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15:02:21 <mscottm2> Zakim, who is here?
15:02:21 <Zakim> sorry, mscottm2, I don't know what conference this is
15:02:22 <Zakim> On IRC I see RRSAgent, Zakim, mscottm2, egombocz, pekkoh, jasone, MacTed, ericP
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15:03:22 <mscottm2> Zakim, this is hcls
15:03:22 <Zakim> ok, mscottm2; that matches SW_HCLS(BioRDF)11:00AM
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15:08:24 <Zakim> + +1.781.431.aadd
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15:17:54 <mscottm2> scribenick: mscottm2
15:18:48 <mscottm2> Jason: I simply wanted to read in a MAGE-ML file and create an RDF representation that is true to the MAGE-ML.
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15:19:25 <JimMcCusker> Hi all
15:19:53 <JimMcCusker> Zakim, I'm 860-995-0490
15:19:53 <Zakim> I don't understand 'I'm 860-995-0490', JimMcCusker
15:20:09 <JimMcCusker> Zakim, who is online?
15:20:09 <Zakim> I don't understand your question, JimMcCusker.
15:20:41 <mscottm2> ..There were useful documents hosted by ArrayExpress describing the MAGE model. I have a copy that can be served from a local tomcat if you are interested.
15:21:09 <mscottm2> I wanted RDF that I could browse in IO's Knowledge Explorer ASAP in order to explore the model.
15:23:54 <mscottm2> ..It doesn't read in CEL files or other data files yet.
15:24:22 <mscottm2> Jim: Jason - Have you tried running this against a non-MAGE-ML source like GEO?
15:24:33 <mscottm2> Jason: Yes, with varying results.
15:26:10 <Zakim> -[IPcaller.a]
15:26:22 <mscottm2> Scott: (to Jason) Can you host the code at github or similar so that we have a URL to point IG note readers to?
15:26:33 <mscottm2> Jason: Yes, but I can't update the code for a few months.
15:26:45 <Zakim> -EricP
15:27:11 <mscottm2> Michael: There are places to enter metadata at GEO but it usually isn't done so it is effectively unavailable.
15:28:24 <mscottm2> ..Imperial College has some nice multi-factor experiment sets. Interesting graph. I'll see if I can dig it up.
15:29:15 <michael> the accession is e-mimr-12
15:29:57 <mscottm2> Jim: You are using your own namespaces as well as MAGE-OM?
15:30:24 <mscottm2> Jason: Yes, still writing own namespaces into the RDF.
15:33:40 <mscottm2> Scott: (to Jim) Is a possible combination of Jason and your code: Use Jason's to traverse the MAGE-OM model for some of the decisions in MAGETAB2RDF
15:33:54 <mscottm2> Jim: yes.
15:34:55 <mscottm2> Jim: I used Limpopo to read in MAGETAB.
15:35:53 <mscottm2> Michael: MAGE-ML has more historical use. You can find some old code that I wrote for Resolver that reads it but most use MAGETAB.
15:36:56 <Zakim> - +1.781.431.aadd
15:37:22 <michael> use of MAGE-ML is pretty much deprecated for MAGE-TAB
15:37:30 <mscottm2> Limpopo MAGE-TAB Parser - http://limpopo.sourceforge.net/extensions.html
15:38:13 <mscottm2> Michael: Which class does the translation to the triples?
15:38:32 <Zakim> +EricP
15:38:38 <mscottm2> Jason: That's done in rdflib. Looks like it's rdflib version 2.4.
15:39:17 <michel> q+
15:42:25 <mscottm2> .. document.py is the class that does the main RDF production work, using rdflib.
15:43:41 <JimMcCusker> http://code.google.com/p/surfrdf/
15:45:17 <Zakim> -EricP
15:45:19 <Zakim> +EricP
15:46:48 <mscottm2> Michael: factor , value - every one of your assays will be associated with a value from each of the factors
15:48:12 <mscottm2> ..Example: one bioassay will be at the 1 second time point with a 100 mg. dosage, can be joined with other bioassays based on the factor / value set.
15:50:27 <JimMcCusker> http://dl.dropbox.com/u/9752413/cshals-2012/combineResults.py
15:50:52 <JimMcCusker> http://dl.dropbox.com/u/9752413/cshals-2012/importArrayExpress.py
15:51:23 <JimMcCusker> http://code.google.com/p/magetab2rdf/wiki/Mappings
15:52:28 <mscottm2> Scott: Any plans to read CEL files into Knowledge Explorer and output analysis results in RDF?
15:52:53 <mscottm2> Jason: Yes, that was the original plan. We just have other priorities at the moment.
15:53:36 <mscottm2> Scott: Could you hand part of the process to an R script (bioconductor) for affy files (that is run on an R server / service)?
15:57:35 <jasone> Knime: http://www.knime.org/
15:59:41 <mscottm2> Jason: Could offer Knowledge Explorer services in Knime (Pipeline tool).
16:00:45 <mscottm2> Scott: <re-explains motivations for IG note, asks Jim about R scripts and demo apps> 
16:01:37 <mscottm2> Jim: Targetting GenePattern with output. Use RDF Data Cube vocabulary to express the output set.
16:01:41 <JimMcCusker> http://publishing-statistical-data.googlecode.com/svn/trunk/specs/src/main/html/cube.html
16:02:48 <mscottm2> ..Have refined MAGETAB converter. Used OBI and EFO. Now also uses PROV.
16:05:19 <mscottm2> Scott: We should align with ArrayExpress (James Malone et al).
16:06:42 <mscottm2> Jim: I'm happy to share my code with James Malone and others.
16:06:58 <JimMcCusker> http://dl.dropbox.com/u/9752413/PROV-Examples/E-MTAB-327.rdf.ttl
16:11:40 <mscottm2> Scott: So, how can this stuff be used by a bioinformaticist who knows nothing of RDF? (from an R script)
16:12:31 <JimMcCusker> https://github.com/jimmccusker/lobi
16:13:44 <Zakim> -EricP
16:13:47 <JimMcCusker> http://lodspeakr.org
16:15:47 <mscottm2> Jim: Project - Linked Open Biomedical Investigations has a java tool, extends a tool called LODspeaker that you point at a triplestore and it publishes it as linked data for you and UI's based on templates.
16:16:49 <michael> have to go, thanks much!
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16:18:47 <mscottm2> Jim: I know that there's a bridge from python into R, but is the reverse true?
16:18:52 <mscottm2> Jason: Yes, there is.
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16:21:33 <Zakim> -egombocz
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16:21:36 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:21:36 <Zakim> Attendees were egombocz, +1.510.705.aaaa, +1.860.995.aabb, +1.206.732.aacc, +1.781.431.aadd, [IPcaller], EricP
16:24:04 <mscottm2>   RRSAgent, please draft minutes
16:24:04 <RRSAgent> I have made the request to generate http://www.w3.org/2012/03/19-HCLS-minutes.html mscottm2
16:24:18 <mscottm2>   RRSAgent, please make log world-visible
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