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Action item: Review of Parkinsons's use case and connection to reagents BioRDF task

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 11 May 2006 01:18:45 -0400
To: public-semweb-lifesci@w3.org
Message-Id: <72114AF5-CBE7-445B-BE17-725FDF5EA1AA@gmail.com>
At the meeting of April 20, I had an action item


AlanR to review http://esw.w3.org/topic/HCLS/ParkinsonUseCase and see  
if BioRDF task for translating data to RDF provide answers to  
questions being asked

I did a quick review of this and came up with the following connections:

1. In the systems physiology view, the question

What proteins (receptors) recognize those chemicals  
(neurotransmitters) and what are the responses that they elicit in  
the neuron?
Concepts of interest: Receptors, Proteins (subtype of Receptors),  
Recognizes, Response_Elicited

Antibodies are a tools for probing the state of proteins. To the  
extent that the responses to neurotransmitters might change the state  
or expression of a protein, antibodies can be used to measure this  
via, e.g. one of the in situ methods. You will be able to link from  
protein/gene to antibodies against that protein, and, probably to  
specific antibodies based on the specific modification of a protein  
you are expecting, and specifically to those antibodies annotated as  
appropriate for use e.g. FISH.

2. Cellular and Molecular Biologist View

Staining by the use of antibodies is a fundamental method for the  
visualization of proteins in cells. Most experimentalists who want to  
work with model systems will use them. So being able to quickly link  
from protein of interest to the antibodies against that protein will  
speed up the process of designing experiments. In addition, although  
the initial antibody database is curated by people interested in  
Alzheimer's research, many of the same proteins are of interest in  
studying other neurological diseases. In the same way that the  
antibodies in this database will be annotated as "being of interest  
to someone studying alzheimers", I expect that other such resources  
will be encoded as "being of interest to someone studying  
parkinsons", once can imagine a situation in which, eventually,  
researchers will be able to query for reagents that have been  
validated for use in their specific area of interest. Such an  
association could eventually mined from research articles, where,  
using NLP one could extract the disease of interest, and from the  
methods sections, any information about antibodies used.

3. Clinical Researcher View

Can a certain diagnostic test (e.g., a blood test for a biomarker or  
an imaging study) provide an approach to diagnosing Parkinsonís  
disease that is superior to or can complement existing diagnostic  
Concepts of interest: Diagnostic test, blood test (subtype of  
diagnostic test), imaging study (subtype of diagnostic test), Test  
Associated With Disease

Antibody tests, particularly ELISA (an antibody assay) are commonly  
used as medical diagnostics. One of the properties annotated for  
antibodies what methods it is useful for and ELISA (and other assay  
types with potential clinical relevance) are in the glossary of such  
methods: see http://www.alzforum.org/res/com/ant/glossary.asp. Or go  
to http://www.alzforum.org/res/com/ant/default.asp and search for  
ELISA as a keyword.

4. Neurologist View

What non-human models exist for Parkinson's Disease? (Last week I  
heard a talk by Leo Pallanck on fruit fly research on Parkinson's  

A small piece of this might be the species reactivity annotations in  
the antibody database. So if a protein is determined as being of  
interest, and an antibody is known against that protein, then there  
might be a suggestion that any species against which the antibody is  
known to be reactive might be candidates for non-human model systems.

That's all for now.


Received on Thursday, 11 May 2006 05:18:59 UTC

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