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13:45:04 <dbooth> rrsagent, make logs public
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13:47:02 <LeeF> zakim, LeeF is in MITKiva
13:47:02 <Zakim> +LeeF; got it
13:47:26 <LeeF> zakim, dbooth is in MITKiva
13:47:26 <Zakim> +dbooth; got it
13:47:30 <LeeF> zakim, ericP is in MITKiva
13:47:30 <Zakim> +ericP; got it
13:48:33 <dbooth> zakim, Justin is in MITKiva
13:48:33 <Zakim> +Justin; got it
13:48:43 <dbooth> zakim, luke is in MITKiva
13:48:43 <Zakim> +luke; got it
13:51:21 <ericP> Zakim, helena is in MITKiva
13:51:21 <Zakim> +helena; got it
13:56:05 <Zakim> + +1.603.770.aacc
13:56:28 <Zakim> - +1.603.770.aacc
13:56:28 <ericP> Q: is there a way to share templates?
13:56:43 <ericP> Lena: we have bioportal
13:59:20 <Lena> new version of my slides: https://confluence.deri.ie:8443/download/attachments/40304735/bos_linkedData4LifeSciences1.pptx
13:59:52 <Lena> these are the slides for the afternoon: https://confluence.deri.ie:8443/download/attachments/40304735/BigLinkedDataLifeSciences_20120827_bos.pptx
14:00:56 <ericP> topic: Introductions
14:01:02 <ericP> scribenick: dbooth 
14:01:30 <ericP> dbooth: David Booth, involved with Cleveland Clinic for several years
14:01:37 <ericP> ... working with SemWeb for research
14:01:55 <ericP> ... worked with Pangenex (SP?) for decision support
14:02:08 <ericP> ... keen user of SPARQL as a rules language
14:02:24 <frago> frago has joined #hack
14:02:29 <bobP> PanGenX
14:03:18 <frago> frago has joined #hack
14:03:19 <dbooth> Maryam: Working in sem in LS. Project in sem in LS.  PubMed.
14:04:21 <dbooth> Nima: Haarvard med school.  Partners Healthcare clinical decision support system.
14:04:50 <dbooth> __: MIT.  Financial models.
14:04:53 <ericP> Maryam Panahiazar - MUlti-Dimensional integrative approach to comparing genes for knowledge DIScovery
14:05:02 <dbooth> HelenaDeus: DERI
14:05:12 <dbooth> ... Cancer research.
14:05:29 <dbooth> Shimu: Research fellow, harvard.  Med records.
14:05:44 <ericP> Sheng Yu
14:05:53 <ericP> s/Shimu:/Sheng Yu/
14:05:57 <ericP> Loren Wilde
14:06:16 <dbooth> ___: Clinician in audiology. 
14:06:27 <ericP> Peter Mager
14:07:06 <dbooth> Peter: CS background.  Looking at gene seq and synth biology.  Also run a seminar series for IEEE.  Having someone from Church lab about writingn thing on DNA sequenses.
14:07:42 <ericP> stuart turner
14:08:24 <dbooth> StuartTurner: Veterinarian.  Post doc in bionfornatics.    Research in biosurveillance.  Want to sem webify a  project ant NCI.
14:09:05 <dbooth> Franz: Entogen, int in deriv of structured data from unstructured.
14:09:13 <dbooth> MattMackdonald: Entogen.
14:09:42 <dbooth> ChrisBouton: Neurobio, engineer, sponsory, triplemapper.
14:10:20 <dbooth> Terence: Up-to-date, CDS, many teaching hospitals.  In charge of info retrieval, and to get better int w EMR sys.
14:11:12 <dbooth> Yakubo: Visiting MIT for dissertation.  Nat Lan Proc to symbolic then computation.  Background philos.   Formal modeling, logic.
14:11:31 <dbooth> Luke: Lead dev SADI, linking dymaic data into SW.
14:11:59 <dbooth> DanielaBourges: Harv Med School, working on SW years, Eagle-I project.
14:13:04 <Lena> (created a tweeter hashtag for this hackaton:  #hclshack)
14:13:05 <dbooth> JustinLancaster: CSO QuickBio BioMedServer.  Dnamic modeling of sys biology.  Came to LS after env sci 10 yrs ago.  Simulate complex sys from the knowledge, in the pattern of OpenBEL, then dev automated hypothesis.
14:13:52 <dbooth> Dipankar: Classifiers, clustering.  Don't work w SW but want to learn.
14:14:10 <ericP> julie mcmurry
14:14:48 <dbooth> ___: Eagle-I, int biomed resource data.  Background in vaccine, immun.
14:15:03 <ericP> juliane schneider
14:15:42 <dbooth> JuliaSchneider: metadata librarian, Harvard Med School.  LD, entity extraction, trying to hook MeSH and Medline and Astrophysics.
14:16:00 <dbooth> s/___/JulieMcMurry/
14:16:26 <julianeschneider> julianeschneider has left #hack
14:17:04 <Frans> small correction - Entagen product is TripleMap - triplemap.com
14:18:56 <Lena> s/Loren/Lorin/
14:19:07 <mattmac> mattmac has joined #hack
14:19:57 <Ray> Ray has joined #hack
14:20:01 <Lena> s/Lorin/Loren/
14:20:35 <Ray> Hi
14:20:59 <nima> nima has joined #hack
14:21:15 <mary> mary has joined #hack
14:22:01 <peter> peter has joined #hack
14:24:29 <Lena> tweethach is #hclshack
14:24:31 <Justin> Hi Justin Lancaster (BiomedServer.com -- kwiKBio project)  justin.lancaster@att.net  --- based in Boston area.
14:24:34 <Lena> tweethacs is #hclshack
14:24:39 <Lena> tweethash is #hclshack
14:26:05 <dbooth> topic: Lee and ericP's SPARQL Tutorial
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14:26:18 <dbooth> slides - http://www.cambridgesemantics.com/sparql-by-example/slides.html
14:26:24 <dbooth> [slide 1]
14:27:02 <Frans> anyone have a link for the meetup just described?
14:27:47 <w3c> w3c has left #hack
14:28:08 <dbooth> -> http://www.meetup.com/The-Cambridge-Semantic-Web-Meetup-Group/ Cambridge Semantic Web Meetup
14:28:21 <dbooth> [slide 2]
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14:29:51 <dbooth> [slide 3]
14:31:25 <frago> frago has joined #hack
14:31:35 <luke> Frans: this looks like the meetup http://www.meetup.com/The-Cambridge-Semantic-Web-Meetup-Group/
14:33:25 <dbooth> [slide 5]
14:33:40 <Frans> thanks - signed up 
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14:37:38 <graham> zakim, who is here?
14:37:38 <Zakim> On the phone I see Bob_Powers (muted), MITKiva, +1.301.906.aaaa (muted), +1.603.570.aabb (muted)
14:37:41 <Zakim> MITKiva has LeeF, dbooth, ericP, Justin, luke, helena
14:37:41 <Zakim> On IRC I see graham, frago, terrence, peter, mary, nima, Ray, mattmac, RRSAgent, dbooth, LeeF, bobP, apo, Lena, Frans, StuartTurner, Justin, luke, Zakim, ericP
14:37:56 <dbooth> [slide 6]
14:39:34 <daniela> daniela has joined #hack
14:41:33 <graham> zakim, who is here?
14:41:33 <Zakim> On the phone I see Bob_Powers (muted), MITKiva, +1.301.906.aaaa (muted), +1.603.570.aabb (muted)
14:41:35 <Zakim> MITKiva has LeeF, dbooth, ericP, Justin, luke, helena
14:41:35 <Zakim> On IRC I see daniela, graham, frago, terrence, peter, mary, nima, Ray, mattmac, RRSAgent, dbooth, LeeF, bobP, apo, Lena, Frans, StuartTurner, Justin, luke, Zakim, ericP
14:44:59 <graham> zakim, who is here?
14:44:59 <Zakim> On the phone I see Bob_Powers (muted), MITKiva, +1.301.906.aaaa (muted), +1.603.570.aabb (muted)
14:45:01 <Zakim> MITKiva has LeeF, dbooth, ericP, Justin, luke, helena
14:45:01 <Zakim> On IRC I see daniela, graham, frago, terrence, peter, mary, nima, Ray, mattmac, RRSAgent, dbooth, LeeF, bobP, apo, Lena, Frans, StuartTurner, Justin, luke, Zakim, ericP
14:46:46 <dbooth> Q: How do you specify where to get the data for the query?
14:46:53 <dbooth> A: That will be explained in a moment.
14:49:34 <dbooth> ... A query interface often has a place to put the URL of the data you wish to query.
14:51:48 <dbooth> [slide 9]
14:51:58 <dbooth> Try query at: http://librdf.org/query/
14:53:52 <ericP> http://128.30.7.30:8001/
14:55:27 <dbooth> [slide 10]
14:55:30 <dbooth> [slide 12]
14:59:09 <dbooth> [slide 14]
14:59:20 <dbooth> [slide 15]
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15:03:46 <Zakim> + +1.603.570.aadd
15:04:16 <dbooth> [slide 18]
15:09:19 <mary> can not get the slides from web<http://www.cambridgesemantics.com/semantic-university/sparql-by-example#q_negation_new_not_exists_r>
15:18:46 <frago> frago has joined #hack
15:20:13 <dbooth> Q: How often are the XML datatype URIs dereferenced?
15:21:09 <dbooth> A: Almost never.  The app doesn't look up the URIs, typically just the developer who needs to look up a detail about that datatype.
15:22:15 <dbooth> Q: SPARQL queries RDF resources.  But how do you create RDF from other data sources and keep it updated?
15:23:17 <dbooth> A: There's a lot of tools to do that.  It isn't standardized.  There are software tools for mapping relational databases to RDF.
15:23:48 <dbooth> ... Same kind of ETL and data integration approaches already existing.
15:24:39 <dbooth> Q: When you design relational DBs, there are design considerations.  Are there similar design considerations for RDF?
15:25:35 <dbooth> A: The design is in the developer's lap.  There are fewer things that the DBA must think about, but it may increase in the future.
15:27:02 <dbooth> Q: In rel DB, there's a limited number of columns.  But in PubMed, you have a gazillion docs, and all free text.  What's the best practice to make sure the user can take advantage of that free text DB?  how do you define the API or protocol between a DB designer and user?
15:27:28 <dbooth> A: SPARQL wiped them out.  Make it so that the person who writes the queries has an intuitive graph pattern to walk.
15:28:00 <dbooth> Q: How do you pick out the data most useful to the users?
15:28:02 <peter> peter has joined #hack
15:28:45 <dbooth> ... If you designed RDF data for PubMed, how do you pick what data is most useful?
15:30:04 <dbooth> A: One approach is the get users together and design what attributes you want.  At the other end of the spectrum, we can pull out tons of information.  But because in RDF we aren't limited by the number of columns, we're going to pull them all out, and let the users do SPARQL queries to pull out what they want.
15:31:32 <dbooth> ... For the first approach you may as well use a rel DB.  For the other extreme, it isn't really practical.  The approach I've seen in practice is an incremental path on that continuum.  But incrementally adding new things on user requrements can be done in RDF without breaking existing data.  You don't have to go back and create new tables.
15:32:05 <dbooth> dbooth: Great answer!
15:32:48 <dbooth> Q: Is the entailment features in SPARQL intended for integrity constraints and checking?
15:33:21 <dbooth> Lee: No.  Different tools and platforms are treating constraints and checking their own way.
15:35:46 <dbooth> EricP: in the TMO (Translational Medicine Ont), we were evolving the ont and it would break the results of SPARQL queries.  We would track what queries broke (went from 5 answers to 0).
15:35:56 <dbooth> [slide 26]
15:36:00 <dbooth> [slide 27]
15:36:30 <dbooth> dbooth: You can also think of constraints as SPARQL queries that look for violations.
15:39:48 <dbooth> Q: Is it possible to query for an artist that has at least one of those attributes?
15:40:45 <dbooth> A: Yes.  BOUND is a SPARQL construct that asks whether a variable has a value in the query, so you can use that.
15:43:02 <dbooth> Lee: I've been interested in doing a life-sciences-specific version of this tutorial.  Let me know if you're interested in helping on that.
15:43:14 <dbooth> [slide 30]
15:44:46 <dbooth> [slide 31]
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15:47:57 <dbooth> [slide 33]
15:48:54 <dbooth> [slide 35]
15:51:06 <dbooth> [slide 36]
15:53:58 <dbooth> Q: Is there  a place where these best practices are being collected?
15:54:13 <dbooth> Lee: Semantic University is one place.
15:54:55 <dbooth> dbooth: A good way to develop a CONSTRUCT query is first to develop and debug it as a SELECT query, and then convert it to CONSTRUCT after you've debugged the WHERE clause.
15:57:01 <dbooth> Q: When would it be better to create a view using CONSTRUCT versus converting the query?
15:57:45 <dbooth> EricP: Question of materializing the view or not.  Same trade-offs as in DB world.
15:58:24 <dbooth> Q: What if a value is unbound when you're doing CONSTRUCT?
15:58:42 <dbooth> A: That triple is automatically filtered out, per the SPARQL standard.
15:58:51 <dbooth> [slide 37]
16:02:13 <dbooth> Q: Are you guaranteed that the Amazon and Nile lengths are in the same units?
16:03:09 <dbooth> A: No.  You'd better be careful in your query.  Good practice that I like (but it bother's ontologists): put the units in the predicate name, e.g. :lengthInKm
16:03:28 <dbooth> [slide 39]
16:03:40 <dbooth> [slide 40]
16:08:14 <dbooth> Q: Queries involving time durations?
16:08:58 <dbooth> A: Yes, there is time arithmetic.
16:09:27 <dbooth> ... They're defined in terms of the XML Schema operators spec.
16:09:44 <dbooth> ... But it isn't required for SPARQL 1.1 conformance.
16:11:44 <dbooth> [slide 42]
16:12:37 <dbooth> [slide 43]
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16:18:40 <dbooth> [slide 46]
16:21:24 <dbooth> Q: Is there a difference between MINUS and using the old !BOUND idiom?
16:21:40 <dbooth> A: They're pretty much the same, except may some edge cases.
16:21:57 <dbooth> [slide 50]
16:22:54 <dbooth> s/may/maybe/
16:23:26 <terrence> terrence has joined #hack
16:23:40 <dbooth> [slide 51]
16:30:45 <dbooth> [slide 53]
16:30:50 <dbooth> [slide 54]
16:30:58 <dbooth> [slide 56]
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16:34:50 <dbooth> EricP:  SADI talk will be next, after lunch, at 1:30pm Eastern.  THen Helena's talk after that.
16:36:00 <Zakim> -Bob_Powers
16:39:44 <graham> graham has joined #hack
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16:45:23 <Zakim> + +1.303.777.aaee
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17:02:01 <luke> Questions from Max:
17:02:01 <luke>   How are triples hashed/indexed?
17:02:01 <luke>   What sits between SPARQL and the web data?
17:02:01 <luke>   Where is the logic stored for the relations?
17:02:01 <luke>   How good are SPARQL queries for proprietary data?
17:10:14 <dbooth> [Lunch break until 1:30pm Eastern US]
17:23:30 <graham> graham has joined #hack
17:25:02 <Zakim> + +1.303.777.aaff
17:27:13 <Ray> Ray has joined #hack
17:29:55 <dbooth> Topic: SADI
17:30:03 <Zakim> + +1.925.377.aagg
17:33:59 <Justin> zakim, who is here?
17:33:59 <Zakim> On the phone I see MITKiva, +1.301.906.aaaa (muted), +1.603.570.aabb (muted), +1.603.570.aadd (muted), +1.303.777.aaff (muted), +1.925.377.aagg (muted)
17:34:02 <Zakim> MITKiva has LeeF, dbooth, ericP, Justin, luke, helena
17:34:02 <Zakim> On IRC I see Ray, graham, terrence, StuartTurner, frago, nima, mattmac, mary, RRSAgent, dbooth, LeeF, bobP, Lena, Frans, Justin, luke, Zakim, ericP
17:34:36 <sanofi> sanofi has joined #hack
17:35:01 <Zakim> +Bob_Powers
17:35:52 <luke> Slides for this talk are at http://sadiframework.org/slides/MIT2012.pdf
17:37:10 <frago> thank you, I was about to ask about the slides
17:38:55 <dbooth> [slide 2]
17:39:10 <ericP> scribenick: ericP
17:39:16 <ericP> [slide 3]
17:40:30 <ericP> luke: use case for computed data
17:40:47 <ericP> ... my clinic recently changed their gold-standard for COPD factors
17:41:02 <ericP> ... was costly 'cause the data was all stored in the old format
17:41:07 <ericP> [slide 4]
17:42:05 <ericP> [slide 5]
17:42:51 <ericP> luke: semantic web services (e.g. OWL-S) aim for the world where the service models the state of the universe before and after
17:43:24 <ericP> ... e.g. tell ciri to purchase plane tickets and do all the debiting etc.
17:43:29 <ericP> [slide 6]
17:43:38 <ericP> [slide 7]
17:44:26 <mary> sadi slide is not avalaible!
17:44:54 <ericP> huh, indeed
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17:45:12 <frago> i'm following from http://sadiframework.org/slides/MIT2012.pdf
17:45:29 <ericP> mary, just takes a while to download
17:45:54 <ericP> [slide 11]
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17:46:14 <ericP> [slide 12]
17:46:50 <ericP> luke: given a db of heights and weights, use a SADI service to query BMI
17:47:16 <mary> thanks
17:47:18 <ericP> [slide 17]
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17:49:57 <ericP> Maryam: can you orchestrate SADI services?
17:50:15 <ericP> Luke: the goal is that *you* don't have to, that it happens for you
17:50:40 <ericP> ... the SHARE client exports the latest Taverna workflow format
17:51:00 <ericP> [slide 19]
17:51:40 <ericP> [slide 20]
17:52:20 <ericP> [slide 22]
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17:52:53 <ericP> [slide 23]
17:53:27 <ericP> luke: the input is a named individual, and the output is the same individual with a hello:greeting property
17:53:57 <ericP> [slide 26]
17:54:45 <ericP> luke: ideally service description would describe services
17:54:54 <ericP> ... for now, use the SADI registry
17:55:12 <ericP> [slide 28]
17:55:42 <ericP> luke: OWL reasoning in Java 'cause thats where the reasoners are
17:55:58 <ericP> [slide 29]
17:56:58 <ericP> luke: SHARE is a SPARQL processor which matchs queries against the local store + the services in the registry
17:57:06 <ericP> ... also decomposes OWL classes
17:57:42 <ericP> ... if you have a bunch of triples which constitute an entity, you can use an OWL class to capture them
17:58:25 <ericP> Maryam: how do you invoke WSDL services?
17:58:34 <ericP> luke: SHARE is for SADI services
17:58:50 <ericP> ... you can describe that in WSDL, but it's just RDF-in/RDF-out
17:59:25 <ericP> ... there are ways to use e.g. SAWSDL or wrappers to make WSDL services available as SADI
18:01:36 <ericP> luke: example: increasing creatinine (blood urea nitrogen) level indicates a rejected transplat
18:02:10 <ericP> [slide 32]
18:02:30 <ericP> includes OWL class patients:AtRiskPatient
18:02:55 <dbooth> http://biordf.net/cardioSHARE/
18:03:27 <Ray> Ray has joined #hack
18:04:31 <ericP> Luke: I want the genes in a pathway and the proteins they code for
18:07:01 <ericP> Luke: interface completes from LSRN (Life Sciences Resources Network)
18:07:17 <ericP> ... could use identifier.org (if they export RDF)
18:09:59 <ericP> [something close to http://sadiframework.org/content/2010/06/10/cardioshare-walkthrough/ ]
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18:19:35 <luke> Download SHARE command-line client: https://code.google.com/p/sadi/wiki/SHAREClient
18:22:19 <luke> SHARE example queries: http://biordf.net/cardioSHARE/queries.html
18:22:53 <Zakim> - +1.603.570.aabb
18:24:01 <Zakim> -Bob_Powers
18:25:26 <ericP> -> http://sadi.googlecode.com/files/SHARE-client-0.1.jar share client jar
18:27:40 <ericP> -> http://biordf.net/cardioSHARE/queries.html example queries
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18:31:40 <graham> zakim, who is here?
18:31:40 <Zakim> On the phone I see MITKiva, +1.301.906.aaaa (muted), +1.603.570.aadd (muted), +1.303.777.aaff (muted), +1.925.377.aagg (muted)
18:31:42 <Zakim> MITKiva has LeeF, dbooth, ericP, Justin, luke, helena
18:31:42 <Zakim> On IRC I see frago, warzeld, sdc, peter, Ray, daniela, nima, mattmac, sanofi, graham, StuartTurner, mary, RRSAgent, dbooth, LeeF, bobP, Lena, Frans, Justin, luke, Zakim, ericP
18:34:41 <Zakim> - +1.925.377.aagg
18:41:32 <frago> frago has joined #hack
18:43:50 <Justin> What was command line string to execute the jar file?
18:44:23 <Justin> ... for the SHARE client
18:50:56 <Zakim> +Bob_Powers
19:01:33 <amy_> amy_ has joined #hack
19:10:55 <mary> if anybody found the link for paper?
19:11:55 <dbooth> justin, java -Xmx1024m -jar SHARE-client-0.1.jar
19:13:02 <ericP> luke: [Re: http://biordf.net/cardioSHARE/queries.html #14]
19:13:35 <ericP> ... phd student in our lap trying to emulate clinical classification in OWL
19:13:44 <dbooth> s/lap/lab/
19:14:01 <ericP> ... i.e. have the OWL reasoner perform diagnosis support like a clinician
19:14:24 <ericP> ... the measurement units in his data were inconsistent and frequently unspecified
19:15:34 <ericP> ... #14 demos that SHARE maps to units to a standard, and can guess them when not specified
19:16:15 <frago> frago has joined #hack
19:18:03 <Zakim> + +1.781.454.aahh
19:19:55 <ericP> Maryam: phylogeny analysis is a hard case
19:20:05 <ericP> Lena: no single tree of life
19:20:18 <ericP> ... also they are huge
19:20:51 <ericP> luke: we needed a stable taxonomy so we're using one from NCBO
19:21:15 <ericP> ... if you build the tree from the ribosomal RNA, you hard-code you biases
19:21:37 <ericP> SADI can't solve the social prob, but can address the size
19:21:42 <ericP> luke: SADI can't solve the social prob, but can address the size
19:22:15 <ericP> ... we had a group using doing molecular modeling
19:22:42 <ericP> ... a query for the polygons on a molecular surface exceeded 4G
19:24:12 <ericP> ... so back to the phylogeny use case, probably need to pack the hierarchy as a literal and unpack when needed
19:25:02 <ericP> Peter Mager: can't you pass a parameter?
19:25:17 <ericP> luke: yep, we have URIs and we can use them for this
19:26:53 <ericP> ... there's a predicate called rdf:isDefinedBy which SADI derefs
19:28:01 <ericP> maryam: phylogeny researchers care about methods used
19:28:23 <ericP> ... can i go through the info for methods?
19:28:32 <ericP> luke: if they write it down, but we don't force them
19:29:42 <ericP> ... Jim McCusker proposed pointing to the code for the service in a public repo
19:31:55 <ericP> ericP: for e.g. homology, you code the way something is known to be homologous
19:32:47 <ericP> luke: we use OWL to infer that e.g. BLAST homology is a form of homology
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19:35:40 <ericP> luke: there are tools to use SAWSDL to make WSDL services be SADI services
19:36:06 <ericP> StuartTurner: where do you see SADI going in the next few years?
19:36:38 <ericP> luke: i described SADI in terms of a toolkit 'cause i work on the toolkit
19:36:52 <ericP> ... but SADI is just a set of practices
19:37:26 <ericP> ... i worked on a submission to W3C
19:37:57 <luke> link to SADI summary/spec: https://code.google.com/p/sadi/wiki/SADITrail
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20:06:12 <ericP> topic: Big Data
20:06:19 <ericP> ericP has changed the topic to: Big Data -- https://confluence.deri.ie:8443/download/attachments/40304735/BigLinkedDataLifeSciences_20120827_bos.pptx
20:06:26 <ericP> -> https://confluence.deri.ie:8443/download/attachments/40304735/BigLinkedDataLifeSciences_20120827_bos.pptx Big Data slides
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20:07:54 <ericP> [slide 15]
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20:25:49 <ericP> [slide 32]
20:31:45 <ericP> ericP: the trust axis can also capture latent nuances which make data more applicable
20:32:47 <ericP> mark: the prob with federation is that we can't move 1k genome sets around on the network 
20:33:06 <ericP> ... (without exotics fiber infrastructure)
20:33:27 <ericP> Lena: but are you using all that data? can you select for the data you need?
20:33:35 <Zakim> - +1.303.777.aaff
20:33:59 <ericP> mark: need to be able to run analysis on computers that you don't own
20:34:05 <nima> nima has joined #hack
20:34:50 <ericP> ... e.g. i don't want to pull the 1k genome data and swissprot to my local computer
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20:39:00 <ericP> ericP: [mumbles about the Grid marrying the SemWeb]
20:39:07 <peter> peter has joined #hack
20:41:27 <ericP> [shipping code to data a la SciDB]
20:44:11 <ericP> Justin: are you losing too much by believing that you will capture all of the understanding of the publishers? [@@corrections please]
20:44:27 <ericP> Lena: i think the question is can we capture that that knowledge
20:44:55 <ericP> ... if we can eliminate human subjectivity, you increase the quality of the data
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20:45:30 <ericP> ... having spent a year manually capturing data, i recognize how imprecise it is
20:46:13 <ericP> Justin: i'm not convinced that letting the machine crank on 1k dimensions will capture the intuitions of the scientist
20:46:59 <ericP> peter: there's a lot of interesting data which is lost
20:47:29 <ericP> ... e.g. astronomers who fedex disk arrays around the country to do fourier analysis
20:49:24 <ericP> ... that data could be still be useful but is not available
20:49:27 <Zakim> - +1.603.570.aadd
20:49:49 <ericP> ericP: [meta data tracking of raw data, e.g. disk arrays]
20:50:12 <ericP> Lena: [fold-it example]
20:54:46 <tez> "Big Data" should enable both cases debated
20:55:49 <ericP> @@1: going back a few slides, you spoke of identifiers disappearing on you. that seems like a higher priority
20:56:40 <tez> How can the "crackpot" be accelerated ? 
20:57:06 <ericP> Lena: yes that's first, but it's basically a solved problem
20:57:20 <ericP> @@1: i don't know what your example was, but how has this been solved?
20:57:47 <ericP> Lena: through frameworks, exposing e.g. RDBs on the SemWeb
20:58:03 <ericP> ... my issue was URLs which were simply non-dereferencable
20:59:20 <ericP> maryam: one of the probs with reactome is that it's just for humans
20:59:46 <ericP> ... on KEGG we can't find a molecule in a pathway on certain days
21:00:01 <ericP> Lena: need to capture context and provenance
21:00:21 <ericP> ... e.g. reactome is curated human data
21:01:22 <ericP> maryam: how can we decide whether KEGG and Reactome is better?
21:02:03 <ericP> Lena: we invented pathways to keep things in boxes
21:02:22 <ericP> ... (like species)
21:02:29 <ericP> ... we need to capture the underlying data
21:03:14 <ericP> ... imo, we need to talk about system states instead of pathways
21:03:25 <Zakim> -Bob_Powers
21:03:57 <ericP> Justin: there are so many variables which can be measured on a patient
21:05:05 <ericP> ... the data mining problem is so huge, but coming at it with a big data approach might allows us to compartmentalize and analyze
21:05:44 <ericP> StuartTurner: in clinical care we have clinical practice to avoid opinion-based medicine
21:06:06 <ericP> ... humans make cognative mistakes and have biases
21:06:20 <ericP> Justin: we want the machine to amplify the human
21:06:43 <ericP> Lena: can't we have the machine perform the standardized tests while humans work on e.g. new methodologies
21:07:57 <Zakim> - +1.617.244.aaii
21:09:54 <Zakim> - +1.301.906.aaaa
21:16:11 <ericP> s/@@1/TFMorris/
21:16:19 <ericP> RRSAgent, draft minutes
21:16:19 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/27-hack-minutes.html ericP
21:16:28 <ericP> RRSAgent, make log world-visible
21:22:05 <ericP> Zakim, who is here?
21:22:05 <Zakim> On the phone I see MITKiva
21:22:06 <Zakim> MITKiva has LeeF, dbooth, ericP, Justin, luke, helena
21:22:06 <Zakim> On IRC I see warzeld, tez, amy_, mary, RRSAgent, dbooth, Lena, luke, Zakim, ericP
21:22:13 <ericP> Zakim, disconnect MITKiva
21:22:13 <Zakim> MITKiva is being disconnected
21:22:15 <Zakim> SW_HCLS(HACK)9:00AM has ended
21:22:15 <Zakim> Attendees were Bob_Powers, [MIT-G449], MITKiva, +1.301.906.aaaa, Lalana, +1.603.570.aabb, LeeF, dbooth, ericP, Justin, luke, helena, +1.603.770.aacc, +1.603.570.aadd,
21:22:17 <Zakim> ... +1.303.777.aaee, +1.303.777.aaff, +1.925.377.aagg, +1.781.454.aahh, +1.617.244.aaii
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