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  Neurodatabase.org Documentation




Upload Overview

PDF version
PDF


Table of Contents

Introduction

If this is your first time submitting, please read the conditions below.

Neurodatabase.org is committed to the following principles governing data sharing for neuroscience:

  • Neurodatabase.org respects and acknowledges the rights of creators and submitters of sharable data. Each dataset and metadata description archived in this database remains the intellectual property of the individuals, laboratories, or organizations responsible for the recording, processing, annotation, and submission of the attributed data. Users of the database must acknowledge this condition and signify that their use of any data from this database will be compliant.
  • We also ask users of shared data to provide appropriate citation of such use, by referencing literature references accompanying sharable data, or by other explicit recognition that includes the names of creators and submitters of data.
  • Neurodatabase.org requires that any shared data obtained from experimental animals conform to recognized standards for animal care, including the Society for Neuroscience Policies as well as standards provided by the U.S. PHS Policy on Humane Care and Use of Laboratory Animals which applies to National Institutes of Health funded research. For research conducted outside the U.S., all policies of the relevant national bodies should be observed as well.
  • We require as well that any shared data obtained from human subjects or patients conform to Society for Neuroscience Policies (scroll to bottom of link) for the use of humans in neuroscience research, as well as other recognized standards for human subject protection and privacy including but not limited to the Common Rule. In particular, all human subject data must be completely de-identified in accordance with privacy requirements of HIPAA part 164.514(b).

Submission of data to neurodatabase.org requires acknowledgement that approval of all co-authors or co-creators has been obtained to grant neurodatabase.org a nonexclusive license to archive and distribute the data and allied metadata, and that any use of experimental animals or human subjects in connection with the generation of these data is compliant with the above requirements.

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Choice of Interfaces

The main interface for uploading data to this repository is a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients.

Java Interface
This implementation, the "Upload Tool", consists of a Java desktop GUI application downloaded and launched on your computer via Java Web Start. To use it you must have Java (runtime) installed. The Upload Tool provides a simple interface for entering your experiment's data and metadata in a format that can be stored and indexed in the neurodatabase.org repository. It will check your submission for completeness and allow you to save your work and resume it later on the same computer. (See system requirements below.)

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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Login is Required

In order to upload an experiment to the database you must have an approved account. This can be verified by entering a username and password to a login window once you start the application.

If you have not yet applied for an account, enter your desired username/password in the boxes to the left and press the "Sign Up" button. You will be asked to enter your basic contact information. Your account request will be submitted for approval to the repository's moderator. Once they approve the request you will receive email.

If you have applied for an account over 2 business days ago and have not received a message from a Neurodatabase.org administrator please email us at neurodatabase.AT.med.cornell.edu.

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Checklist for Submission

Before starting the application to submit your data, you should have:

  • full contact information for the primary contributor, as well as names and institutions of all contributors;
  • full citation information for any literature references to be attached to the submission;
  • identifiers and basic information for all animals/preparations and neurons recorded from;
  • all data to be submitted, either in text format (comma or whitespace-delimited) or in an application such as Excel that is able to provide text data to the clipboard for paste operations.

Click the menu on the left or the links here for more information on the application, or for a description of the data model used.

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Java Interface Requirements

To run the Java Upload 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 Upload 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.

The XML accepted conforms to the BrainML-X protocols (description, and definition) and the data model describing the submission format. The response (receipt acknowledgement or error report) will also conform to the data model schema.

It is possible to just validate the XML instead of actually submitting it. This is done on the text-box web form by checking the "Validate Only" checkbox. When accessing directly using HTTP POST, you can either use '/validate.do' in place of '/upload.do' or add 'validateOnly=true' to the query string.

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Acknowledgements

The BrainML Data Server and Client tools Version 3.0 were developed using Java tools by Sun Microsystems, the Apache-Jakarta Project, and others.

Credits:

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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