12 Dec 2006

See also: IRC log


Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty, Helen_Chen, Davide_Zaccagnini, Amit_John




<vipul> set logs, world-visible

<vipul> Helen's page for Parkinson's Disease http://esw.w3.org/topic/ParkinsonsDisease

<vipul> http://esw.w3.org/topic/ParkinsonsDisease

Vipul: intro - context - Don, Helen, & Vipul - discussed on ACPP TCon to extend current UC to bedside (see Helen's PD URL)

DD: see PD UC - biological causes w/cites - discussed associtated dimentia & olfactory impairment - many specific to PD
... locus coeruleus damage - correlate neuron loss w/NE depletion & dimentia - there is a lot of subtlety to interpreting phenotype correlations
... e.g. - S.nigra loss associated with motor problems - e.g. dyskinesia
... l.c. loss appears related to cognitive impairment - memory, executive functions, visual-spatial mapping, language, etc.
... l.c. AND nuc. basalis of Meynart - associated w/biochem deficits & cog. impairment
... still roughed out - but will continue to enhance

VK: can you step through from molecular effect to dimentia - covering intervening entities?

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.
... remember any specific Use Case (UC) glosses over many related issues - must limit UC

VK: glossing fine, as long as we can provide additional value through links derived from those entities that are covered in the UC

Amit: what is the role of literature informatics in this semantic approach to describing the data related to an UC

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.

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.

<helen> three well established nuroscience literature corpus:brainmap.org

<helen> three well established nuroscience literature corpus:brainmap.org

<vipul> Thanks, Helen!

<helen> trying to get the other two sites

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

VK: well-known migraine study by Swanson - can use VK lab tool to automatically derive info
... Amit tool semantic mining - we are focussed on semantically well-founded data integration now.

Amit: see those 2 as intimately linked

VK: agreed - but focussing first on integration

HC: focus on PD clinical guidelines - have references to specific dtb ref numbers - use those to assemble biological causes
... symptoms = clinical features in the clinical guidelines
... drew entity graphs for these features

VK: how link to what DD is doing

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.
... each feature comes with a model - hypothesis including where & how of biological entities involved.

DD: you fleshed out PD depression & some of the olfactory symptoms - could you do this with dimentia

HC: need to tie in neural systems pathways

DD: pathways = connections from one brain region to another

BAMS: http://brancusi.usc.edu/bkms/

BAMS XML dumps: http://brancusi.usc.edu/bkms/bamsxml.html

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)

DD: put out more detail in the biological causes

HC: work with DD to add more links from clinical features to dtb refs - represented as "triples"
... go to literature to add some supporting info for diagnosis - weight assertions based on certainty of observations found in lit.

VK: when to meet next?

HC & DD: will meet next week to reconnoiter - determine whether covered all the available details

CocoMac - Untangling the Brain -

DD & HC: work more on the BMC Bioinformatics manuscript

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.127 (CVS log)
$Date: 2006/12/12 16:47:01 $

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Default Present: Vipul_Kashyap, Bill_Bug, John_Barkley, Don_Doherty, Helen_Chen, Davide_Zaccagnini, Amit_John
Present: Vipul_Kashyap Bill_Bug John_Barkley Don_Doherty Helen_Chen Davide_Zaccagnini Amit_John

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Got date from IRC log name: 12 Dec 2006
Guessing minutes URL: http://www.w3.org/2006/12/12-hcls-minutes.html
People with action items: 

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<dbooth> Topic: Review of Amy's report

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