17:12:46 <RRSAgent> RRSAgent has joined #hcls
17:12:46 <RRSAgent> logging to http://www.w3.org/2010/11/23-hcls-irc
17:12:48 <Zakim> + +1.832.386.aabb
17:12:53 <ssahoo2> Scott: Use of SWObjects by the HCLS BioRDF task force not clear to others
17:12:57 <ssahoo2> Scott: Use the Microarray RDF data as the use case for disseminating correct information about HCLS BioRDF
17:13:23 <ssahoo2> Lena: Tried to install SWObjects
17:13:27 <Lena> Lena has joined #hcls
17:14:19 <ssahoo2> Lena: Need a server to permanently host the dataset and SWObjects
17:15:05 <Zakim> - +1.832.386.aabb
17:15:06 <ssahoo2> Scott: Servers at W3C, Netherlands, or DERI are possible candidates
17:15:20 <ericP> Zakim, please dial plh-office
17:15:20 <Zakim> I am sorry, ericP; I do not know a number for plh-office
17:15:28 <ericP> Zakim, please dial philippe-office
17:15:28 <Zakim> I am sorry, ericP; I do not know a number for philippe-office
17:15:40 <ssahoo2> Matthias: The Microarray RDF dataset can be added to the HCLS knowledgebase
17:15:57 <Zakim> + +1.832.386.aacc
17:16:02 <Lena> Lena has joined #hcls
17:16:31 <Zakim> +Philippe
17:16:34 <ssahoo2> Scott: Possible to leave the data in current server for demonstration in Berlin?
17:19:48 <ssahoo2> Eric: Except for performance, accessing remote or local copy of the dataset will not be a problem
17:20:24 <mscottm> ACTION: Eric creates new windows build of SWObjects to let Lena try
17:21:18 <ssahoo2> Lena: GenomeBrowser has good visualization tool, that can be used for the Microarray RDF dataset
17:22:03 <ssahoo2> Scott: Earlier used a similar approach for chip-on-chip dataset
17:23:06 <ssahoo2> Scott: Additional information (e.g. Uniprot) can also be added to the Microarray RDF dataset
17:24:33 <ssahoo2> Scott: Will soon meet with James Mallone, Robert Stevens and others. Was Software ontology used for SWPM paper?
17:24:48 <ssahoo2> Lena: Software ontology terms were used
17:25:55 <ssahoo2> Lena: What are the solutions for resolving the issue of mismatched identifiers/terms of an entity?
17:27:18 <ssahoo2> Lena: Should we rely on URIs only or focus on technologies that can be used to reconcile heterogeneous identifiers
17:28:34 <ssahoo2> Scott: An intermediate solution is a good approach - will often need to map terms
17:29:04 <ssahoo2> Scott: NCBO funding has been renewed, so purl URI will persist
17:32:50 <ssahoo2> Scott: Spoke to Carole Goble about Open Pharmacological Space, which may be relevant 
17:34:45 <ssahoo2> Scott: Shared names is a viable alternative, suggested to Open Pharmacological Space
17:35:58 <ssahoo2> Scott: Generating the URI for the Microarray RDF dataset can be outlined as a multi-step process
17:37:28 <ssahoo2> Scott: Concept Web ids are also a possible option
17:41:04 <ssahoo2> Scot: Can create an application to automatically re-use Concept Web ids, in case ontological ids are not available
17:42:36 <ssahoo2> Lena: We can start with using a specific URIs and creating mappings to other available URIs for given concept
17:44:23 <ssahoo2> Scott: We can also discuss with Translational Medicine Ontology to use an appropriate identifier 
17:45:03 <ssahoo2> Scott: Start with listing our options
17:46:33 <ssahoo2> Lena: It would be useful to have a centralized resource to identify all available URIs for an entity
17:46:51 <matthias_samwald> http://sameas.org/
17:46:55 <ssahoo2> Matthias: These services are already available
17:49:41 <ssahoo2> Lena: Is there a programmatic access available for Shared Names?
17:50:40 <egonw> egonw has joined #HCLS
17:51:18 <ssahoo2> Scott: An application can be build on top of Shared names infrastructure for URI resolution
17:52:10 <ssahoo2> Matthias: Will the work on Shared names be continued?
17:52:33 <ssahoo2> Scott: Yes
17:53:10 <Zakim> -Philippe
17:53:45 <ericP> Zakim, please dial ericP-office
17:53:45 <Zakim> ok, ericP; the call is being made
17:53:47 <Zakim> +EricP
17:54:13 <mscottm> ACTION: Matthias adds microarray RDF to HCLS KB
17:54:18 <ssahoo2> Scott: When can the dataset be loaded into the HCLS knowledgebase at DERI
17:54:29 <Zakim> -EricP
17:54:34 <ssahoo2> Matthias: Will be completed by next week
17:54:56 <ericP> sorry, lost one phone. will join in a few if you guys linger a bit
17:55:39 <ssahoo2> Scott: With respect to provenance, will use a URI for a named graph
17:59:34 <ssahoo2> Scott: If URIs are used for identifying named graphs, we can use RDFS labels for user readability
18:05:13 <ssahoo2> Scott: Next week, a presentation discussing how to derive triples from text and provenance aspect
18:07:06 <ericP> Zakim, please dial ericP-office
18:07:06 <Zakim> ok, ericP; the call is being made
18:07:07 <Zakim> +EricP
18:15:55 <Lena> i have to go, bye all and thanks
18:16:18 <ssahoo2> I also have to leave now
18:16:52 <Zakim> -ssahoo2
18:17:53 <mscottm> oh no!
18:21:23 <mscottm> http://genome.csdb.cn/cgi-bin/hgTables?db=rn4&hgta_group=genes&hgta_track=knownGene&hgta_table=knownGene&hgta_doSchema=describe+table+schema
18:24:14 <mscottm> http://genomewiki.ucsc.edu/index.php/UCSC_Genes_Staging_Process
18:24:16 <Lena> Lena has joined #hcls
18:24:26 <Lena> genome@soe.ucsc.edu
18:27:21 <mscottm> UniProt Database (e.g. sp080707)
18:27:50 <mscottm> http://genomewiki.ucsc.edu/index.php/UCSC_Genes_Staging_Process#Details_About_UniProt_and_Proteome_Databases
18:31:19 <ericP> hi, this is what we're up to
18:31:34 <Lena> Lena has joined #hcls
18:31:38 <ericP> we'd like advice on two db's that have data we could link
18:31:50 <matthias_samwald> have to leave now too, bye!
18:31:56 <Zakim> -[IPcaller]
18:32:01 <matthias_samwald> matthias_samwald has left #hcls
18:32:40 <ericP> we invite you to join us at 9am PST, 12EST, 18CST on #hcls2
18:33:00 <Zakim> - +1.832.386.aacc
18:41:22 <mscottm> http://www.integrativebioinformatics.nl/histone/HistoneDataIntegration.html
18:48:36 <ericP> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
18:56:25 <ericP> select * from encodeSangerChipH3K4me3 limit 3;
18:58:50 <mscottm> select * from tfbsConsSites limit 3;
19:01:57 <mscottm> (tStart1 <= tEnd2 AND tEnd1 >= tStart2)
19:03:00 <mscottm> WHERE chrom1 = chrom2 AND 
19:04:45 <ericP> select * from encodeSangerChipH3K4me3 AS encode, tfbsConsSites AS trans WHERE encode.chrom="chr22" AND trans.chrom="chr22" AND encode.chromStart>=trans.chromStart && encode.chromEnd<=trans.chromEnd limit 3;
19:07:24 <ericP> select chrom,count(*) from encodeSangerChipH3K4me3 group by chrom
19:09:18 <ericP> use uniProt
19:09:26 <ericP> select chrom,count(*) from TFBSConsSites.tfbsConsSites group by chrom;
19:09:37 <ericP> ERROR 1142 (42000): SELECT command denied to user 'genome'@'31-35-62.wireless.csail.mit.edu' for table 'tfbsConsSites'
19:15:47 <ericP> SELECT * FROM toto.x AS t INNER JOIN toy.IOUs AS o ON t.name=o.fname;
19:20:14 <Zakim> -mscottm
19:21:05 <Zakim> -EricP
19:21:06 <Zakim> Team_(hcls)17:01Z has ended
19:21:08 <Zakim> Attendees were mscottm, ssahoo2, +1.832.386.aaaa, [IPcaller], +1.832.386.aabb, +1.832.386.aacc, Philippe, EricP
20:30:36 <Zakim> Zakim has left #hcls
22:00:43 <mscottm> mscottm has joined #hcls
23:32:08 <mscottm>   RRSAgent, please draft minutes
23:32:08 <RRSAgent> I have made the request to generate http://www.w3.org/2010/11/23-hcls-minutes.html mscottm
23:32:15 <mscottm>   RRSAgent, please make log world-visible