IRC log of hcls on 2006-12-12

Timestamps are in UTC.

16:00:50 [RRSAgent]
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logging to
16:00:57 [vipul]
set logs, world-visible
16:01:26 [Zakim]
16:02:22 [BillBug]
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16:02:38 [vipul]
rrsagent, set logs world-visible
16:02:44 [Don]
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16:03:01 [Zakim]
16:03:32 [Zakim]
16:03:52 [vipul]
Zakim, who's on the call?
16:03:53 [Zakim]
On the phone I see Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty
16:05:44 [vipul]
Helen's page for Parkinson's Disease
16:05:50 [Zakim]
16:07:00 [Zakim]
16:07:18 [vipul]
Zakim, who's on the call?
16:07:18 [Zakim]
On the phone I see Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty, Helen_Chen, Davide_Zaccagnini
16:08:13 [Zakim]
16:08:59 [vipul]
16:09:19 [helen]
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16:09:33 [BillBug]
Vipul: intro - context - Don, Helen, & Vipul - discussed on ACPP TCon to extend current UC to bedside (see Helen's PD URL)
16:11:12 [BillBug]
DD: see PD UC - biological causes w/cites - discussed associtated dimentia & olfactory impairment - many specific to PD
16:12:59 [BillBug]
DD: locus coeruleus damage - correlate neuron loss w/NE depletion & dimentia - there is a lot of subtlety to interpreting phenotype correlations
16:13:25 [BillBug]
DD: e.g. - S.nigra loss associated with motor problems - e.g. dyskinesia
16:14:30 [BillBug]
DD: l.c. loss appears related to cognitive impairment - memory, executive functions, visual-spatial mapping, language, etc.
16:15:27 [BillBug]
DD: l.c. AND nuc. basalis of Meynart - associated w/biochem deficits & cog. impairment
16:15:41 [BillBug]
DD: still roughed out - but will continue to enhance
16:16:32 [BillBug]
VK: can you step through from molecular effect to dimentia - covering intervening entities?
16:18:48 [BillBug]
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 [BillBug]
DD: remember any specific Use Case (UC) glosses over many related issues - must limit UC
16:20:10 [BillBug]
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 [BillBug]
Amit: what is the role of literature informatics in this semantic approach to describing the data related to an UC
16:22:32 [BillBug]
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 [BillBug]
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 [helen]
three well established nuroscience literature
16:27:35 [helen]
three well established nuroscience literature
16:28:30 [vipul]
Thanks, Helen!
16:29:52 [helen]
trying to get the other two sites
16:31:43 [BillBug]
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 [BillBug]
VK: well-known migraine study by Swanson - can use VK lab tool to automatically derive info
16:32:57 [BillBug]
VK: Amit tool semantic mining - we are focussed on semantically well-founded data integration now.
16:33:07 [BillBug]
Amit: see those 2 as intimately linked
16:33:16 [BillBug]
VK: agreed - but focussing first on integration
16:33:50 [Zakim]
16:34:07 [BillBug]
HC: focus on PD clinical guidelines - have references to specific dtb ref numbers - use those to assemble biological causes
16:34:33 [BillBug]
HC: symptoms = clinical features in the clinical guidelines
16:34:54 [BillBug]
HC: drew entity graphs for these features
16:35:03 [BillBug]
VK: how link to what DD is doing
16:36:33 [BillBug]
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 [BillBug]
HC: each feature comes with a model - hypothesis including where & how of biological entities involved.
16:37:54 [BillBug]
DD: you fleshed out PD depression & some of the olfactory symptoms - could you do this with dimentia
16:38:40 [BillBug]
HC: need to tie in neural systems pathways
16:40:34 [BillBug]
DD: pathways = connections from one brain region to another
16:40:56 [BillBug]
16:41:11 [BillBug]
BAMS XML dumps:
16:42:15 [BillBug]
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 [BillBug]
DD: put out more detail in the biological causes
16:43:18 [BillBug]
HC: work with DD to add more links from clinical features to dtb refs - represented as "triples"
16:43:53 [BillBug]
HC: go to literature to add some supporting info for diagnosis - weight assertions based on certainty of observations found in lit.
16:44:01 [BillBug]
VK: when to meet next?
16:44:52 [BillBug]
HC & DD: will meet next week to reconnoiter - determine whether covered all the available details
16:45:14 [BillBug]
CocoMac - Untangling the Brain -
16:45:40 [BillBug]
DD & HC: work more on the BMC Bioinformatics manuscript
16:46:24 [Zakim]
16:46:25 [Zakim]
16:46:25 [Zakim]
16:46:26 [Zakim]
16:46:27 [Zakim]
16:46:28 [Zakim]
16:46:30 [Zakim]
SW_HCLS(Bio-Ont WG)11:00AM has ended
16:46:31 [Zakim]
Attendees were Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty, Helen_Chen, Davide_Zaccagnini, Amit_John
16:46:47 [vipul]
rrsagent, create minutes
16:46:47 [RRSAgent]
I have made the request to generate vipul
16:47:24 [BillBug]
BB: please review section 4.3 of BMC Bioinformatics manuscript "Interactions with other communities" - very focussed on community ontology development.
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