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ALFRED: the AL lele FRE quency D atabase

ALFRED: the AL lele FRE quency D atabase. Kenneth K. Kidd and the ALFRED Team. Department of Genetics and Center for Medical Informatics Yale University School of Medicine. Supported by the U.S. National Science Foundation. ALFRED Home Page http://alfred.med.yale.edu/. Overview.

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ALFRED: the AL lele FRE quency D atabase

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  1. ALFRED: the ALlele FREquency Database Kenneth K. Kidd and the ALFRED Team Department of Genetics and Center for Medical Informatics Yale University School of Medicine Supported by the U.S. National Science Foundation

  2. ALFRED Home Pagehttp://alfred.med.yale.edu/

  3. Overview ALFRED,theALleleFREquencyDatabase, is designed to serve as a central repository of frequencies for DNA sequence variation in the human genome - curated and cross referenced to molecular and ethnographic databases. Who’s Looking at ALFRED? ALFRED receives hits from approximately 450 unique hosts per month.

  4. ALFRED System Overview Input Data Sources Kidd Lab Data HAPLO Program PhenoDB Collaborators Others (e.g. literature) Data Curation and Integrity Check External Data Resources (dbSNP, HGVBase) Client Browser IIS Web Server (ASP) ODBC ALFRED (Oracle) Public JDBC Curators Tomcat Server (java, servlet, jsp) Client Browser Windows 2000 Server

  5. New Features - Summary • New Homepage options. • New “additional info” button. • XML Dump (with DTD). • Graphical overview for populations per site and sites per population. • More detailed allelic definitions. • Increased flexibility in frequency search results.

  6. 1. New Homepage options • Ethics Statement • Statement regarding the ethical issues pertaining to the use of ALFRED data. • Links • Links to other databases containing allele frequency data on specific populations • If you are aware of any useful links not included in this list, please let us know • Downloads • Options for downloading ALFRED data

  7. 2. New “Additional Info” button • The icon will be used throughout ALFRED whenever additional information can be provided. • Example #1: Click here to get additional info

  8. Example #2: Click here to get additional information

  9. 3. XML Dump 1st A Document Type Definition (DTD) has been developed for importing and exporting ALFRED data in XML format. 2nd Currently, twice a month the staff generate two compressed versions of the “data dump” of the entire contents of ALFRED in the declared XML format. 3rd The data dump’s include either all relevant information (including descriptions) or only the data relevant to statistical analyses. 4th Researchers can download either version by following the “Download” link on the main page.

  10. 4. Graphical Overview A. Populations per site • Ordered by number of population’s typed (Multiple different samples of a population are not distinguished in this summary)

  11. B. Sites per population • Ordered by number of sites typed (Multiple different samples of a population are not distinguished in this summary)

  12. 5. Allelic Definitions When possible we provide 10 to 15 nucleotide sequences upstream and downstream of the nucleotide variants (polymorphic site)

  13. 6. Increased Flexibility • From graphical and tabular formats of the frequency search results, users can link to both population information and sample information • For example: Clicking here will give you population information Clicking here will give you sample information

  14. Table Summary NumbersAs of April 15, 2003 The number of frequency tables has increased from 6,667 to 11,505 in the last year

  15. What’s in ALFRED’s Future? • Electronic submission of allele frequency data by researchers • We encourage researchers to submit their data to ALFRED. This is YOUR database; everyone will benefit from more complete data. Please contact ALFRED staff who will supply an appropriate template for your submission. • New Public Interface • More search options • Including searching for citations • User-friendly graphical interface • Interactive geographic map • Interactive chromosome map

  16. Interactive Geographic Map • The geographic map is generated dynamically by querying geographical and population data stored in the database to create an SVG (scalar vector graphic, which is an XML-based markup language for manipulating graphical data) document which is displayed in the browser. • As the user moves the mouse over the map, geographical and population information is displayed.

  17. An Example of the Prototype When your pointer is hovering above a population, data pertaining to that population is displayed The point on the map that the mouse is pointing to. List of populations in the selected box

  18. ALFRED:TheALleleFREquencyDatabase http://alfred.med.yale.edu/ Suggestions and comments are welcome.

  19. The ALFRED Team Senior Faculty Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.) Perry Miller, M.D., Ph.D., Director of Center for Medical Informatics Curators Hongyi Deng, M.S., Research Associate Shannon Stein, B.S., Research Assistant Programmers Haseena Rajeevan, Ph. D., Systems Programmer Nicholas P. Tosches, M.D., Associate Research Scientist Lyudmila Druskin, M.D., Postdoctoral Fellow and Associate Consultants Andrew J. Pakstis, Ph. D., Research Scientist Judith R. Kidd, Ph. D., Research Scientist Kei-Hoi Cheung, Ph. D., Assistant Professor

  20. The ALFRED Advisory Board • Ken Weiss, Ph.D., Chair • Guido Barbujani, Ph.D. • Francesc Calafell, Ph.D. • Jonathan Friedlaender, Ph.D. • Michael Gribskov, Ph.D. • Bartha Knoppers, Ph.D. • Jeffrey C. Long, Ph.D. • Partha Majumder, Ph.D. • Dennis O'Rourke, Ph.D.

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