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14:57:21 <kei> Zakim, this will be BioRDF
14:57:21 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 3 minutes
14:57:57 <kei> agenda+ intro [kei]
14:58:15 <kei> agenda+ rat genome database [simon]
14:59:00 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
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14:59:30 <kei> agenda+ paper [all]
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15:03:36 <mscottm> Zakim, who is here?
15:03:36 <Zakim> On the phone I see +1.510.527.aaaa, Kei_Cheung, +1.414.456.aabb, +1.832.386.aacc, mscottm
15:03:39 <Zakim> On IRC I see Simon, mscottm, Lena, ChuckRockey, RRSAgent, Zakim, kei, egonw, ericP
15:03:40 <Simon> Slideshare URL for todays presentation: http://www.slideshare.net/stwigger/ncbo-dbp
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15:11:31 <kei> scribenick kei
15:11:41 <kei> ncbo biological project rat model
15:12:00 <kei> a variety of data including gene annotation data
15:12:10 <kei> good use of ontologies to help annotate these data
15:12:21 <kei> phenotype, trait, etc
15:12:36 <kei> rate genome database
15:12:54 <kei> linking bench work to informatics
15:12:59 <ericP> Zakim, please dial ericP-office
15:12:59 <Zakim> ok, ericP; the call is being made
15:13:01 <Zakim> +EricP
15:13:27 <kei> use rat model for hypertension
15:13:38 <kei> quantitative trait loci
15:14:04 <kei> link genes within the loci to high blood pressure phenotype
15:14:54 <kei> gene expression in different genes, different rat strains, ...
15:15:10 <kei> use of geo microarray data at ncbi
15:15:21 <kei> use ncbo anntotator
15:15:40 <kei> run geo data through annotator
15:15:48 <kei> get ontology anntotation
15:16:02 <kei> rat strain ontology (obo format)
15:16:27 <kei> mouse anatomy ontology (small difference between mouse and rat)
15:16:46 <kei> rat strain, tissue (metadata)
15:17:20 <kei> give an example (slide 7) of geo series entry
15:17:42 <Simon> gminer.mcw.edu
15:17:54 <kei> gminer shows the results
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15:18:11 <kei> web application to provide tag cloud
15:18:44 <kei> who has done particular experiments on certain rat samples
15:19:03 <kei> for example, neuromicroarray experiment metadata
15:19:51 <kei> annotator tool is used with some noise term removal
15:20:11 <kei> provide the ability to pick ontology during the automatic anntation process
15:21:48 <kei> nomenclature inconsistency create some problem with annotation
15:22:11 <kei> some problem with annotation in affy chips
15:22:15 <ericP> agenda+ remaining Sample and Series data is the hard (ambiguous) stuff?
15:22:55 <ericP> agenda+ comparative cost if annotation/specification work were pushed upstream
15:24:10 <kei> slide 12 probsets corresponding to babra1 receptor
15:24:57 <kei> link to genecard database
15:26:07 <kei> ontologies may help make the interpretation of data meaningful
15:26:34 <kei> data aggregation based on QTL
15:26:59 <kei> genes with QTL may be linked to hypertension
15:27:21 <kei> hypergraph structure is created using semantic web
15:27:37 <kei> slide 14: use of allegragraph
15:28:00 <kei> linking phenotype and disease
15:28:35 <kei> multiple sources of data are formatted in rdf and loaded into rdf store
15:28:43 <kei> ruby/rail was used
15:28:57 <ericP> agenda+ contentment with results so far
15:29:00 <kei> a number of owl ontology are used
15:29:52 <ericP> agenda+ sharing derived ontology alignment
15:30:10 <kei> in addition to rat data, annotations are collected for humn
15:30:44 <kei> annotated data are updated periodically
15:30:54 <kei> ontologies are access via bioportal
15:31:35 <kei> how to take functional info about genes and use sparql to do queries 
15:31:59 <kei> rdg in relational database converted to rdf
15:32:13 <kei> with alignment with existing ontologies such as SO
15:33:52 <kei> try to figure the best way to model entities
15:35:03 <kei> support front end interface development
15:35:34 <kei> future work: register PURL for RGD
15:35:49 <kei> how to represent RGD data in RDF
15:36:20 <kei> avoid blank nodes in the RDF representation
15:37:18 <kei> rdf provenance
15:37:28 <kei> make data accessible and reliable
15:37:44 <ericP> agenda?
15:38:29 <Zakim> - +1.510.527.aaaa
15:39:07 <kei> eric: how to resolve ambuiguity
15:39:28 <kei> simon: in some case, curators need to go back to the paper for answer
15:40:13 <kei> eric: how upstream one can push annotation
15:41:08 <kei> simon: full automation is difficult because the nature of annotation can be complex
15:43:02 <kei> simon: excel might be ontologized
15:43:17 <kei> simon: curation is a challenge even with the use of ontologies
15:43:51 <kei> eric: ontology alignment when mutliple alternative ontologies are available
15:44:45 <kei> simon: ontology mappings are increasingly available through ncbo
15:46:38 <kei> eric: relational vs rdf -- painful (short term vs long term)
15:50:07 <kei> scott: swobject might be helpful
15:50:45 <kei> scott: tie with geo?
15:51:34 <kei> scott: arrayexpress aims at rdf format in the future
15:52:41 <kei> michael: biologists need to add detailed enough annotation into geo and arrayexpress
15:56:28 <Lena> (I'm sorry... I will have to leave to another meeting :-( I will send the co-authors a list of notes I have on written on the paper's reviewer comments)
15:56:37 <Lena> (bye)
15:56:43 <kei> thanks, lena
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16:07:04 <kei> RRSAgent, please draft minutes
16:07:04 <RRSAgent> I have made the request to generate http://www.w3.org/2010/09/27-hcls-minutes.html kei
16:07:09 <Zakim> disconnecting the lone participant, EricP, in SW_HCLS(BioRDF)11:00AM
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16:07:12 <kei> RRSAgent, please make log world-visible 
16:07:13 <Zakim> Attendees were +1.510.527.aaaa, Kei_Cheung, +1.414.456.aabb, +1.832.386.aacc, mscottm, +1.206.605.aadd, +1.414.678.aaee, EricP
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