eXtensible Neuroimaging Archive Toolkit (XNAT)

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eXtensible Neuroimaging Archive Toolkit (XNAT)

• Washington University Neuroinformatics Group

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What is XNAT?

• An environment for developing experimental data
  archives (data store archiving tools).
• Data store
• relational database for non-image data
• specified directory structure for image data.
• Archiving tools
• Web application for uploading, entering,
  searching, visualizing, and otherwise exploring
  data.
• Command-line tools for batch handling data.

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Why do we need XNAT (or something like it)?
Assessments
Metadata
Processed images
Derived data
Demographics
Raw images
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Why do we need XNAT (or something like it)?
Assessments
Raw
Processed
Subject
MR Session
Derived
Demographics
Metadata
Secure User Interface
Integrated Data Store
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What is XML Schema?

• XML Schema is a language for describing the
  structure and contents of an XML document.

XML
XML Schema
ltClassgtBirdlt/Classgt
ltxselement nameClass"gt ltxssimpleTypegt
ltxsrestriction base"xsstring"gt
ltxsenumeration value"Bird"/gt
ltxsenumeration value"Mammal"/gt
ltxsenumeration value"Reptile"/gt
ltxsenumeration value"Fish"/gt
lt/xsrestrictiongt lt/xssimpleTypegt lt/xselementgt
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XML Schema is the lingua franca for data exchange

• Data exchange requires standard open data
  formats.
• XML Schema is the language in which these open
  formats are defined.
• Many fields (e.g. genetics, medicine) have
  already implemented XML Schema-based standards.
• So an application that automatically archives,
  searches, and displays XML Schema-based data
  would be really useful

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Welcome to XNAT
Data Documents
Database Schema
Java Classes
HTML Pages
CRATE TABLE table ( name, VARCHAR(50),
idMethod, VARCHAR(50), DEFAULT 'null,
type, VARCHAR(50), ID INT UNSIGNED, NOT NULL
AUTO_INCREMENT, PRIMARY KEY (ID) ) CREATE
TABLE table_column ( name VARCHAR(50)
javaName VARCHAR(50) primaryKey VARCHAR(50)
XML Schema
public class Experiment extends
org.cnl.cnda.om.BaseExperiment implements
Persistent public static final long
MILLIS_IN_DAY 86400000 public static long
getDays(Calendar c1, Calendar c2)
long time1 c1.getTime().getTime()
lt?xml version"1.0" encoding"UTF-8"?gt ltxsschema
xmlnsxnat"xnat.xsd" xmlnsxs"http//www.w3.org/
2001/XMLSchema" elementFormDefault"qualified"
attributeFormDefault"unqualified"gt ltxselement
name"Database"gt ltxsannotationgt ltxsappinfogt ltxna
tdbinfo database.name"CNDA" database"MYSQL"/gt lt
/xsappinfogt lt/xsannotationgt lt/xselementgt ltxsel
ement name"wm_mod_scheltens"gt ltxscomplexTypegt ltx
ssequencegt ltxselement ref"experiment"/gt ltxsele
ment name"session_id" type"xsstring"/gt ltxselem
ent name"assessment"gt
lt!DOCTYPE html PUBLIC "-//W3C//DTD HTML
3.2//EN"gt page.setTitle("CNDA -- Integrating
the Neurouniverse") page.setLinkColor(ui.alink)
page.setVlinkColor(ui.vlink) lthtmlgt ltbodygt ltta
ble border"0"gt lttrgt lttd bgcolor"336600"gt

lt?xml version"1.0" encoding"UTF-8"?gt ltsession
id"050202_vc1000"gt ltsubject map_num"0001"
lab_id"0001"gt ltagegt78lt/agegt
ltgendergtmalelt/gendergt lthandednessgtrightlt/h
andednessgt ltcohortgtADRClt/cohortgt
lt/subjectgt ltsession_infogt
ltacq_dategt5/1/2002lt/acq_dategt ltpigtRandy
Bucknerlt/pigt ltoperatorgtDan
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This XML schema structure
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becomes this database table
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More complicated elements
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yield more complicated tables
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XNAT is a three-tiered architecture
Data Store
User Interface
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The web application emphasizes usability and
quality control

• Clean user interface
• Search and download, no statistics.
• Quality control

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Security is pretty important too

• Password protected login and session timeout.
• Secondary password and IP-address restriction on
  most sensitive data.
• User access privileges set by data type and meta
  data values (e.g. Dan can view but not edit R
  Buckners fMRI data.)
• Signed approval on new user accounts and changes
  to existing accounts.
• Logins, queries, and downloads written to daily
  log files.

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XNAT is completely open source

• All of XNATs dependencies are open source.
• Turbine (Apache Jakarta) provides a servlet
  based framework that allows developers to
  quickly build web applications.
• ImageJ (NIH) provides the foundation for the
  image viewer.
• MySQL and PostgreSQL databases are supported.

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XNAT improvements are on the way

• Data quarantine
• Data history
• Direct XML?? Database exchange
• Improved image viewer with subcortical
  segmentation and fMRI plugins.
• Improved mechanisms for controlling display of
  data.
• Improved mechanisms for validating user input
  from web forms.