14:58:52 <RRSAgent> RRSAgent has joined #hcls
14:58:52 <RRSAgent> logging to http://www.w3.org/2010/07/19-hcls-irc
14:59:12 <jun> zakim, this will be biordf
14:59:12 <Zakim> ok, jun; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 1 minute
14:59:28 <jun> zakim, space for 10
14:59:28 <Zakim> I don't understand 'space for 10', jun
15:00:45 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
15:00:52 <Zakim> +??P3
15:01:07 <jun> zakim, ??P3 is jun
15:01:07 <Zakim> +jun; got it
15:01:33 <Zakim> +[IPcaller]
15:01:47 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
15:01:47 <Zakim> +matthias_samwald; got it
15:02:53 <mscottm> mscottm has joined #hcls
15:02:56 <jun> zakim, mute me
15:02:56 <Zakim> jun should now be muted
15:03:05 <jun> zakim, unmute
15:03:05 <Zakim> I don't understand 'unmute', jun
15:03:10 <jun> zakim, unmute me
15:03:10 <Zakim> jun should no longer be muted
15:03:32 <Zakim> + +1.832.386.aaaa
15:04:01 <Zakim> +Daniel_Rubin
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15:05:00 <mscottm> Zakim, who is here?
15:05:00 <Zakim> On the phone I see jun, matthias_samwald, +1.832.386.aaaa, Daniel_Rubin
15:05:02 <Zakim> On IRC I see LenaDeus, mscottm, RRSAgent, matthias_samwald, Zakim, jun, egonw, ericP
15:06:00 <mscottm> Zakim, Daniel_Rubin is mscottm
15:06:00 <Zakim> +mscottm; got it
15:06:08 <Zakim> + +44.122.383.aabb
15:07:14 <mscottm> Zakim, +44.122.383.aabb is James_Malone
15:07:14 <Zakim> +James_Malone; got it
15:07:26 <mscottm> Zakim, +44.122.383.aabb is James_Malone
15:07:26 <Zakim> sorry, mscottm, I do not recognize a party named '+44.122.383.aabb'
15:07:34 <jun> scribenick mscottm
15:07:34 <mscottm> Zakim, who is here?
15:07:34 <Zakim> On the phone I see jun, matthias_samwald, +1.832.386.aaaa, mscottm, James_Malone
15:07:36 <Zakim> On IRC I see LenaDeus, mscottm, RRSAgent, matthias_samwald, Zakim, jun, egonw, ericP
15:07:51 <mscottm> Zakim, +1.832.386.aaaa is LenaDeus
15:07:51 <Zakim> +LenaDeus; got it
15:07:56 <jun> zakim, scribenick mscottm
15:07:56 <Zakim> I don't understand 'scribenick mscottm', jun
15:08:37 <mscottm> scribenick mscottm
15:11:00 <mscottm> James: Haven't been able to get sample RDF for you yet
15:11:33 <mscottm> ..We have created Experimental Factor Ontology (EFO) as a bridging ontology
15:11:38 <jun> Topic: James introduce EFO
15:12:39 <mscottm> ..You can see an example of an application of EFO in the Gene Atlas that lets you look for microarray studies with certain specific attributes
15:13:03 <mscottm> ..pulling out genes as they relate to disease and experiments using EFO
15:13:17 <mscottm> ..So, EFO is a subset of the sort of data that we have in Gene Atlas
15:13:46 <mscottm> ..Not sure if we how soon we will create a SPARQL endpoint. We will begin with export of RDF.
15:14:16 <mscottm> ..We have a position open at the moment for student internship with funding.
15:15:10 <mscottm> ..Some attributes of interest are disease, genes, cell types, cell lines, compounds, acids, instrumentation, software
15:16:29 <mscottm> Jun: We are also trying to model disease, brain region, etc. Would be interesting to link to other related data sets through extra attributes.
15:17:00 <mscottm> ..I don't see specific statistical values modeled yet in EFO.
15:17:44 <mscottm> James: We don't have statistics in EFO yet. We could do that if you have a small list of things to add.
15:18:25 <mscottm> Lena: Yes, I would like to refer to statistics as provenance.
15:18:43 <mscottm> James: What sort of values would you like to use?
15:18:56 <mscottm> Lena: fold change and corrected p-value
15:19:37 <mscottm> James: Yes, these are some of the sorts of classes that OBI is meant to cover. We could add these.
15:20:46 <jun> scott: it's quite important to express the method or the software used to derive the p-value
15:20:59 <mscottm> Scott: Would like to refer to the method/software that was used to arrive at the p-values
15:23:09 <mscottm> Lena: But studies sometimes use more than one method.
15:23:28 <mscottm> Scott: Most don't, and this level of detail is not required.
15:26:08 <mscottm> Lena: But software packages change so any reference to the software will be stale over the years.
15:28:17 <mscottm> Scott: Many types of provenance will go stale but essential information about the origins of the information (provenance), such as the method used to produce the p-values, is important to anyone reusing the data. They want to know whether it's from LIMMA or MANOVA, just as they want to know Affy vs. other types of arrays.
15:29:07 <mscottm> Jun: RESTful API? 
15:29:34 <mscottm> James: Yes, RESTful API's are available.
15:29:38 <jun> Jun: how to access ArrayExpress programmatically?
15:29:52 <jun> James: through Restful APIs, but no SPARQL endpoint yet
15:30:34 <jun> James: There are some provenance kind of information, tracking e.g. probes used in the experiments, publications, etc, but not expressed using ontologies
15:30:58 <mscottm> Scott: Do you notice any differences between our RDF and others that you are aware of?
15:30:59 <jun> James: we say a lot less about the statistical information about the experiments, about the data
15:31:23 <jun> James: sometimes not all the information is submitted, because it's not required as part of the minimum information
15:31:41 <jun> James: we think species, diseases, regions, etc, as high priority
15:33:55 <jun> James: we are not curating the same level of details as the BioRDF use case
15:36:18 <jun> Scott: where do you see as the bottleneck as using RDF to express the information (general speaking)?
15:38:19 <jun> James: EFO takes bits and pieces from the community that are useful for our cases. and it has been useful
15:40:51 <jun> Jun: have you had any difficulties of dealing with changes of ontologies
15:41:09 <jun> James: we have tools to help us deal with that; so it's not a big problem for us
15:43:10 <jun> Scott: in our application we are interested in linking to related data, for cases, such as translational medicine
15:43:26 <jun> James: we are on the same page for this. that's one of the primary reasons for us to convert datasets into RDF
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15:57:25 <Zakim> -James_Malone
15:57:27 <Zakim> -LenaDeus
15:57:31 <Zakim> -jun
15:57:34 <Zakim> -mscottm
15:57:57 <LenaDeus> (good job scribing, Scott, you may not need coffee after all ;) )
15:58:40 <mscottm> tx!
15:59:58 <jun> rrsagent, set log public
16:00:04 <jun> rrsagent, draft minutes
16:00:04 <RRSAgent> I have made the request to generate http://www.w3.org/2010/07/19-hcls-minutes.html jun
16:01:08 <jun> rrsagent, set log public
16:03:37 <jun> scribenick jun
16:03:43 <jun> rrsagent, draft minutes
16:03:43 <RRSAgent> I have made the request to generate http://www.w3.org/2010/07/19-hcls-minutes.html jun
16:03:49 <jun> rrsagent, set log public