A new Graphical User Interface for ALFRED:

the ALALlele FREFREquency DDatabase

A new Graphical User Interface for ALFRED:

the ALALlele FREFREquency DDatabase

Nicholas P. Tosches, M.D., M.S.2, Haseena Rajeevan, Ph.D.2, Kei-Hoi Cheung, Ph.D.2, Shannon Stein, B.S.1, Hongyi Deng,

M.S.1, Judith R. Kidd, Ph.D.1, Andrew J. Pakstis, Ph.D.1, Perry L. Miller, M.D., Ph.D.2, Kenneth K. Kidd, Ph.D.1

1Department of Genetics, Yale University School of Medicine

2Center for Medical Informatics, Yale University School of Medicine

http://alfred.med.yale.eduSupported by the U.S. National Science Foundation

ALFRED is Moving in Three Directions:

1. A new GIS-based graphical interface to display population data on a map 2. A new reusable search interface that is based on Extensible Markup Language (XML)3. Expansion of the database by increasing the quantity, quality, and accessibility of data in ALFRED

The GIS-based graphical interface 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. This new interface will enable a user to make selections from the map based on geographic locations and follow the links for population information or allele frequency tables. This will facilitate retrieval of data on all populations in an arbitrarily defined geographic region without prior knowledge of the identities of the populations. Possibilities of further expanding this interface to include displaying chromosomes using ideograms of a karyotype where the typed loci for a population or set of populations can be plotted are being investigated.

The new reusable search interface will enhance the graphical user interface of ALFRED by allowing the display of data in a hierarchical tree format from which the user can format queries, launch searches, and display results. The interface can be reused to display data about populations, chromosomes, loci, etc. by changing the XML message used to construct the interface.

ALFRED currently has information on 917 polymorphic sites typed on at least one population sample and 383 populations typed for at least one polymorphism for a total of 18,299 frequency tables (one sample typed for one site). The database is updated on a daily basis. In addition to the major enhancements described above, several specific retrieval options have been implemented in the past year. For example, the list of publications underlying the data can now be searched by the name of any author and all allele frequency data from a publication quickly retrieved. In addition, researchers can now download data useful for analysis into a single compressed "data dump" file or smaller files of each table separately in the declared XML format. The XML files are updated twice a month.

ALFRED New Home Page

Improvements to the present interface continue with a new tabbed menu for easier navigating

Frequency Search Results in Tabular Format

Frequency Search Results in Graphical Format

GIS-based World Map Interface

Fields from the database can be selected to narrow down a search for specific populations. Here the Geographic Region of Africa was chosen and the resultant

populations displayed on the map (Scalar Vector Graphic).

GIS-based World Map Interface

Once the populations are displayed, a selection tool can be used to further filter the initial selection (selected population points shown in yellow). These populations are then

listed in the text box above and can be forwarded to an additional page which in this instance shows the loci typed for at least one of the populations.

TreeView and TabForm Displays of Population Data

The TreeView and TabForm controls are assembled from an XML message. Data is displayed in a hierarchical tree format (left) from which selections can be made to show

detailed information regarding the selection in a tabbed-form (right). The code that constructs the skeleton of the tree and tabbed-form can be reused to display loci or

chromosome data, for instance, by changing the XML message so that it contains loci or chromosome data selected from the database.

TreeView Control

TabForm Control

XML message generating Tree and TabForm displays (partial)

The data and instructions for the tree view and tabbed-form are contained in this XML message sent by the server to the browser. This message is the result of a

specific query on the database. An alternate query would result in different data and metadata but would reuse the same skeletal TreeView and TabForm controls.

XML-based Query Interface

Individual fields can be selected and combined as a Boolean expression in order to filter a complex search of Frequency data. The query is constructed in XML, sent to the server where a standard SQL query is issued to the database. The results are then sent back to the browser in the form of

XML and can be displayed in various formats such as HTML, XML and Text. These results can then be copied and pasted into an Excel spreadsheet if desired.

The The ALFREDALFRED Team TeamThe The ALFREDALFRED Team TeamSenior FacultySenior FacultyKenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.)Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.)Perry Miller, M.D., Ph.D., Director of Center for Medical InformaticsPerry Miller, M.D., Ph.D., Director of Center for Medical Informatics

CuratorsCuratorsHongyi Deng, M.S., Research AssociateHongyi Deng, M.S., Research AssociateShannon Stein, B.S., Research AssistantShannon Stein, B.S., Research Assistant

ProgrammersProgrammersHaseena Rajeevan, Ph. D., Systems ProgrammerHaseena Rajeevan, Ph. D., Systems ProgrammerNicholas P. Tosches, M.D., Associate Research ScientistNicholas P. Tosches, M.D., Associate Research ScientistLyudmila Druskin, M.D., Postdoctoral Fellow and AssociateLyudmila Druskin, M.D., Postdoctoral Fellow and Associate

ConsultantsConsultantsAndrew J. Pakstis, Ph. D., Research ScientistAndrew J. Pakstis, Ph. D., Research ScientistJudith R. Kidd, Ph. D., Research ScientistJudith R. Kidd, Ph. D., Research ScientistKei-Hoi Cheung, Ph. D., Assistant ProfessorKei-Hoi Cheung, Ph. D., Assistant Professor