examples to follow
<Jun> slide 7
<mscottm> scribenick: Jun
<Jun> Janos: computed it against a couple of LOD datasets, 4 of the
LODD, DailyMed, LinkedCT, DrugbankRDF, RxNorm
<Jun> ... BioGrid database: an open access DB on Protein and Genetic
Interactions
<Jun> ... BioPAX: pathways in BioPAX format
<Jun> ... bioGrid can be downloaded via OWL format
<Jun> ... VIVO: NIH funded project for scientific networking
<Jun> .... got n-triples for VIVO dataset
* amrapali (8b120872@64.62.228.82) Quit (Quit: http://www.mibbit.com
ajax IRC Client)
<Jun> ... go through by the number of triples desc
<Jun> slide 8
<Jun> Janos: top subjects, top classes, predicates, etc
* markthompson (9158d121@78.129.202.38) has joined #hcls
<Jun> ... give you a good idea of how people use ontologies
* egonw_ (egonw@145.20.139.203) Quit (Ping timeout)
<Jun> ... LinkCT: 40% are literals, objects have 80% repetition
<Jun> ... three dominant classes
<Jun> Michael: have you done this analysis on the GO ontology?
<Jun> Janos: not yet
<Jun> Michael: expecting more diverse coverage
<Jun> Janos: would be interesting to look at
<Jun> slide 9
<Jun> Janos: BioGrid in BioPAX
<Jun> ... 50MB in owl but 40 millions triples in n-triple format
<Jun> ... again, subject, object coverage, and top classes. they are not LOD yet
* egonw_ (egonw@145.20.139.203) has joined #HCLS
<Jun> ... get a good sense of what's actually in the content
<Jun> slide 10
<Jun> Janos: RxNorm
<Jun> ... only 6 classes. pretty small
<Jun> ... quite a bit of literals. structure data is higher than other datasets
<Jun> Q: do you see a big structure differences from these datasets?
<Jun> Janos: TBD
* egonw_ (egonw@145.20.139.203) Quit (Ping timeout)
<Jun> slide 11
<Jun> Janos: 1.2 million triples
<Jun> ... data about publications, such as Authorship, Person ...
<Zakim> -??P15
<Jun> ... publication is dominant data source there. pretty good
subject/object coverage
<Jun> slide 12
<Jun> Janos: it has a lot of links to outside datasets, have a much
higher object coverage
<Jun> slide 13
<Jun> Janos: top predicate: owl:sameAs. again has a lot of links to
outside datasets
* matthias_samwald1 (m@128.131.167.8) Quit (Ping timeout)
<Jun> Scott: any idea about how one type of matrix could be more
useful than another, or searching for others?
<Jun> s/Scott/mscottm/
<Jun> slide 14
<mscottm> s/matrix/metric/
<Jun> Janos: there are a lot of tools for graph vis and analysis, but
not so good with RDF data
* ericP Zakim please dial ericP-office
* ericP Zakim, please dial ericP-office
* Zakim ok, ericP; the call is being made
<Zakim> +EricP
<Jun> slide 15
<Jun> Janos: the twist is to allow multiple paths between 2 nodes
<Jun> slide 16
<Jun> Janos: there are ways to collapse the parallel edges, or put RDF
into XML, in order to use some graph analysis tools
<Jun> slide 17
<Jun> Janos: show some examples
<Jun> ... get co-authors that are only members of a site, to get a
smaller co-author network
<Jun> slide 18
<Jun> Janos: do some basic graph analysis using Mathematica
<Jun> ... basic in-degrees, out-degrees, histograms, one/two degree
separation etc
<mscottm> Nice!
<Jun> slide 19
<Jun> Janos: Gephi doesn't support parallel edges. you have to do some
pre-processing
<Zakim> -tlebo
<Jun> slide 20
<Jun> Janos:some links
<Jun> q+ have you thought about encoding some of the statistics using VoID?
* Zakim Jun, you typed too many words without commas; I suspect you
forgot to start with 'to ...'
<michael> thanks, janos, i need to drop off
<Zakim> - +1.206.732.aaff
* rkiefer (81b0c518@207.192.75.252) Quit (Quit: http://www.mibbit.com
ajax IRC Client)
<Zakim> -Tony
<Jun> Eric: any further analysis on some of the results, like the
social network?
<Jun> <mscottm, I have to leave for another meeting>
<mattgamble> First how do you work out which metrics are useful?
* ericP away again
<Zakim> -EricP
<Zakim> - +46.7.08.13.aadd
* bbalsa (d5723e05@109.169.29.95) Quit (Quit: http://www.mibbit.com
ajax IRC Client)
<egombocz> Our Knowledge Explorer also provides metrics for weighing
of connections in several ways
* BobF (81b0c518@78.129.202.38) Quit (Quit: http://www.mibbit.com ajax
IRC Client)
<Zakim> -??P1
<chimezie> Zakim, unmute me
<Zakim> Chimezie should no longer be muted
<mscottm> Chime - would you please jot your comment/question into IRC?
I received an urgent call exactly when you started.. :(
<Zakim> -Tony.a
<chimezie> My question was whether he had considered using rdflib
(https://github.com/RDFLib)
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<Zakim> - +1.510.705.aaaa
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<Zakim> - +1.857.250.aagg
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ajax IRC Client)
* markthompson (9158d121@78.129.202.38) Quit (Quit:
http://www.mibbit.com ajax IRC Client)
* Jun (81431aef@78.129.202.38) Quit (Quit: http://www.mibbit.com ajax
IRC Client)
* Amit (826c0136@109.169.29.95) Quit (Quit: http://www.mibbit.com ajax
IRC Client)
<Zakim> -Chimezie
* chimezie (chimezie@99.59.109.32) Quit (Quit: chimezie)
<mscottm> CTSA Connect - ISF - Integrated Semantic Framework: core is
combining VIVO ontology and eagle-i ontology
<HarryH> Thanks , Janos - very interesting!
<ram> Thanks Janos
* HarryH (8231b338@64.62.228.82) Quit (Quit: http://www.mibbit.com
ajax IRC Client)
<Stella> thanks all, bye
<Zakim> - +1.412.623.aaee
* ram (31f97127@78.129.202.38) Quit (Quit: http://www.mibbit.com ajax
IRC Client)
<Zakim> -Scott_Marshall
<Zakim> -??P13
<Zakim> - +1.631.444.aabb
<mscottm> bye all
<Zakim> -??P9
<Zakim> SW_HCLS(BioRDF)11:00AM has ended
<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
* Stella (80fd5743@78.129.202.38) Quit (Quit: http://www.mibbit.com
ajax IRC Client)
<mscottm> Zakim, please draft minutes
<Zakim> I don't understand 'please draft minutes', mscottm
<mscottm> RRSagent, draft minutes
<RRSAgent> I have made the request to generate
http://www.w3.org/2012/05/21-HCLS-minutes.html mscottm
<mscottm>  rrsagent, make log world-visible
<RRSAgent> I have made the request, mscottm

On Tue, May 22, 2012 at 1:22 AM, M. Scott Marshall
<mscottmarshall@gmail.com> wrote:
> Here are the minutes from today's meeting:
> http://www.w3.org/2012/05/21-HCLS-minutes.html
>
> I see large potential for using tools like Janos's to describe /
> characterize datasets and their RDF representations for selection and
> eventual query patterns - something essential in a linked data
> marketplace.
>
> My apologies for not anticipating more participants and increasing the
> default parameter for Zakim. If you were unable to join and have
> questions or comments after reading the minutes, please send them to
> the list or I will do my best to answer (or find someone who can).
>
> Thanks to Jun for scribing! Thanks to Janos for presenting!
>
> Richard Boyce will present work to us in early June. Stay tuned for details.
>
> Cheers,
> Scott



-- 
M. Scott Marshall, PhD
https://plus.google.com/u/0/114642613065018821852/posts
http://www.linkedin.com/pub/m-scott-marshall/5/464/a22

Received on Tuesday, 22 May 2012 05:50:04 UTC