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RE: BioRDF [Telcon]

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Tue, 12 Dec 2006 15:48:46 -0500
Message-ID: <2BF18EC866AF0448816CDB62ADF65381055CC143@PHSXMB11.partners.org>
To: "June Kinoshita" <junekino@media.mit.edu>
Cc: <public-semweb-lifesci@w3.org>


This use case below is a great one. Thanks for sharing it with us!
I guess some of the questions can be answered using PubMed queries on the
literature and some of them can be answered using "facts/hypotheses" stored on
the Alzheimer's Forum.

I would presume that the act of posting hypotheses on the Alzheimer's Forum
would be a manual step, but this would later enable automatic answering of other

Wondering how one could "integrate" this use case with the Parkinson's Disease
Use Case snd whether it would be feasible or make sense.



An interesting list of hypotheses that you enumerate are:

> A hypothesis about
> ADDL causing memory loss in AD is posted on Alzforum.

> The ADDL Hypothesis on Alzforum suggests that ADDL (= Abeta*56?)
> disrupts LTP.
> The literature indicates CA1 hippocampal neurons, and A- and D-type K
> channels are involved in LTP. BrainPharm data state that CA1
> hippocampal neurons have A-channels.  What's more, the A-current is
> reduced by Abeta.
> Question: Would an antibody directed against ADDL / Abeta*56 restore
> A-current in the mouse model hippocampal neuron (e.g. in an
> organotypic slice prep)?
> A query locates an antibody to ADDL and where to obtain it.
> Question 2 is what determines vulnerability to encephalilitis among
> immunized patients?
> A literature search finds interferon-gamma (INFG) may be a player.
> This comes from both mouse and human trial data (need to check this).
> Question: Do polymorphisms in INFG, or differences in INFG
> regulation, correlate with inflammatory response to vaccine?
> Question: Why did the mouse models not develop encephalitis in
> preclinical studies?
> Our investigator queries pathway databases to identify the gene
> network involved in IFNG regulation, and also SNP databases for
> differences between mouse strains, mouse and human. He narrows down a
> group of genes and queries the AlzGene database to see if any gene
> association studies have shown a correlation between any of these
> genes and AD risk.
> Our investigator proposes a study to genotype participants in the
> failed vaccination trial to find out whether the encephalitis
> response correlates with specific SNPs in the candidate genes.
> On Dec 8, 2006, at 3:16 PM, Susie Stephens wrote:
> >
> > Here's a reminder for Monday's BioRDF call.
> >
> > Date of Call: Monday December 11, 2006
> > Time of Call: 11:00am Eastern Time
> > Dial-In #: +1.617.761.6200 (Cambridge, MA)
> > Participant Access Code: 246733 ("BIORDF")
> > IRC Channel: irc.w3.org port 6665 channel #BioRDF
> > Duration: ~1 hour
> >
> > Agenda
> > Matthias Samwald and Alan Ruttenberg will be providing task updates.
> > Bill Bug, Elizabeth Wu and Scott Marshall will be discussing the
> > scientific queries that they have been researching.
> >
> > Kind regards,
> >
> > Susie
> >
Received on Tuesday, 12 December 2006 20:49:06 UTC

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