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  BrainML Data Server Documentation

Query Overview

PDF version

Table of Contents


There are three primary interfaces for querying data from this repository: a web-based browse interface, a web-based HTML query form, and a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients.

Browse Interface
The browse interface allows access to the database contents without explicit querying. It may be accessed by clicking "Browse Database" in the left-hand navigation bar. Each link on the resulting page represents a data field. Clicking on a link will call up all data submissions with a value set for that field, sorted by that value.

Query Form
The query form implements a structured search paradigm, allowing you to enter one or more values which are searched for in specific metadata fields amongst the submissions. The resulting query is a logical 'AND' of all the conditions entered. All text field queries will be searched as substrings. This form may be accessed by clicking "HTML Form" on the left.

Java Interface
A more interactive experience is available using the Java interface. This implementation, accessed by the "Java Web Start" link on the left, consists of a Java desktop GUI application downloaded and launched on your computer via Java Web Start. To use it you must have the Java runtime installed. (See system requirements in the next section.)

XML Interface
For developers interested in interfacing directly with the data server in software, we provide an XML interface. Ordinarily (see below), this interface is accessed directly over HTTP by a software client other than a browser. However, for testing purposes, a form is provided in which an XML query can be edited and passed to the server for processing. This is accessed by clicking "XML (Expert)" on the left.

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Java Interface Requirements

To run the Java Query Tool, you will need:

  • Internet Ready Computer with Windows XP/2000 (NT and 98 may work), Linux, or Mac OS X. Solaris and IRIX may work.
  • Java 1.4 or above installed. On the Mac, note that Java comes installed on OS X.
  • Browser with MIME mapping for Web Start helper application enabled. Note this is enabled by default in recent Java installations on Windows and Mac; see this page if you have problems, or if you are running Linux/Unix.

The Query Tool has been tested on the following systems:

  • Mac OS X, running Java 1.4 or 1.5.
  • Windows XP with IE 6 or Firefox 1.5 running Java 1.4 or 1.5.
  • Linux with Firefox 1.0+ or Galeon and Java 1.4.
It may run on other systems with Java 1.4 or higher and Web Start installed.

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XML Interface

The XML interface can be accessed through the form as mentioned above, or by direct HTTP POST to URL /query.do under parameter 'xml'. In the latter case, the response will also be in XML, unless the 'format' parameter is also present and set to one of 'html' or 'pdf'.

The XML accepted conforms to the BrainML-X protocols (description, and definition) and the data model describing the submission format. The response will also conform to the data model schema and is identical to that which can be obtained by selecting XML output from one of the browser-based query methods.

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The BrainML Data Server and Client tools were developed using Java tools by Sun Microsystems, the Apache-Jakarta Project, and others.


Original design: Michael Abato, Daniel Gardner
Server Support: Kevin Knuth
Development version 1: Robert DeBellis, Thomas White, Youping Xiao
Development, version 2: Ajit Jagdale, David Markowitz, Adrian Robert
Development, version 3: Eliza Chan, Ajit Jagdale, Adrian Robert

© 2001-2008 Weill Medical College of Cornell University

Additional tools are being developed in collaboration with Bruxton Corporation.

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