ALFRED ALFRED: the ALlele FREquency Database ALFRED: the A AA ALlele F FF FREquency D DD 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

ALFRED Home Page ALFRED Home Page

Overview ALFRED, the ALlele FREquency Database, 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.

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

New Features - Summary 1. New Homepage options. 2. New “additional info” button. 3. XML Dump (with DTD). 4. Graphical overview for populations per site and sites per population. 5. More detailed allelic definitions. 6. Increased flexibility in frequency search results.

1. New Homepage options n Ethics Statement –Statement regarding the ethical issues pertaining to the use of ALFRED data. n 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 n Downloads –Options for downloading ALFRED data

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

n Example #2: Click here to get additional information

3. XML Dump 1 st A Document Type Definition (DTD) has been developed for importing and exporting ALFRED data in XML format. 2 nd 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. 3 rd The data dump’s include either all relevant information (including descriptions) or only the data relevant to statistical analyses. 4 th Researchers can download either version by following the “Download” link on the main page.

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

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

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

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

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

What’s in ALFRED’s Future? n 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. n New Public Interface –More search options Including searching for citationsIncluding searching for citations –User-friendly graphical interface –Interactive geographic map –Interactive chromosome map

Interactive Geographic Map n 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. n As the user moves the mouse over the map, geographical and population information is displayed.

n 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

ALFRED: The ALlele FREquency Database Suggestions and comments are welcome.

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

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.