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

Thanks David!

I will look for angle brackets in the log if it happens again.

Could some sort of error message be sent back to IRC if the minutes aren't
generated? Just a thought. No need to reply to the list.

In any case, I will try to remember to check the links from now on before
sending them out. :)

-Scott
On May 22, 2012 3:22 PM, "David Booth" <david@dbooth.org> wrote:

> Attached are formatted minutes.  I don't know why they weren't generated
> as expected.  The only weird thing I noticed in the log was one line
> that said:
>
>  <Jun> <mscottm, I have to leave for another meeting>
>
> Possibly the angle brackets around "mscottm, I have to leave for another
> meeting" confused the minutes generator, since angle brackets are
> normally only expected around IRC names.
>
> David
>
>
> On Tue, 2012-05-22 at 07:49 +0200, M. Scott Marshall wrote:
> > 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)
> > * BrianLowe (8054fe2e@78.129.202.38) Quit (Ping timeout)
> > <Zakim> - +1.510.705.aaaa
> > * egombocz (42758fa2@207.192.75.252) Quit (Quit: http://www.mibbit.com
> > ajax IRC Client)
> > * michael (d17cbd27@64.62.228.82) has left #hcls
> > <Zakim> - +1.857.250.aagg
> > * mattgamble (801e06c7@64.62.228.82) Quit (Quit: http://www.mibbit.com
> > 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
> >
> >
> >
>
> --
> David Booth, Ph.D.
> http://dbooth.org/
>
> Opinions expressed herein are those of the author and do not necessarily
> reflect those of his employer.
>