Harvard:Biophysics 101/2007/Project

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(Disease Name -> Useful Patient Info (Medical search engines))
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===RS Number -> Disease Name (OMIM)===
===RS Number -> Disease Name (OMIM)===
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===RS Number -> Disease Name (PubMed)===
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===RS Number (OMIM) -> PubMed PMIDs===
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* Resmi
+
====PubMed PMIDs -> Mesh Terms====
 +
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-24|code]] (1) parses OMIM XML to (2) get PubMed PMIDs to (3) get Mesh Terms
-
====Mesh Terms -> Disease Name (in-house code, prevalence algorithm)====
+
 
 +
=====Mesh Terms -> Disease Name (in-house code, prevalence algorithm)=====
* Deniz
* Deniz
=====Disease Name -> Useful Patient Info (Medical search engines)=====
=====Disease Name -> Useful Patient Info (Medical search engines)=====
* Deniz:  
* Deniz:  
-
* Tiff: [[TChan/Notebook/2007-4-24|code]] (1) displays relevant URLs, (2) collects lists of drugs, clinical trials, experts, etc.
+
* Tiff: [[TChan/Notebook/2007-4-24|code]] (1) displays relevant URLs, (2) returns lists of drugs, clinical trials, experts, etc.
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-5|code]] (1) displays PubMed reviews
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-5|code]] (1) displays PubMed reviews
 +
 +
 +
=====Disease Name -> PMIDs=====
 +
* (Uncertain about whether or not this was the point of the code?)
 +
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-19|code]] returns Mesh Terms
=Path 2: Using GenBank and PolyPhen=
=Path 2: Using GenBank and PolyPhen=

Revision as of 21:29, 30 April 2007

Biophysics 101: Genomics, Computing, and Economics

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Contents

Overview

  • Project Goal: To develop tools to aid in analysis of personal DNA sequences.

We would like to develop software and documentation that will help people get from sequence to diagnosis. At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise. We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon. Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.


Path 1: Using OMIM

Sequence -> RS Number (BLAST SNP)

  • Xiaodi

RS Number -> Mesh Terms (PubMed)

  • Cynthia

RS Number -> Disease Name (OMIM)

RS Number (OMIM) -> PubMed PMIDs

PubMed PMIDs -> Mesh Terms

  • Resmi: code (1) parses OMIM XML to (2) get PubMed PMIDs to (3) get Mesh Terms


Mesh Terms -> Disease Name (in-house code, prevalence algorithm)
  • Deniz
Disease Name -> Useful Patient Info (Medical search engines)
  • Deniz:
  • Tiff: code (1) displays relevant URLs, (2) returns lists of drugs, clinical trials, experts, etc.
  • Resmi: code (1) displays PubMed reviews


Disease Name -> PMIDs
  • (Uncertain about whether or not this was the point of the code?)
  • Resmi: code returns Mesh Terms

Path 2: Using GenBank and PolyPhen

Sequence -> Gene Name (BLAST)

  • Zach

Gene Name -> Mutations (GenBank)

  • Xiaodi

Gene Name -> ??? (PolyPhen)

  • Mike

Mutations -> Disease Name (OMIM)

  • Xiaodi

Disease Name -> Useful Patient Info (Medical search engines)

  • Deniz and Tiff


Diagram

Project Diagram

Project-in-Progress

Project-in-Progress notes have been moved to their own page.

Project Ideas

Project ideas have been moved to their own page.
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