IRC log of hcls on 2007-02-06

Timestamps are in UTC.

15:59:48 [RRSAgent]
RRSAgent has joined #hcls
15:59:48 [RRSAgent]
logging to
15:59:59 [vipul]
rrsagent, make logs world-visible
16:00:28 [Zakim]
SW_HCLS(Bio-Ont WG)11:00AM has now started
16:00:29 [Zakim]
16:00:48 [Zakim]
16:01:31 [Zakim]
16:01:53 [Don]
Don has joined #hcls
16:03:25 [Zakim]
16:03:51 [vipul]
16:05:21 [helen]
helen has joined #hcls
16:05:32 [helen]
sorry I am late
16:05:39 [vipul]
no problem
16:05:39 [helen]
still dial in now
16:05:46 [helen]
16:06:53 [Zakim]
16:07:12 [vipul]
Zakim, who's on the call?
16:07:12 [Zakim]
On the phone I see Vipul_Kashyap, Don_Doherty, Bill_Bug, John_Barkley, [IPcaller]
16:08:10 [helen]
Zakim, [IPcaller] is Helen
16:08:10 [Zakim]
+Helen; got it
16:09:35 [BillBug]
VK: Review Use of PATO statements for AD & PD Use Cases
16:10:19 [BillBug]
DD: We assume SWAN will produce RDF for use in the HCLSIG demo. Will this also be made avaialble in the Science Commons for future use?
16:11:22 [vipul]
Action: Look at the RDF Graphs and figure out architectural best practices to refer to Distilled Knowledge Resources
16:12:31 [BillBug]
DD: AD folks do this work full-time; DD (and others) does PD Use Case work doing this gratis on top of other work.
16:14:04 [vipul]
DD: Action Item 1 to be owned by Bill, Don and Helen
16:15:32 [BillBug]
Action: create data flow diagram for demo - Demo script --> BioRDF sources --> Distilled KRs
16:18:25 [vipul]
DD: Start with a simple interface, e.g., PubMed
16:18:37 [vipul]
DD: Match against strings in RDF data sets
16:19:53 [vipul]
DD: Look for relations to Distilled knowledge sources
16:20:44 [vipul]
DD: Present as a next step as refining query
16:21:17 [vipul]
DD: Menus pre-populated from most frequently occurring DKR concepts
16:21:50 [vipul]
DD: Faceted browser inspired by an ontology
16:22:33 [Don]
Vipul, the previous statements are by BB
16:22:36 [vipul]
VK: M Scott Marshall could take a look at these things
16:22:40 [vipul]
16:22:53 [vipul]
Replace DD by BB
16:24:11 [BillBug]
HC: Can't start with free text - no clear way to map into RDF statement
16:28:52 [vipul]
16:29:12 [BillBug]
16:36:18 [helen]
16:36:48 [vipul]
BB: Bill will post the URLs of two papers/presentations by Amarnath on the BIRN Mediator
16:42:22 [BillBug]
BIRN Data & Tools:
16:42:24 [BillBug]
BIRN neuroimaging metadata XML Schema: XCEDE -
16:42:26 [BillBug]
BIRNLex ontology (OWLDocs view - avaialble as OWL files, too):
16:42:28 [BillBug]
BIRN data relevant to HCLSIG Demo:
16:42:30 [BillBug]
* Cell-Centered Database:
16:43:01 [Don]
Bill, are the BIRNLex OWL files available now?!
16:58:38 [BillBug]
Yes - I can distribute what I have. There have been some URI problems for the imports (BIRNLex is 6 OWL files, some of which are other public ontologies imported via owl:import).
17:01:14 [Zakim]
17:04:32 [BillBug]
Recent BIRN Mediator articles (Amarnath Gupta et al.):
17:04:34 [BillBug]
* Semantically Based Data Integration Environment for Biomedical Research
17:04:36 [BillBug]
Vadim Astakhov, Amarnath Gupta, Jeffrey S. Grethe, Edward Ross, David Little, Aylin Yilmaz, Xufei Qian, Simone Santini, Maryann Martone, Mark Ellisman.
17:04:38 [BillBug]
Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)
17:04:39 [BillBug]
* Data Integration and Ontologies for Biomedical Applications
17:04:41 [BillBug]
Amarnath Gupta, Vadim Astakhov, and Christopher Condit
17:04:42 [BillBug]
VLDB 2006
17:04:44 [BillBug]
form PDF, see
17:04:45 [BillBug]
* OntoQuest: Exploring Ontological Data Made Easy
17:04:47 [BillBug]
Li Chen, Maryann Martone, Amarnath Gupta, Lisa Fong, Mona Wong-Barnum
17:04:48 [BillBug]
VLDB 2006
17:04:50 [BillBug]
form PDF, see
17:05:03 [BillBug]
Ooops - those VLDB2006 articles are both the same thing - download the SLIDES not the PAPER.
17:06:05 [vipul]
Thanks, Bill!
17:06:19 [vipul]
This could be posted on the wiki when we get Amarnath to speak
17:24:08 [Zakim]
17:24:10 [Zakim]
17:24:12 [Zakim]
17:24:16 [Zakim]
17:24:17 [Zakim]
SW_HCLS(Bio-Ont WG)11:00AM has ended
17:24:18 [Zakim]
Attendees were Vipul_Kashyap, Don_Doherty, Bill_Bug, John_Barkley, Helen
17:24:30 [BillBug]
VK: Helen made many wonderful points through her presentation - lessons learned - etc. Please write up and add to Wiki along with presentation.
17:24:32 [BillBug]
HC: Will try to do.
18:18:29 [Zakim]
Zakim has left #hcls