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14:58:02 <RRSAgent> logging to http://www.w3.org/2010/06/07-hcls-irc
14:58:11 <kei> Zakim, this will be BioRDF
14:58:11 <Zakim> ok, kei, I see SW_HCLS(BioRDF)11:00AM already started
14:58:28 <kei> agenda+ introduction [kei]
14:58:36 <kei> agenda+ lipid ontology [chris]
14:58:56 <kei> agenda+ genelist representation [Lena, Jun, Satya, Scott]
14:59:07 <kei> Zakim, take up next agendum
14:59:07 <Zakim> agendum 1. "introduction" taken up [from kei]
14:59:48 <Zakim> +Kei_Cheung
14:59:53 <Zakim> + +1.832.386.aabb
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15:02:40 <Zakim> + +1.206.605.aacc
15:04:31 <kei> https://transfer.med.yale.edu/upload/data/39YObdi808qV4ftL3FY1588AL5AAC2AKLpS/Baker_-_BioRDF_-_W3C_-_HCLS_Lipid-Ontology_and_Reuse_Cases.pptx
15:04:50 <kei> https://transfer.med.yale.edu/upload/data/39YObdi808qV4ftL3FY1588AL5AAC2AKLpS/Baker_-_BioRDF_-_W3C_-_HCLS_Lipid-Ontology_and_Reuse_Cases.pdf
15:04:50 <kei> Cheers,
15:04:50 <kei> -Kei 
15:07:15 <Zakim> +mscottm
15:07:42 <ericP> Zakim, please dial ericP-office
15:07:42 <Zakim> ok, ericP; the call is being made
15:07:44 <Zakim> +EricP
15:08:35 <Zakim> +[IPcaller]
15:08:52 <mscottm> Zakim, who is here?
15:08:52 <Zakim> On the phone I see +1.506.648.aaaa, Kei_Cheung, +1.832.386.aabb, +1.206.605.aacc, mscottm, EricP, [IPcaller]
15:08:54 <Zakim> On IRC I see michael, mscottm, RRSAgent, Zakim, kei, LenaDeus, jodi, Chris, matthias_samwald, trackbot, ericP
15:09:02 <jodi> jodi has left #HCLS
15:09:23 <Zakim> +??P9
15:10:38 <mscottm> Zakim, +[IPcaller] is matthias_samwald
15:10:38 <Zakim> sorry, mscottm, I do not recognize a party named '+[IPcaller]'
15:10:39 <rfrost> rfrost has joined #HCLS
15:10:43 <mscottm> Zakim, [IPcaller] is matthias_samwald
15:10:43 <Zakim> +matthias_samwald; got it
15:11:07 <mscottm> Zakim, ??P9 is rfrost
15:11:07 <Zakim> +rfrost; got it
15:11:25 <Zakim> + +1.937.775.aadd
15:12:56 <rfrost> kei, would you mind repasting the slide link?
15:13:11 <kei> kei: lipid ontology -- started with text mining and then formal ontology
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15:13:41 <kei> kei: data integration is important and challenging in the context of lipid
15:14:11 <kei> IUPAC is older (1970's) challenge in adoption
15:14:32 <kei> LIPIDMAPS came along but still has issues such as inconsistencies
15:14:57 <kei> objectives: available through OBO
15:15:43 <kei> OBO compliance (e.g., continuant entity ... small molecule)
15:16:30 <kei> semantically expressive
15:17:15 <kei> use of owl in terms of necessary and sufficient condiitions and cardinality
15:18:03 <kei> started with 32 organic groups and another 63 are needed to define lipids
15:20:39 <kei> different functional groups can be defined
15:21:52 <kei> some entities are from the lipidmap and new entities have been added
15:22:59 <kei> reasoning can be performed based on the owl structure
15:23:51 <kei> use of checkmol and open babel for conversion into n3 format from mol files
15:25:02 <kei> go through all the instances and use rules/axioms to reason over the structure
15:25:22 <kei> to make sure structural group assignments are correct
15:25:42 <kei> this is an iterative process with interaction/collaboration/curation with community
15:26:31 <kei> 715 classes, 901 restrictions, and 41 properties
15:26:52 <kei> scientists discovering new lipids can submit through web services
15:27:27 <kei> position the ontology as a bridge between lipid community, obo, and chebi
15:27:47 <kei> leverage the skills of the ontology community and the expertise of lipid community
15:27:57 <kei> semantic assistant
15:28:40 <kei> use of racer, sparql, and other related tools
15:29:24 <kei> use of text mining to help populate the ontology
15:30:03 <kei> normalizing terms into canonical names
15:30:58 <kei> looked at 8000 abstracts involving ovarian cancer
15:31:19 <kei> linked dimensions of lipid/protein to classes
15:31:32 <kei> linked to the sentence level
15:32:39 <kei> signal pathways are also included
15:33:17 <kei> knowledge finder: user can submit keyword can be mapped to a set of natural language queries for users to select
15:33:37 <kei> in addition, visual query tool has been developed
15:34:36 <kei> semantic desktop assistant: web service paradigm
15:35:22 <kei> lipid annotation: input can be abstract text for example
15:35:39 <kei> using the GATE annotation pipeline
15:36:56 <kei> client side application is open office
15:37:06 <kei> semantic assistant is free for download
15:39:31 <kei> acknowledgement: mutliple institutions are involved
15:41:21 <matthias_samwald> (need to leave now as well. bye!)
15:41:25 <Zakim> -matthias_samwald
15:42:31 <kei> thanks, matthias
15:43:11 <kei> scott, could you also do the scribing from this point on?
15:45:31 <kei> I'm leaving now ...thanks!
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15:47:26 <Zakim> -Kei_Cheung
15:52:39 <Zakim> - +1.937.775.aadd
15:52:55 <Zakim> -EricP
16:02:04 <Zakim> -rfrost
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16:08:02 <Zakim> - +1.832.386.aabb
16:08:05 <Zakim> -mscottm
16:08:06 <Zakim> - +1.206.605.aacc
16:08:06 <Zakim> - +1.506.648.aaaa
16:08:08 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:08:10 <Zakim> Attendees were +1.506.648.aaaa, Kei_Cheung, +1.832.386.aabb, +1.206.605.aacc, mscottm, EricP, matthias_samwald, rfrost, +1.937.775.aadd
16:08:38 <mscottm> possible followup meeting to look at genelists: Thu morning HCLS timeslot 11AM ET
16:09:34 <mscottm> Lena: Have some concerns about the current relation between genes and samples
16:09:55 <mscottm> Scott: Yes, let's talk about that some more - possibly this week?
16:10:27 <mscottm> ..anybody else interested in this?
16:10:28 <mscottm> MichaelMiller: I would be interested
16:28:55 <mscottm>   RRSAgent, please draft minutes
16:28:55 <RRSAgent> I have made the request to generate http://www.w3.org/2010/06/07-hcls-minutes.html mscottm
16:28:59 <mscottm>   RRSAgent, please make log world-visible
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