Harvard:Biophysics 101/2007/Project: Difference between revisions
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===RS Number -> Disease Name (OMIM)=== | ===RS Number -> Disease Name (OMIM)=== | ||
===RS Number -> | ===RS Number (OMIM) -> PubMed PMIDs=== | ||
* 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) | * 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 18:29, 30 April 2007
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-in-Progress
Project-in-Progress notes have been moved to their own page.
Project Ideas
Project ideas have been moved to their own page.