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12:36:22 <RRSAgent> logging to http://www.w3.org/2012/08/28-hack-irc
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12:50:22 <Zakim> SW_HCLS(HACK)9:00AM has now started
12:50:29 <Zakim> +[MIT-G449]
12:51:39 <Zakim> +EricP
12:52:02 <ericP> Zakim, unmute [MIT-G449]
12:52:02 <Zakim> [MIT-G449] should no longer be muted
12:52:17 <ericP> Zakim, unmute ericP 
12:52:17 <Zakim> EricP should no longer be muted
12:52:25 <ericP> Zakim, mute ericP 
12:52:25 <Zakim> EricP should now be muted
12:52:51 <Zakim> -EricP
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13:00:28 <Zakim> + +1.301.906.aaaa
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13:10:03 <Zakim> + +1.781.454.aabb
13:10:46 <Zakim> - +1.781.454.aabb
13:13:07 <dbooth> zakim, who is here?
13:13:07 <Zakim> On the phone I see [MIT-G449], +1.301.906.aaaa (muted)
13:13:08 <Zakim> On IRC I see dbooth, frago, daniela, Lena, RRSAgent, Zakim, amy_, ericP
13:13:56 <apo> apo has joined #hack
13:13:58 <dbooth> Topic: Day 2, introductions
13:14:13 <Frans> Frans has joined #hack
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13:15:07 <dbooth> Curran: PhD student Lowell, working on Data Cubes.
13:15:25 <dbooth> TedSlater: Consulting at Selventa, working on OpenBEL.
13:15:32 <luke> luke has joined #hack
13:15:56 <dbooth> OliverRuebenacker: Working at PanGenX, also working on turning biological odels into math models
13:16:40 <dbooth> Mamatau: From Quebec, was CS prof w int in SW.  Int in health care apps, editing a book and looking for people int in joining in.
13:17:18 <dbooth> SophiiaCheng: Working on Eagle-I team.
13:17:25 <dbooth> s/ii/i/
13:17:36 <dbooth> Eric: We
13:17:42 <Zakim> + +1.781.454.aacc
13:18:01 <dbooth> Eric: We'll do lightning talks, if anyone wants to do one.
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13:18:56 <dbooth> Topic: Tool for integrating data, Helena Deus
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13:19:16 <Zakim> - +1.781.454.aacc
13:19:17 <Frans> scribenick: Frans
13:19:29 <Zakim> + +1.781.454.aadd
13:20:48 <dbooth> s/Tool/SWObjects, a tool/
13:21:28 <Frans> tools for converting data to RDF:  google refine
13:22:05 <Frans> code.google.com/p/google-refine/
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13:22:33 <ericP> -> http://code.google.com/p/google-refine/wiki/Downloads Google Refine download
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13:23:13 <Frans> question: google refine is a web application? privacy concerns?
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13:23:32 <ericP> s/question: google/mark: google/
13:23:38 <Frans> answer: no, can be run locally or on server. 
13:23:59 <ericP> s/answer: no,/lena: no/
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13:27:23 <Frans> lena:  google refine needs RDF extension.  available at refine.deri.ie.
13:27:35 <ericP> -> http://refine.deri.ie/ google refine RDF extension
13:27:41 <frago> frago has joined #hack
13:28:34 <Justin> Justin has joined #hack
13:28:46 <Frans> … downloaded folder should be dropped into "extensions" dir of google refine.
13:29:36 <Frans> … restart refine service
13:29:44 <Justin> Justin has joined #hack
13:31:30 <dbooth> Installation docs: http://refine.deri.ie/installationDocs
13:32:53 <ericP> unpack http://refine.deri.ie/download-latest in google-refine-2.5/webapp/extensions
13:33:00 <Zakim> - +1.781.454.aadd
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13:33:29 <ericP> a la unzip -q ~/Downloads/grefine-rdf-extension-0.8.0.zip
13:34:28 <ericP> then:
13:34:30 <ericP>   cd ../..
13:34:35 <ericP>   bash refine
13:34:59 <dbooth> actually: bash ./refine
13:35:30 <ericP> then browse http://127.0.0.1:3333/
13:35:52 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/28-hack-minutes.html ericP
13:36:25 <dbooth> rrsagent, make logs public
13:37:25 <Lena> example file: https://dl.dropbox.com/u/61307320/example.xlsx
13:41:04 <Frans> lena: sindice (sindice.com) is a semantic web crawler
13:41:32 <Frans> … indexes everything it crawls.  does both explicit and inferred triples.
13:42:48 <Frans> … used by google refine extension for reconciliation of imported data.
13:43:34 <ericP> -> http://sindice.com/ sindice server
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13:49:07 <ericP> -> https://dl.dropbox.com/u/61307320/example.xlsx drop box example
13:50:03 <ericP> Addresses::Facet::Text Facet
13:53:24 <dbooth> From google refine, in upper right: RDF-->Edit RDF Skeleton
13:53:51 <dbooth> Then edit Base URI
13:54:10 <dbooth> ... to be whatever URI you want for your prefix/base
13:54:25 <dbooth> ... e.g. http://example/
13:54:33 <ericP> yup, lena used http://example.com/
13:55:26 <dbooth> Then click "(row index)" to tell it how to generate a URI from the ID column
13:55:33 <dbooth> ... Select "ID"
13:55:55 <dbooth> ... use the default "as a URI"
13:58:02 <ericP> OK to leave RDF Node dialog
13:59:11 <ericP> delete all of the properties except the one with "Names cell" at the right
13:59:45 <ericP> click on "property"
14:00:07 <ericP> you will see "search for property". enter "name"
14:00:27 <Frans> lena:  google refine is connected to prefix.cc from which it derives prefixes, predicates
14:00:48 <Frans> … allows for voting on newly submitted prefixes
14:03:22 <ericP> after a second, you will see "rdfs:label"
14:04:07 <ericP> (of course, we'd have liked to see "foaf:name", but time will apparently fix that.)
14:04:31 <RRSAgent> I have made the request to generate http://www.w3.org/2012/08/28-hack-minutes.html ericP
14:04:50 <ericP> ericP has changed the topic to: http://www.w3.org/2012/08/28-hack-minutes
14:06:14 <Frans> lena: you can create your own identifiers, don't have to use the suggestions of Refine.
14:06:26 <Frans> … "somelabel: "
14:08:17 <dbooth> Lena: After you've defined your first property, you can clice the "RDF Preview" tab to see the RDF you'll get.
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14:21:22 <ericP> OK to leave the RDF template
14:22:23 <ericP> click on the Age menu, Edit Cells::Common Transforms::To Text
14:23:01 <ericP> this gives you e.g. an Age of 23.0
14:23:16 <dbooth> (which is NOT an xsd:int)
14:23:57 <ericP> now in the Age menu, Edit Cells::Transform
14:25:13 <ericP> change the input box from 'value' to 'value.split(".")[0]'
14:27:34 <ericP> back to RDF (upper right) ::Edit RDF Skeleton
14:27:46 <ericP> add property (should be blue)
14:28:16 <ericP> you will see a new arrow with the text "property" -> "Configure?"
14:28:39 <ericP> click "property" and enter "foaf:age"
14:28:56 <ericP> then click "Configure?" and select "Age"
14:29:20 <ericP> the RDF preview should now give yield:
14:29:30 <ericP> <http://127.0.0.1:3333/1.0> rdfs:label "John" ; foaf:age "23" .
14:29:30 <ericP> ...
14:30:31 <dbooth> And it would be good to do the same thing for the ID column, so that it comes out as an integer like http://example.com/
14:31:04 <dbooth> s|com/|com/3|
14:31:05 <Frans> Lena: to get RDF do Export drop-down as choose Turtle.
14:31:36 <Frans> s/as choose/and choose/
14:31:43 <ericP> now click "Add type" (under the ID on the left)
14:32:03 <ericP> enter foaf:Person
14:32:31 <ericP> RDF Preview should now reflect the new types
14:32:51 <ericP> "OK" to leave the RDF Pain pane
14:34:36 <ericP> in the upper right of the regular Google Refine pane, click Export::RDF as Turtle
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14:42:49 <dbooth> Eric: I forgot to set the datatype for the Age (foaf:age).  I should have set it to xsd:int or xsd:integer.  xsd:integer is arbitrary length, whereas xsd:int is 4 bytes.
14:43:41 <dbooth> Lee: the default type in Turtle for a bare number (with no decimal point) is xsd:integer, so that should be used.
14:44:01 <Frans> eric:  exported file should be in Downloads folder - "example-xlsx.ttl"
14:45:51 <Frans> eric: after break we will be using SWObjects tool to analyze exported file.
14:46:10 <Frans> -> http://sourceforge.net/apps/mediawiki/swobjects/index.php?title=Main_Page  SWObjects
14:47:27 <Justin> zakim, who is here?
14:47:27 <Zakim> On the phone I see [MIT-G449], +1.301.906.aaaa (muted)
14:47:28 <Zakim> On IRC I see Justin, mattmac, peter, LeeF, skc, ted_, StuartTurner, julianeschneider, luke, graham, Frans, apo, dbooth, daniela, Lena, RRSAgent, Zakim, amy_, ericP
14:48:11 <dbooth> http://128.30.7.30:8088/
14:48:21 <dbooth> that's eric's server
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14:49:49 <ericP> -> http://sourceforge.net/projects/swobjects/files/ SWObjects download
14:49:57 <dbooth> Topic: SWObjects
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14:52:31 <Lena_> https://docs.google.com/document/d/170GFtfwcuXt5vvhzvZLyCJChMnDeWJbrLd4_7LuUQGQ/edit#
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14:53:22 <Lena_> https://docs.google.com/document/d/170GFtfwcuXt5vvhzvZLyCJChMnDeWJbrLd4_7LuUQGQ/edit#
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14:57:58 <Lena_> also: tinyurl.com/swobjects
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15:02:25 <Lena_> alias sparql=/Applications/Sparql.app/Contents/MacOS/Sparql 
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15:22:40 <LeeF> [11:16] <LeeF> c:\Program Files (x86)\W3C\SPARQL\
15:22:42 <LeeF> [11:16] <LeeF> then run SPARQL.exe --version
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15:38:20 <Lena_> https://dl.dropbox.com/u/61307320/gorydetails.map.txt
15:39:36 <Justin> Getting Parse Error -- ":1.1: syntax error, unexpected end of file, expecting IT_DELETE or IT_INSERT"  --??????
15:39:37 <Justin> ---- Q&D SPARQL Server Parsing Error
15:39:45 <Justin> OK, fixed, thanks to Bob -- problem was directing to "... localhost:8080/SPARQL, instead of simply browsing to "... localhost/8080"
15:40:27 <dbooth> http://tinyurl.com/swobjects
15:46:51 <StuartTurner> Getting same error as Justin
15:47:00 <StuartTurner> Ah, thanks
15:50:04 <peter_> try the following 3 variations of SELECT * and note which fields (columns) are displayed:
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15:51:14 <peter_> SELECT * WHERE {   ?geneA a <http://purl.org/net/biordfmicroarray/ns#gene> ;       <http://purl.org/net/biordfmicroarray/ns#probe_set_id> ?probeId BIND(IRI(concat("http://bio2rdf.org/affymetrix:", ?probeId)) as ?probe_URI)    SERVICE <http://affymetrix.hcls.deri.org/sparql> {     ?probe_URI  <http://bio2rdf.org/ns/affymetrix#xGene_Ontology_Biological_Process> ?go .    }  SERVICE <http://go.bio2rdf.org/sparql> {    ?go <http://www.w3.org/2000/01/rdf-schema#label>
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15:52:06 <peter_> vs  SELECT * WHERE {   ?geneA a <http://purl.org/net/biordfmicroarray/ns#gene> ;       <http://purl.org/net/biordfmicroarray/ns#probe_set_id> ?probeId BIND(IRI(concat("http://bio2rdf.org/affymetrix:", ?probeId)) as ?probe_URI)    SERVICE <http://affymetrix.hcls.deri.org/sparql> {     ?probe_URI  <http://bio2rdf.org/ns/affymetrix#xGene_Ontology_Biological_Process> ?go .    }  } 
15:53:26 <peter_> without the extra SERVICE with ?gofunction, fewer fields are displayed.  The additional fields are also displayed in the non-federated version of the query.
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16:35:01 <Lena_> scribenick:Lena_
16:35:14 <Lena_> scribenick: Lena_
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16:39:35 <dbooth> Topic: OpenBEL, Ted Slater
16:41:48 <dbooth> Ted: Selventa used to be called GenStruct
16:42:12 <dbooth> s/OpenBEL/OpenBEL and RDF
16:46:20 <bobP> 3 textminers for BEL
16:46:27 <bobP> 1) Linguamatics
16:46:39 <bobP> 2) Martin Wolfman(?) Bonn
16:46:50 <bobP> 3) Larry Hunter, U. of Colorado
16:48:09 <ericP> Frans: what's your assessment of text processing accuracy?
16:48:23 <bobP> probability correct used to be 60%; now higher
16:48:41 <bobP> Linguamatics is now getting north of 80%
16:48:48 <ericP> ted: we tested linguamatics and @@3 against a gold standard
16:50:09 <ericP> @@4: is there a gold standard available?