15:51:05 RRSAgent has joined #BioRDF 15:51:05 logging to http://www.w3.org/2008/11/17-BioRDF-irc 15:51:26 Zakim, this will BioRDF 15:51:26 I don't understand 'this will BioRDF', kei 15:51:35 Zakim, this will be BioRDF 15:51:35 ok, kei; I see SW_HCLS()11:00AM scheduled to start in 9 minutes 15:51:56 agenda+ introduction [kei] 15:52:19 agenda+ gene wiki [Andrew] 15:52:33 agenda+ web visualization [Maged] 15:52:48 agenda+ Q&A [All] 15:53:01 Zakim, take up next agendum 15:53:01 agendum 1. "introduction" taken up [from kei] 15:58:03 SW_HCLS()11:00AM has now started 15:58:09 +AndrewSu 15:58:41 +??P1 15:58:59 Zakim, please dial ericP-office 15:58:59 ok, ericP; the call is being made 15:59:01 +EricP 15:59:03 -AndrewSu 15:59:04 +Kei_Cheung 15:59:15 +AndrewSu 15:59:22 Zakim, who is here? 15:59:22 On the phone I see ??P1, EricP, Kei_Cheung, AndrewSu 15:59:23 On IRC I see RRSAgent, Zakim, kei, ericP 16:00:36 +[IPcaller] 16:01:01 ericP-test has joined #BioRDF 16:01:13 +??P8 16:01:58 maged has joined #BIORDF 16:02:07 + +1.781.662.aaaa 16:02:16 i think it works now 16:02:29 Zakim, who is here? 16:02:29 On the phone I see ??P1, EricP, Kei_Cheung, AndrewSu, [IPcaller] (muted), ??P8, +1.781.662.aaaa 16:02:30 ty 16:02:34 On IRC I see maged, ericP-test, RRSAgent, Zakim, kei, ericP 16:02:46 Susie has joined #BioRDF 16:02:50 ipcaller maged 16:02:53 Zakim, [IPcaller] is Huajan 16:02:58 +Huajan; got it 16:03:00 Jun has joined #biordf 16:03:10 Zakim, +1.781.662.aaaa is Susie 16:03:10 +Susie; got it 16:03:43 Zakim, ??P8 is Andrew 16:03:45 Huajun has joined #BioRDF 16:03:46 +Andrew; got it 16:03:53 + +86528aabb 16:04:08 Zakim, +86528aabb is Jun 16:04:08 +Jun; got it 16:04:21 Zakim, ??P1 is maged 16:04:21 +maged; got it 16:04:29 Zakim, who is here? 16:04:29 On the phone I see maged, EricP, Kei_Cheung, AndrewSu, Huajan (muted), Andrew, Susie, Jun 16:04:31 On IRC I see Huajun, Jun, Susie, maged, ericP-test, RRSAgent, Zakim, kei, ericP 16:04:51 scribenic: kei 16:05:19 rfrost has joined #BioRDF 16:05:38 meeting: BioRDF weekly telecon 2008-11-17 16:05:42 topic: introductions 16:06:36 maged: lecturer at plymouth univ. UK, presenter today 16:07:11 http://www.plymouth.ac.uk/staff/mnkamelboulos 16:07:51 ericP has changed the topic to: BioRDF Task Force meeting http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-11-17 16:08:31 jun: postdoc at oxford, flyweb project 16:08:38 http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-11-17?action=AttachFile&do=get&target=20081117_BioRDF_TC_20081116.ppt 16:09:03 Zakim, take up the next agendum 16:09:03 I don't understand 'take up the next agendum', kei 16:09:41 andrew: patten of citation follows power law 16:10:03 Susie has joined #BioRDF 16:10:10 -> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-11-17?action=AttachFile&do=get&target=20081117_BioRDF_TC_20081116.ppt The Gene Wiki, from a BioRDF-naïve perspective 16:10:26 Zakim, take up next agendum 16:10:26 agendum 2. "gene wiki" taken up [from Andrew] 16:10:45 andrew: bottleneck in data annotation/curation 16:11:07 andrew: long tail vs. short head 16:11:32 andrew: wikipedia emphasizes large community contribution 16:12:48 andrew: concern about wiki (e.g., accuracy) reported in Nature (comparing Britanaca and Wikipedia) 16:13:16 andrew: open model of content generation producing a huge breadth of data 16:13:53 andrew: why this paradigm applies to gene annotation 16:14:39 andrew: structured view (e.g., entrez gene) vs. unstructured wiki text (machine vs human readability) 16:14:49 we have just published on this: see http://www.ncbi.nlm.nih.gov/pubmed/18998977 and Clauson KA, Polen HH, Kamel Boulos MN, Dzenowagis JH. Scope, completeness, and accuracy of drug information in Wikipedia. The Annals of Pharmacotherapy. 2009; 43: in press 16:15:24 andrew: may be easier to incorporate things like images into unstructured text 16:16:47 andrew:wiki keeps a nice history of revisions -- two way commumnication works well for gene annotation 16:17:38 andrew: gene stubs creation -- complementary to existing manual creation of gene articles 16:18:03 andrew: gene wiki added 7500 automatically generated gene stubs 16:18:42 andrew: info box gene annotation databases (e.g., entrez genes, ensembl, references, etc) 16:19:14 andrew: most biologists more likely edit existing articles than creating new articles ... 16:19:47 andrew: critical mass of articles linked to/from 16:20:11 andrew: there is an active group of molecular biologists actively participating in the wikipedia project 16:23:23 andrew: evaluation of gene wiki - increase of editing activities was observed 16:24:59 andrew: solicit postive feedback loops 16:25:32 andrew: it is hoped that the gene stubs would attract more readers who can introduce some edits ... 16:27:26 andrew: the model of community editing is shown in wikipedia 16:30:48 andrew: getting data in first, before worrying too much about getting data out in standard format 16:31:21 -> http://www.w3.org/mid/200807101203.19705.kanzure@gmail.com "massive plaintext disaster" 16:32:04 q+ to ask about the payback for gene infoboxes 16:32:42 andrew: semantic annotation -- how to do it right and who should do it? 16:33:03 andrew: authorative source vs community contribution 16:33:35 andrew: pipeline of getting data out of WP? 16:33:55 ack me 16:33:55 ericP, you wanted to ask about the payback for gene infoboxes 16:34:59 ericP: people wants consistently coded way of presenting info using info boxes, how is this applied to gene annotation ... 16:35:08 Susie has joined #BioRDF 16:35:42 you create a wiki template for each 16:36:26 andrew: how dbpedia works? 16:38:03 ericP: infobox info extraction? 16:42:09 Susie: who is the person you mentioned who do the infobox extraction? 16:43:21 concrete steps in is identify things in infoboxes and identify those missing in the infoboxes 16:44:01 Chris Bizer has been involved in the Linked Data project from the start 16:44:20 Zakim, take up next agendum 16:44:20 agendum 3. "web visualization" taken up [from Maged] 16:44:36 Jun has joined #biordf 16:44:41 kei, slides link? 16:44:53 http://www.google.com/intl/en/press/annc/20081112_earthrome.html 16:44:54 http://healthcybermap.org/MNKB--Why_visualize_RL_data_in_SL.zip 16:45:41 maged: mirror world transforms into 3D world 16:46:17 maged: navigation in 3D space -- 3D wiki? 16:47:29 maged: chat room, teleconference -- future worlds bring face-to-face meetings into 3D virtual environment 16:48:01 maged: people who are geographically distributed can meet in vitural worlds like second life 16:49:32 maged: avartars (simulated people) can be created to reflect reality closely 16:50:28 maged: cognitive skills incorporated into VW 16:50:32 -Andrew 16:51:30 maged: human interactions are spatial in nature 16:53:05 maged: bringing google earth environment into Second Life 16:53:15 -Huajan 16:54:25 maged: why we need 3D for collaborative environment 16:55:59 http://www.slideshare.net/sl.medic/3d-realvirtual-worlds-for-health-and-healthcare/ 16:56:35 maged: performance is governed by hardware which is descreasing in costs 16:57:41 maged: iso standard -- mpeg V -- 17:00:01 -Susie 17:00:02 -AndrewSu 17:00:02 -maged 17:00:03 mpeg-v http://www.chiariglione.org/mpeg/working_documents/mpeg-v/mpeg-v_Reqs.zip 17:00:04 -Jun 17:00:04 -Kei_Cheung 17:00:06 -EricP 17:00:08 SW_HCLS()11:00AM has ended 17:00:09 Attendees were AndrewSu, EricP, Kei_Cheung, Huajan, Susie, Andrew, Jun, maged 17:00:17 RRSAgent, please draft minutes 17:00:17 I have made the request to generate http://www.w3.org/2008/11/17-BioRDF-minutes.html ericP 17:00:22 RRSAgent, please make log world-visible