14:50:41 <RRSAgent> RRSAgent has joined #hcls
14:50:41 <RRSAgent> logging to http://www.w3.org/2010/04/19-hcls-irc
14:51:27 <jun> zakim, list conferences
14:51:27 <Zakim> I see Team_SysWeb()10:00AM, SW_HCLS(Disc)10:00AM, WAI_PFWG(ARIA)10:00AM, VB_VBWG(ConvApps)10:00AM, GA_SVGWG()10:30AM active
14:51:30 <Zakim> also scheduled at this time are MM_MMI()11:00AM, T&S_Team()10:00AM, SW_HCLS(BioRDF)11:00AM, XML_SchemaW()10:00AM
14:51:56 <jun> what conference is this?
14:52:32 <jun> zakim, what conference is this?
14:52:32 <Zakim> no conference has been selected, jun
14:54:01 <jun> trackbot, prepare telcon
14:54:01 <trackbot> Sorry... I don't know anything about this channel
14:54:01 <trackbot> If you want to associate this channel with an existing Tracker, please say 'trackbot, associate this channel with #channel' (where #channel is the name of default channel for the group)
14:54:53 <jun> zakim, this is SW_HCLS(Disc)
14:54:53 <Zakim> ok, jun; that matches SW_HCLS(Disc)10:00AM
14:55:03 <jun> zakim, what conference is this?
14:55:03 <Zakim> this is SW_HCLS(Disc)10:00AM conference code 42572
14:55:09 <Donald_Doherty> Donald_Doherty has joined #HCLS
14:55:12 <jun> trackbot, prepare telcon
14:55:12 <trackbot> Sorry... I don't know anything about this channel
14:55:12 <trackbot> If you want to associate this channel with an existing Tracker, please say 'trackbot, associate this channel with #channel' (where #channel is the name of default channel for the group)
14:56:47 <jun> Zakim, space for 5?
14:56:50 <Zakim> sorry, jun; could not schedule an adhoc conference; passcode overlap; if you do not have a fixed code you may try again
14:58:37 <jun> zakim, who is here?
14:58:37 <Zakim> On the phone I see +03120485aaaa, ??P15, Tim, [IPcaller], Joanne_Luciano, +03539149aacc, [IPcaller.a], +1.212.186.aadd, +1.856.528.aaee
14:58:39 <Zakim> On IRC I see Donald_Doherty, RRSAgent, Zakim, jun, jodi, AlexPassant, trackbot, ericP
14:58:41 <kei> kei has joined #HCLS
14:58:54 <jun> zakim, ??P15 is jun
14:58:54 <Zakim> +jun; got it
14:59:06 <LenaDeus> LenaDeus has joined #hcls
15:00:05 <mscottm> mscottm has joined #hcls
15:02:11 <kei> Zakim, this will be BioRDF
15:02:11 <Zakim> ok, kei, I see SW_HCLS(BioRDF)11:00AM already started
15:02:43 <mccuskej> mccuskej has joined #hcls
15:03:01 <mscottm> Zakim, who is here?
15:03:01 <Zakim> On the phone I see jun, +1.860.673.aabb, +1.832.386.aacc, mscottm
15:03:03 <Zakim> On IRC I see mccuskej, mscottm, LenaDeus, kei, Donald_Doherty, RRSAgent, Zakim, jun, jodi, AlexPassant, trackbot, ericP
15:03:07 <jun> http://prezi.com/pr7qkiw_5yk2/
15:03:12 <Zakim> +Kei_Cheung
15:03:42 <jodi> jodi has left #HCLS
15:04:01 <Zakim> +Don_Doherty
15:04:32 <LenaDeus> on the agenda: Jim McKuster talk 
15:04:47 <jun> scribenick, LenaDeus
15:05:04 <LenaDeus> Jim: programmer at Yale
15:05:17 <LenaDeus> Jim: rdfizing mage tab documents
15:05:17 <mscottm> s/McKuster/McCusker/
15:05:18 <jun> zakim, mute me
15:05:18 <Zakim> jun should now be muted
15:05:52 <Donald_Doherty> http://prezi.com/pr7qkiw_5yk2/rdf-izing-mage-tab-magetab2magerdf/
15:06:24 <jun> zakim, unmute me
15:06:24 <Zakim> jun should no longer be muted
15:06:37 <LenaDeus> mccuskej: tool is magetab2rdf
15:07:11 <LenaDeus> mccuskej: jim's piece is called magetab2magerdf
15:07:57 <Zakim> + +1.937.775.aadd
15:08:32 <mscottm> http://prezi.com/pr7qkiw_5yk2/
15:08:32 <ssahoo2> ssahoo2 has joined #HCLS
15:08:32 <LenaDeus> mccuskej: usage: downoad the script, provide url, run
15:09:02 <LenaDeus> mccuskej: Jena is used to handle the RDF
15:09:59 <LenaDeus> mccuskej: reusing most of the classes from mged ontology; introducing a few more classes
15:11:23 <Zakim> + +1.206.605.aaee
15:11:54 <mmiller> mmiller has joined #hcls
15:11:58 <LenaDeus> re-used: person; protocol package; biomaterial package
15:14:14 <LenaDeus> mccuskej: biospeciment characteristics - describes diagnosis, age, etc
15:14:46 <LenaDeus> mccuskej: tried to reconstruct the uri of biospeciment characteristic
15:20:45 <LenaDeus> mmiller: arrayexpress can be usde
15:20:48 <LenaDeus> mmiller: arrayexpress can be used
15:21:16 <LenaDeus> mmiller: cannot always rely on arrayexpress (institution may not be submitting to arrayexpress)
15:21:22 <LenaDeus> mccuskej: cannot always rely on arrayexpress (institution may not be submitting to arrayexpress)
15:21:36 <LenaDeus> mccuskej: how best to create the uri?
15:22:25 <LenaDeus> mccuskej: no specific field saying that this is an arrayexpress experiment
15:23:17 <LenaDeus> mccuskej: need an easy to read arrayexpress
15:24:35 <LenaDeus> jun: any plans to publish the rdf graph on the web?
15:24:47 <LenaDeus> mccuskej: yes, that is the goal of using accession numbers in URI
15:25:01 <LenaDeus> mccuskej: autogenerated uri, if possible, to link between experiments~
15:26:22 <LenaDeus> mccuskej: accession nr can be used to create a uri (by inverseFunctionalProperty)
15:27:30 <LenaDeus> kei: depending on the context, treat the accession nr as URI or literal value
15:27:49 <LenaDeus> ssahoo2: does it conform to mged schema?
15:27:56 <LenaDeus> mccuskej: where it can, it does
15:31:31 <LenaDeus> mmiller: magetab started informally; internally accession nr could be transformed into key; therefore in some cases accession nrs are literals, today, if submitted to arrayexpress, they are already converted to URI
15:32:03 <LenaDeus> ssahoo2: some accession nrs are not resolvable today, they can be treated differentelly at the schema level
15:33:01 <LenaDeus> ssahoo2: the current state can be reflected in terms of solvable or non-solvable accession nrs, it does not affect the quality of the RDF
15:33:52 <LenaDeus> mccuskej: if there is a deferencenceable uri for a protocol, that is the one used;
15:34:38 <LenaDeus> mmiller: for example, investigationTitle is often the array accession, but programatically there is no way to know that
15:36:15 <LenaDeus> mccuskej: SDRF portion
15:36:36 <LenaDeus> biosource
15:38:43 <LenaDeus> mccuskej: disease state as a type of tumor cell line
15:39:58 <LenaDeus> kei: the disease state can be revisited for the microarray use case
15:40:25 <LenaDeus> mmiller: along with the data, this is the most important part of sdrf
15:44:54 <LenaDeus> mccuskej: last slide: hybridization, set of experimental values;
15:47:30 <LenaDeus> mccuskej: factor values are used in the same way as parameters
15:48:59 <Zakim> - +1.832.386.aacc
15:49:14 <mscottm> Thanks Jim!
15:50:17 <Zakim> + +1.832.386.aaff
15:51:28 <jun> Kei: the future with MAGE and OBI
15:51:37 <jun> Jim: I would prefer to use OBI
15:52:36 <LenaDeus> LenaDeus has joined #hcls
15:53:41 <LenaDeus> jun: satya to give update on the microarray use case
15:54:39 <LenaDeus> ssahoo2: created schema with set of concepts; created a placeholder schema that jun is using to generate proper RDF
15:56:18 <LenaDeus> Affy ID for gene1 in genelist2: http://bio2rdf.org/page/affymetrix:1556743_at
16:01:11 <mscottm> http://SharedName.org is about to provide URI's to ncbi genes.
16:04:09 <Zakim> - +1.937.775.aadd
16:04:20 <Zakim> - +1.206.605.aaee
16:04:30 <Zakim> - +1.860.673.aabb
16:04:31 <Zakim> - +1.832.386.aaff
16:04:34 <Zakim> -Don_Doherty
16:04:35 <Zakim> -mscottm
16:04:40 <Zakim> -Kei_Cheung
16:04:43 <Zakim> -jun
16:04:44 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:04:45 <mccuskej> At Yale I am using the bio2rdf gene and trancript URIs.
16:04:45 <Zakim> Attendees were jun, +1.832.386.aaaa, +1.860.673.aabb, +1.832.386.aacc, mscottm, Kei_Cheung, Don_Doherty, +1.937.775.aadd, +1.206.605.aaee, +1.832.386.aaff
16:04:50 <jun> rrsagent, set log public
16:04:51 <mccuskej> mccuskej has left #hcls
16:05:04 <jun> rrsagent, draft minutes
16:05:04 <RRSAgent> I have made the request to generate http://www.w3.org/2010/04/19-hcls-minutes.html jun
16:05:44 <jun> trackbot, end telcon
16:06:29 <jun> zakim, excuse us
16:06:29 <Zakim> Zakim has left #hcls
16:10:30 <mscottm>   RRSAgent, please make log world-visible
16:33:51 <mscottm> http://www.franz.com/agraph/services/conferences_seminars/
16:33:51 <mscottm> semantic_technologies_v21.lhtml
17:48:58 <egonw> egonw has joined #hcls