16:00:50 RRSAgent has joined #hcls 16:00:50 logging to http://www.w3.org/2006/12/12-hcls-irc 16:00:57 set logs, world-visible 16:01:26 +Bill_Bug 16:02:22 BillBug has joined #hcls 16:02:38 rrsagent, set logs world-visible 16:02:44 Don has joined #hcls 16:03:01 +John_Barkley 16:03:32 +Don_Doherty 16:03:52 Zakim, who's on the call? 16:03:53 On the phone I see Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty 16:05:44 Helen's page for Parkinson's Disease http://esw.w3.org/topic/ParkinsonsDisease 16:05:50 +Helen_Chen 16:07:00 +Davide_Zaccagnini 16:07:18 Zakim, who's on the call? 16:07:18 On the phone I see Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty, Helen_Chen, Davide_Zaccagnini 16:08:13 +Amit_John 16:08:59 http://esw.w3.org/topic/ParkinsonsDisease 16:09:19 helen has joined #hcls 16:09:33 Vipul: intro - context - Don, Helen, & Vipul - discussed on ACPP TCon to extend current UC to bedside (see Helen's PD URL) 16:11:12 DD: see PD UC - biological causes w/cites - discussed associtated dimentia & olfactory impairment - many specific to PD 16:12:59 DD: locus coeruleus damage - correlate neuron loss w/NE depletion & dimentia - there is a lot of subtlety to interpreting phenotype correlations 16:13:25 DD: e.g. - S.nigra loss associated with motor problems - e.g. dyskinesia 16:14:30 DD: l.c. loss appears related to cognitive impairment - memory, executive functions, visual-spatial mapping, language, etc. 16:15:27 DD: l.c. AND nuc. basalis of Meynart - associated w/biochem deficits & cog. impairment 16:15:41 DD: still roughed out - but will continue to enhance 16:16:32 VK: can you step through from molecular effect to dimentia - covering intervening entities? 16:18:48 DD: Oooh - tough - try executive function deficits - problems (e.g., like following company protocols or manners - inappropriate outburst) - this correlates with decr. Choline Acetyle Transferase (ChAT) in frontal crtx - therefore neurochem. Rx for low ChAT may assist in recovering exec. func. 16:19:35 DD: remember any specific Use Case (UC) glosses over many related issues - must limit UC 16:20:10 VK: glossing fine, as long as we can provide additional value through links derived from those entities that are covered in the UC 16:20:58 Amit: what is the role of literature informatics in this semantic approach to describing the data related to an UC 16:22:32 VK: our ontology is spare - mostly basic bio science - not clinical & medical, yet. HC working on this - focus of demo is to use avaialble primary and accessory data repositories - data FACTS - as opposed to their distillation in the lit. 16:25:33 Amit: tools to create idea graphs by extracting UMLS & MeSH terms from a defined lit. corpus; also - if you have multiple data sets in RDF, can do correlations across graphs - extension to SPARQL to specify constraints based on specified sub-graphs and node traversal limits. 16:27:35 three well established nuroscience literature corpus:brainmap.org 16:27:35 three well established nuroscience literature corpus:brainmap.org 16:28:30 Thanks, Helen! 16:29:52 trying to get the other two sites 16:31:43 VK & Amit: have a focussed working session on UC, specific queries & data sets (early next year) - include students from Amit's lab to build demo - based on F2F UC w/known answers as a metric 16:32:24 VK: well-known migraine study by Swanson - can use VK lab tool to automatically derive info 16:32:57 VK: Amit tool semantic mining - we are focussed on semantically well-founded data integration now. 16:33:07 Amit: see those 2 as intimately linked 16:33:16 VK: agreed - but focussing first on integration 16:33:50 -Amit_John 16:34:07 HC: focus on PD clinical guidelines - have references to specific dtb ref numbers - use those to assemble biological causes 16:34:33 HC: symptoms = clinical features in the clinical guidelines 16:34:54 HC: drew entity graphs for these features 16:35:03 VK: how link to what DD is doing 16:36:33 HC: Rx side - different types of Rx - medication in particular symptom (did already for depression) - could pick PD dementia - look at pharm Rx - link back to biochem. based on known biological role of pharm agent. 16:37:03 HC: each feature comes with a model - hypothesis including where & how of biological entities involved. 16:37:54 DD: you fleshed out PD depression & some of the olfactory symptoms - could you do this with dimentia 16:38:40 HC: need to tie in neural systems pathways 16:40:34 DD: pathways = connections from one brain region to another 16:40:56 BAMS: http://brancusi.usc.edu/bkms/ 16:41:11 BAMS XML dumps: http://brancusi.usc.edu/bkms/bamsxml.html 16:42:15 HC: tie behavior to molecules - e.g., olfactory oderant links to olf-receptor - then on to biochem, specific neurons in the Olf Epithelium and connectivity (see SenseLab for support in making this leap) 16:42:28 DD: put out more detail in the biological causes 16:43:18 HC: work with DD to add more links from clinical features to dtb refs - represented as "triples" 16:43:53 HC: go to literature to add some supporting info for diagnosis - weight assertions based on certainty of observations found in lit. 16:44:01 VK: when to meet next? 16:44:52 HC & DD: will meet next week to reconnoiter - determine whether covered all the available details 16:45:14 CocoMac - Untangling the Brain - http://134.95.56.239/home.asp 16:45:40 DD & HC: work more on the BMC Bioinformatics manuscript 16:46:24 -John_Barkley 16:46:25 -Davide_Zaccagnini 16:46:25 -Bill_Bug 16:46:26 -Helen_Chen 16:46:27 -Vipul_Kashyap 16:46:28 -Don_Doherty 16:46:30 SW_HCLS(Bio-Ont WG)11:00AM has ended 16:46:31 Attendees were Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty, Helen_Chen, Davide_Zaccagnini, Amit_John 16:46:47 rrsagent, create minutes 16:46:47 I have made the request to generate http://www.w3.org/2006/12/12-hcls-minutes.html vipul 16:47:24 BB: please review section 4.3 of BMC Bioinformatics manuscript "Interactions with other communities" - very focussed on community ontology development. 18:24:30 Zakim has left #hcls 19:40:02 matt_h has joined #hcls