Scott: Use of SWObjects by the HCLS BioRDF task force not clear to others
... Use the Microarray RDF data as the use case for disseminating correct information about HCLS BioRDF

Lena: Tried to install SWObjects
... Need a server to permanently host the dataset and SWObjects

Scott: Servers at W3C, Netherlands, or DERI are possible candidates

Matthias: The Microarray RDF dataset can be added to the HCLS knowledgebase

Scott: Possible to leave the data in current server for demonstration in Berlin?

Eric: Except for performance, accessing remote or local copy of the dataset will not be a problem

<mscottm> ACTION: Eric creates new windows build of SWObjects to let Lena try [recorded in http://www.w3.org/2010/11/23-hcls-minutes.html#action01]

Lena: GenomeBrowser has good visualization tool, that can be used for the Microarray RDF dataset

Scott: Earlier used a similar approach for chip-on-chip dataset
... Additional information (e.g. Uniprot) can also be added to the Microarray RDF dataset
... Will soon meet with James Mallone, Robert Stevens and others. Was Software ontology used for SWPM paper?

Lena: Software ontology terms were used
... What are the solutions for resolving the issue of mismatched identifiers/terms of an entity?
... Should we rely on URIs only or focus on technologies that can be used to reconcile heterogeneous identifiers

Scott: An intermediate solution is a good approach - will often need to map terms
... NCBO funding has been renewed, so purl URI will persist
... Spoke to Carole Goble about Open Pharmacological Space, which may be relevant
... Shared names is a viable alternative, suggested to Open Pharmacological Space
... Generating the URI for the Microarray RDF dataset can be outlined as a multi-step process
... Concept Web ids are also a possible option

Scot: Can create an application to automatically re-use Concept Web ids, in case ontological ids are not available

Lena: We can start with using a specific URIs and creating mappings to other available URIs for given concept

Scott: We can also discuss with Translational Medicine Ontology to use an appropriate identifier
... Start with listing our options

Lena: It would be useful to have a centralized resource to identify all available URIs for an entity

<matthias_samwald> http://sameas.org/

Matthias: These services are already available

Lena: Is there a programmatic access available for Shared Names?

Scott: An application can be build on top of Shared names infrastructure for URI resolution

Matthias: Will the work on Shared names be continued?

Scott: Yes

<mscottm> ACTION: Matthias adds microarray RDF to HCLS KB [recorded in http://www.w3.org/2010/11/23-hcls-minutes.html#action02]

Scott: When can the dataset be loaded into the HCLS knowledgebase at DERI

Matthias: Will be completed by next week

<ericP> sorry, lost one phone. will join in a few if you guys linger a bit

Scott: With respect to provenance, will use a URI for a named graph
... If URIs are used for identifying named graphs, we can use RDFS labels for user readability
... Next week, a presentation discussing how to derive triples from text and provenance aspect

<Lena> i have to go, bye all and thanks

I also have to leave now

<mscottm> oh no!

<mscottm> http://genome.csdb.cn/cgi-bin/hgTables?db=rn4&hgta_group=genes&hgta_track=knownGene&hgta_table=knownGene&hgta_doSchema=describe+table+schema

<mscottm> http://genomewiki.ucsc.edu/index.php/UCSC_Genes_Staging_Process

<Lena> genome@soe.ucsc.edu

<mscottm> UniProt Database (e.g. sp080707)

<mscottm> http://genomewiki.ucsc.edu/index.php/UCSC_Genes_Staging_Process#Details_About_UniProt_and_Proteome_Databases

<ericP> hi, this is what we're up to

<ericP> we'd like advice on two db's that have data we could link

<matthias_samwald> have to leave now too, bye!

<ericP> we invite you to join us at 9am PST, 12EST, 18CST on #hcls2

<mscottm> http://www.integrativebioinformatics.nl/histone/HistoneDataIntegration.html

<ericP> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A

<ericP> select * from encodeSangerChipH3K4me3 limit 3;

<mscottm> select * from tfbsConsSites limit 3;

<mscottm> (tStart1 <= tEnd2 AND tEnd1 >= tStart2)

<mscottm> WHERE chrom1 = chrom2 AND

<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;

<ericP> select chrom,count(*) from encodeSangerChipH3K4me3 group by chrom

<ericP> use uniProt

<ericP> select chrom,count(*) from TFBSConsSites.tfbsConsSites group by chrom;

<ericP> ERROR 1142 (42000): SELECT command denied to user 'genome'@'31-35-62.wireless.csail.mit.edu' for table 'tfbsConsSites'

<ericP> SELECT * FROM toto.x AS t INNER JOIN toy.IOUs AS o ON t.name=o.fname;

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Got date from IRC log name: 23 Nov 2010
Guessing minutes URL: http://www.w3.org/2010/11/23-hcls-minutes.html
People with action items: adds eric matthias microarray rdf

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