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13:00:17 <RRSAgent> RRSAgent has joined #hack
13:00:17 <RRSAgent> logging to http://www.w3.org/2012/08/30-hack-irc
13:00:23 <dbooth> zakim, who is here?
13:00:23 <Zakim> sorry, dbooth, I don't know what conference this is
13:00:25 <Zakim> On IRC I see RRSAgent, Zakim, dbooth, bobP, amy_, lorin, ericP
13:00:32 <dbooth> zakim this is #hack
13:00:54 <dbooth> zakim, this will be #hack
13:00:54 <Zakim> I do not see a conference matching that name scheduled within the next hour, dbooth
13:01:05 <dbooth> zakim, what conferences?
13:01:05 <Zakim> I see WAI_RDWG()9:30AM, Team_(w3m)12:00Z active
13:01:07 <Zakim> also scheduled at this time are Team_Global(review)8:00AM, SW_HCLS(HACK)9:00AM, UW_UWA()9:00AM, WF_TF()9:00AM, IA_WebApps(Widgets)9:00AM
13:01:24 <dbooth> zakim, this will be sw_hcls
13:01:24 <Zakim> ok, dbooth; I see SW_HCLS(HACK)9:00AM scheduled to start now
13:01:48 <dbooth> rrsagent, make logs public
13:02:09 <dbooth> Meeting: W3C HCLS Hackathon at MIT
13:02:22 <dbooth> Chair: EricP
13:02:39 <ericP> zakim, this will be #hack
13:02:39 <Zakim> I do not see a conference matching that name scheduled within the next hour, ericP
13:02:41 <Zakim> SW_HCLS(HACK)9:00AM has now started
13:02:48 <Zakim> +Bob_Powers
13:03:23 <ericP> zakim, this will be hack
13:03:23 <Zakim> ok, ericP, I see SW_HCLS(HACK)9:00AM already started
13:03:28 <ericP> Zakim, who is here?
13:03:28 <Zakim> On the phone I see Bob_Powers
13:03:29 <Zakim> On IRC I see RRSAgent, Zakim, dbooth, bobP, amy_, lorin, ericP
13:04:10 <ericP> Zakim, please dial MITKiva
13:04:10 <Zakim> ok, ericP; the call is being made
13:04:11 <Zakim> +MITKiva
13:04:54 <ericP> Zakim, unmute MITKiva
13:04:54 <Zakim> MITKiva should no longer be muted
13:05:13 <bobP> yes I can hear
13:05:16 <bobP> sort of
13:05:27 <Justin> Justin has joined #hack
13:05:39 <bobP> I can hear good
13:05:46 <Justin> well, well
13:05:47 <bobP> can you hear me now?
13:06:05 <Justin> no, because you're muted
13:06:16 <Justin> and Eric is scared of feedback
13:06:21 <ericP> Zakim, unmute Bob_Powers
13:06:21 <Zakim> Bob_Powers should no longer be muted
13:06:21 <bobP> hold on for coffee
13:06:29 <Justin> YES!
13:11:43 <mary> mary has joined #hack
13:16:58 <Lena> Lena has joined #hack
13:17:28 <luke> luke has joined #hack
13:18:45 <graham> graham has joined #hack
13:20:38 <Lena> any scribe volunteers?
13:20:48 <Lena> or should we "volunterize" someone ;)
13:26:22 <LeeF> LeeF has joined #hack
13:30:24 <graham> graham has joined #hack
13:37:39 <dbooth> Topic: Lightning talk by Maryam Panahiazar: Using Semantic Technology and Phyloinformatics in Translational Bioinformatics
13:42:04 <Lena> scribenick: Lena
13:43:19 <Lena> Topic: Lightning talk by David Booth - RDF Pipeline Framework
13:43:25 <Lena> automating data production pipelines
13:43:29 <Lena> open source project
13:43:34 <Lena> hosted on google code
13:43:40 <bobP> http://code.google.com/p/rdf-pipeline/
13:43:45 <dbooth> http://dbooth.org/2012/pipeline/
13:44:59 <Lena> idea: when doing apps using sem web techs, we get data from somewhere and we massage it using some data production pipeline
13:45:25 <Lena> slide 7 - modelled after the cleveland clinic pipeline
13:45:35 <Lena> each node represent processing and data storage
13:45:47 <Lena> e.g. patients represents some sort of patient data
13:46:29 <Lena> when we have large amounts of data, it is used by many different applications
13:46:39 <Lena> e.g. cardiology vs immunology
13:46:52 <iker> iker has joined #hack
13:46:54 <Lena> why do we want data production pipelines? - 
13:47:04 <Lena> from applications to RDF - from RDF to applications
13:47:41 <Lena> dbooth: app developers tend to be  miopic - they only see their application
13:47:57 <Lena> dbooth: what should go on in the semantic data integration cloud to make it work?
13:48:14 <Lena> the pipeline can have as many outputs as you want
13:48:50 <Lena> pipeline itself is described as rdf
13:49:10 <Lena> each node is an http node that "knows" rest
13:52:32 <Lena> data and programming language agnostic
13:52:40 <Lena> although it was designed around an rdf use case
13:54:26 <Lena> the framework transforms code (e.g. shell scripts) into REST services
13:56:12 <Lena> output can be RDF but not necessarily
13:56:21 <Lena> lazy update policy
13:58:41 <Lena> it won't update unless the data changes
13:59:26 <Lena> data manipulation using SPARQL
13:59:32 <Lena> because it is a rules language
13:59:45 <Lena> use inserts to keep the data in the server
14:07:58 <Lena> different from a workflow because there is no central controller!
14:08:26 <Lena> each node sees and uses the same description of pipeline
14:09:32 <Lena> somewhat event-driven
14:20:16 <iker> http://www.topquadrant.com/products/TB_install.php
14:20:21 <mary> mary has joined #hack
14:21:26 <iker> http://www.topquadrant.com/products/TB_install.php
14:23:30 <dbooth> i/topq/Topic: Elsevier - Semantic Web in HCLS for Commercial Applications, Iker Huerga
14:26:05 <dbooth> rrsagent, draft minutes
14:26:05 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/30-hack-minutes.html dbooth
14:32:54 <ericP> http://www.w3.org/People/Eric/ericP-foaf#ericP
14:42:44 <daniela> daniela has joined #hack
14:47:06 <dbooth> Topic: Tutorial - SPARQL Rules, Iker Huerga
14:49:36 <dbooth> Download of TopBraid Composer Free edition: http://www.topquadrant.com/products/TB_install.php
14:55:36 <iker> http://topbraid.org/examples/purchases
15:02:26 <Zakim> -Bob_Powers
15:04:49 <Zakim> +Bob_Powers
15:11:31 <Lena> Lena has joined #hack
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15:21:06 <dbooth> dbooth has joined #hack
15:21:21 <Lena> Lena has joined #hack
15:22:26 <luke> luke has joined #hack
15:24:44 <dbooth> zakim, who is here?
15:24:44 <Zakim> On the phone I see MITKiva, Bob_Powers (muted)
15:24:45 <Zakim> On IRC I see luke, Lena, dbooth, LeeF, Justin, RRSAgent, Zakim, bobP, amy_, lorin, ericP
15:26:29 <iker> iker has joined #hack
15:26:33 <iker> SELECT ?x WHERE { LET (?x := smf:parseDate("12/3/09","MM/dd/yy")). }
15:26:59 <mary> mary has joined #hack
15:28:17 <Lena> drag and drop topbraid-spin-spin.ttl into imports tab
15:30:15 <Lena> right click on spin function
15:30:19 <Lena> create subclass
15:30:26 <Lena> name it ISO8601
15:31:28 <iker> http://www.topquadrant.com/spin/tutorial/SPARQLRulesTutorial.pdf
15:32:25 <Lena> click spin contrain and select "create from spin template"
15:32:38 <Lena> go to predicate, click on + sign
15:33:05 <Lena> click rdf:property and then arg1
15:33:23 <iker> This transforms a date into mmddyy ISO8601
15:36:27 <graham> graham has joined #hack
15:36:56 <Lena> click on spin body - add empty row
15:37:10 <iker> SELECT ?x WHERE { LET (?x := smf:parseDate("12/3/09","MM/dd/yy")). }
15:38:10 <dbooth> Then modify it to be: SELECT ?x WHERE { LET (?x := smf:parseDate(?arg1,"MM/dd/yy")). }
15:38:20 <StuartTurner> StuartTurner has joined #hack
15:40:25 <iker> SELECT ?x WHERE { LET (?x := :ISO8601("3/6/09")).  } 
15:47:10 <Lena> (paste the above query in sparql editor)
15:54:51 <Lena> now go to right hand side and click add property
15:55:38 <Lena> select datatypeproperty
15:55:43 <Lena> call it invoiceDate
15:56:54 <Lena> add range
15:56:59 <Lena> xsd:date
15:58:51 <iker> iker has joined #hack
15:58:56 <iker> CONSTRUCT {?s :invoiceDate ?idate } WHERE { ?s purchases:date ?date . LET (?idate := :ISO8601(?date)) . }
16:00:31 <Lena> double click purchase
16:00:45 <Lena> spin rule - add empty row
16:00:55 <Lena> paste the construct that works
16:01:24 <Lena> replace ?s with ?this
16:01:43 <Lena> click ok (tiny little ok on the right hand side of the textbox)
16:01:44 <dbooth> so the spin:rule becomes:
16:01:45 <dbooth> [[
16:01:47 <dbooth> CONSTRUCT {
16:01:47 <dbooth>     ?this :invoiceDate ?idate .
16:01:47 <dbooth> }
16:01:47 <dbooth> WHERE {
16:01:49 <dbooth>     ?this purchases:date ?date .
16:01:51 <dbooth>     BIND (:ISO8601(?date) AS ?idate) .
16:01:53 <dbooth> }
16:01:55 <dbooth> ]]
16:02:32 <Lena> go to instances tab, double click on one of them
16:03:08 <Lena> go to "Inference" menu, click "Run Inferences"
16:07:51 <iker> http://topbraid.org/spin/api/1.2.0/index.html
16:11:07 <Lena> Lena has left #hack
16:17:18 <graham> graham has joined #hack
16:20:21 <dbooth> Topic: Lightning talk: Justin Lancaster, Integrated Monitoring, Modeling and Management
16:25:27 <iker> iker has joined #hack
16:29:17 <graham> graham has joined #hack
16:37:18 <Frans> Frans has joined #hack
16:38:38 <iker> sorry guys but I need to leave to catch the train, very nice hackathon, congratulations Eric and thx everyone 
16:38:50 <dbooth> Topic: Using Jena, by Ian Jacoby
16:40:51 <dbooth> s/Jacoby/Jacobi/
16:41:47 <Justin> Justin has joined #hack
16:46:19 <dbooth> Luke: Jena also has a Dataset interface that has a default graph and a set of named graphs, but it's read only.
16:51:56 <luke> Dataset.getDefaultModel(), Dataset.getNamedModel(String graphURI) will get you the Model objects out of the Dataset object. You could probably modify those.
16:54:41 <ericP> -> http://purl.org/hcls/2007/kb-sources/addgene.ttl sample data for jena hacking demos
17:01:47 <ericP> -> http://www.w3.org/2012/Talks/0830-JenaIntroBio.pdf slides
17:02:19 <ericP> also linked from the agenda
17:03:04 <dbooth> Letest release of maven eclipse extension: http://download.eclipse.org/technology/m2e/releases
17:03:11 <Justin> RE: Lightning Talk -- JUSTIN LANCASTER -- kwiKBio(tm) Project -- slides accessible at http://biomedserver.com/kwiKBio%20Project_AUG%202012.pdf 
17:03:17 <dbooth> linked from http://www.eclipse.org/m2e/download/
17:08:08 <amy_> amy_ has joined #hack
17:09:12 <dbooth> Eclipse IDE for Java Developers: http://www.eclipse.org/downloads/packages/eclipse-ide-java-developers/junor
17:26:54 <dbooth> After eclipse startup, File-->New-->Project-->Maven->Maven Project
17:27:04 <dbooth> ... select "Create a simple project"
17:27:34 <dbooth> ... Group id: org.example
17:27:42 <dbooth> ... Artifact Id: simplejena.example
17:27:59 <dbooth> ... Finish
17:29:21 <Zakim> -Bob_Powers
17:30:39 <dbooth> Then double click on: Package Explorer--> simplejena.example->src->pom.xml
17:30:50 <dbooth> ... go to Dependencies tab
17:31:15 <dbooth> ... Group Id: org.apache.jena
17:31:27 <dbooth> ... Artifact Id: jena-core
17:31:45 <dbooth> ... Version: 2.7.3
17:32:19 <dbooth> ... Okay
17:32:25 <dbooth> ... SAVE
17:33:03 <dbooth> ... and that will cause it to load jena from maven, and put it into the classpath.
17:33:52 <dbooth> Then note in Package Explorer->simplejena.example->Maven Dependencies, that jena stuff is there.
17:35:43 <dbooth> Then File->New->Class
17:35:49 <dbooth> ... Package: org.example.simplejenaexample
17:35:57 <dbooth> ... Name: SimpleJenaExample
17:36:10 <dbooth> ... Select "public static voic main(...)
17:44:26 <dbooth> http://purl.org/hcls/2007/kb-sources/addgene.ttl
17:45:29 <bobP> bobP has joined #hack
17:46:18 <ericP> prefix sc: <http://purl.org/science/owl/sciencecommons/>
17:49:33 <Zakim> +Bob_Powers
17:50:49 <dbooth> http://purl.org/science/articles/pmid/15169870
18:01:39 <Frans> Frans has joined #hack
18:04:19 <dbooth> Complete code in SimpleJenaExample.java tab: 
18:04:20 <dbooth> [[
18:04:21 <dbooth> package org.example.simplejenaexample;
18:04:21 <dbooth> import com.hp.hpl.jena.rdf.model.Model;
18:04:21 <dbooth> import com.hp.hpl.jena.rdf.model.ModelFactory;
18:04:21 <dbooth> import com.hp.hpl.jena.rdf.model.Property;
18:04:24 <dbooth> import com.hp.hpl.jena.rdf.model.Resource;
18:04:25 <dbooth> import com.hp.hpl.jena.rdf.model.StmtIterator;
18:04:27 <dbooth> import com.hp.hpl.jena.vocabulary.RDFS;
18:04:29 <dbooth> public class SimpleJenaExample {
18:04:32 <dbooth> 	/**
18:04:34 <dbooth> 	 * @param args
18:04:35 <dbooth> 	 */
18:04:38 <dbooth> 	public static void main(String[] args) {
18:04:39 <dbooth> 		Model m = ModelFactory.createDefaultModel();
18:04:41 <dbooth> 		m.read("http://purl.org/hcls/2007/kb-sources/addgene.ttl", "N3");
18:04:43 <dbooth> 		Property is_described_by = m.createProperty(m.getNsPrefixURI("sc"), "is_described_in");
18:04:45 <dbooth> 		StmtIterator itr = m.listStatements(null, is_described_by, m.createResource("http://purl.org/science/articles/pmid/15169870"));
18:04:49 <dbooth> 		while (itr.hasNext()) {
18:04:52 <dbooth> 			Resource subject = itr.nextStatement().getSubject();
18:04:54 <dbooth> 			StmtIterator name_itr = subject.listProperties(RDFS.label);
18:04:56 <dbooth> 			while (name_itr.hasNext()) {
18:04:58 <dbooth> 				System.out.println(name_itr.nextStatement().getString());
18:05:00 <dbooth> 			}
18:05:03 <dbooth> 		}
18:05:04 <dbooth> 	}
18:05:06 <dbooth> }
18:05:09 <dbooth> ]]
18:05:46 <ericP> -> http://pastebin.com/5j8PKhiU slide4 task
18:06:34 <dbooth> Ian: To use SPARQL, you need to add Arq as a dependency.
18:13:57 <dbooth> To add Arq dependency: Package Explorer->simplejena.example->src->pom.xml->(right click)->Maven->Add dependency
18:14:46 <dbooth> ... Group Id: org.apache.jena
18:14:55 <dbooth> ... Artifact Id: jena-arq
18:15:08 <dbooth> ... Version: 2.9.3
18:15:16 <dbooth> ... OK
18:21:20 <ericP> java -cp $(echo apache-jena-2.7.3/lib/*.jar | tr ' ' ':'):. Slide4
18:32:44 <dbooth> Luke: Warning "log4j:WARN No appenders could be found for logger (com.hp.hpl.jena.sparql.mgt.ARQMgt)." can be ignored.  Jena has its own logger that will bind at runtime to your preferred logger, so this warning is saying that it failed to do so.  You can correct it by adding a logger to your maven dependencies.
18:32:57 <Lena> Lena has joined #hack
18:33:32 <dbooth> s/has its own/uses an abstract/
18:33:44 <ericP> -> http://pastebin.com/kirx9eLh query demo
18:36:26 <dbooth> Working code is in the above pastebin uri.
18:44:20 <dbooth> Luke: For using SPARQL 1.1 Update, you can use a Jena Dataset.
18:47:13 <dbooth> Interactive SPARQL editor SparqlEd from Sindice: http://www.sindicetech.com/blog/?p=14&preview=true
18:50:51 <luke> For Jena SPARQL update syntax on a local Model, the syntax looks like:
18:50:51 <luke> Model model;
18:50:51 <luke> String query;
18:50:51 <luke> UpdateRequest request = UpdateFactory.create(query);
18:50:51 <luke> UpdateAction.execute(request, model);
18:52:01 <mary> thansk for SPARQL editor
18:54:05 <dbooth> Topic: SPARQL Editor: SparqlEd, From Sindice
18:54:15 <dbooth> Interactive SPARQL editor SparqlEd from Sindice: http://www.sindicetech.com/blog/?p=14&preview=true
18:59:17 <ericP> RRSAgent, please draft minutes
18:59:17 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/30-hack-minutes.html ericP
18:59:25 <ericP> RRSAgent, please make log world-visible
18:59:49 <ericP> Zakim, unmute bob_powers
18:59:49 <Zakim> Bob_Powers should no longer be muted
19:02:14 <Lena> Lena has left #hack
19:02:54 <dbooth> http://hcls.sindicetech.com/sparql-editor/
19:03:08 <luke> complete, working Jena update example: http://pastebin.com/faWHGfY2
19:31:11 <StuartTurner> StuartTurner has joined #hack
19:33:21 <amy> amy has joined #hack
19:35:31 <Justin> THANKS TO ERIC, LENA and all other organizers and contributors for a really terrific session!!  Ciao. Justin
20:06:15 <amy_> amy_ has joined #hack
20:27:00 <Zakim> -MITKiva
20:27:09 <Zakim> -Bob_Powers
20:27:10 <Zakim> SW_HCLS(HACK)9:00AM has ended
20:27:10 <Zakim> Attendees were Bob_Powers, MITKiva
20:44:56 <luke> luke has joined #hack
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21:05:14 <Zakim> Zakim has left #hack
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21:34:17 <dbooth> rrsagent, draft minutes
21:34:17 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/30-hack-minutes.html dbooth
21:35:41 <dbooth> i/Using Jena/scribenick: dbooth
21:36:34 <dbooth> YES, THANK YOU ERIC AND HELENA FOR A FANTASTIC HACKATHON!
21:37:25 <dbooth> AND THANK YOU ENTAGEN, W3C and DERI FOR SPONSORING IT!
21:37:44 <dbooth> ADJOURNED
21:38:02 <dbooth> rrsagent, draft minutes
21:38:02 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/30-hack-minutes.html dbooth
22:34:53 <StuartTurner> StuartTurner has joined #hack
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