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HDD Access Release Notes - October 2012

HDD Access Release Notes

October 2012

This is the October 2012 release of terminology content for HDD Access – the public version of the 3M™ Healthcare Data Dictionary (HDD).  There is no new software release this month.  The release notes cover the following topics:

  • Supported technologies
  • System requirements
    • Operating system, hardware, software, network resources
    • Compatibility with earlier releases
    • Known issues
    • Documentation
    • Support
    • Content integrity
    • Licenses
Content Version 3

HDD Access terminology content version 3 contains 216,722 unique concepts.  This release has added respiratory disorders and findings to cardiovascular problems, and is intended to provide a subset of terminology content to help the user get familiar with HDD Access software.  A sampling of other domains, such as allergy, medication, language and religion, is also included.  You can see the list of domains in the left sidebar (“Search Domains”) of the HDD Access browser.  Clicking the triangle to the left of each domain will open sub-domains.  There is also content created to help users test and understand the HDD Access Web Services API v1.1 that was released in September 2012.

Standard terminologies included are:

  • ICD-9-CM Diagnoses (codes and hierarchies)
  • ICD-9-CM Procedures (codes and hierarchies)
  • ICD-10-CM (codes and hierarchies)
  • ICD-10-PCS (codes but not attributes/hierarchies)
  • HCPCS Level II
  • HCPCS Modifiers
  • MS-DRG
  • TRICARE/CHAMPUS MS-DRG
  • APC
  • MS-DRG MDC
  • TRICARE/CHAMPUS MS-DRG MDC

HDD Access content will be incremented monthly in subsequent releases.

HDD Access Table Row Count September 2012(Content v2) Row Count October 2012(Content v3)
CONCEPT 215,658 216,722
CONCEPT_RELATION 442,522 444,482
RSFORM  1,126,417  1,129,357
RSFORM_CONTEXT  1,421,899 1,710,112

Installer Version 1.2

The HDD Access installer v1.2 was released September 2012 and will install content v2, database v1.2, browser v1.2 and API v1.1, for both Linux and Windows.

In Windows, after installing HDD Access, the user can see the following menu items in the Windows Start Menu → All Programs→ HDD Access:

  • Create Search Index
  • HDD Access Browser
  • HDD Access Uninstaller
  • Shutdown HDD Access
  • Start HDD Access
  • Update Content

Current users who have installed the September 2012 HDD Access on Windows can update the content to v3 by clicking the menu option “Update Content”.  You will see the following:

Clicking on “here” will bring you to the HDD Access content and documentation download page.  Select “HDD Access terminology content v3 (UPDATE)” and save the file in your system, then come back to the HDD Content Update dialog window to browse for the file and click “Update” to complete the process.

For Linux CentOS, while the server is running, current users who have installed the September 2012 HDD Access can see the “Update Content” function in the Applications Menu → Other:

  • Browse
  • Create Search Index
  • Load Content
  • Shutdown Server
  • Start Server
  • Update Content

New users who have not installed HDD Access previously should install the current release and then follow the same process to update the content to v3.

Note that you should rebuild the search index for the HDD Access browser, using the “Create Search Index” function, after you have updated the content.

Database Version 1.2

HDD Access users will have the option of installing HDD Access to operate under any of the following database management systems (DBMS).  Each DBMS is listed with the version with which it was tested.  Previous or later versions may also work but have not been tested:

  • Oracle 11g
  • MySQL 5.1
  • H2 1.3

A denormalized table named PREFERREDNAME to hold thepreferred 3M Display Name(Context_NCID 45821, Preferred_Score 0) ofactiveconcepts (Status_NCID 1024) has been added in the September 2012 release to improve performance of the HDD Access browser and the HDD Access Web Services API.

For October 2012, the database remains at v1.2 with no changes.

Browser Version 1.2

The HDD Access browser has the functionalities listed below:

  • Search by text string – this uses HyperSearch, a heuristic search engine developed by 3M, which searches for synonyms, abbreviations, abbreviation expansions, inflectional variants, spelling variations and word order variations of the input string.
  • Constrain text search by domain
  • Search by NCID (Numeric Concept IDentifier)

In the September 2012 release, a link has been added in the HDD Access menu to (re)create the search engine index – the “Create Search Index” function (see the section on Installer Version 1.2) – whenever the user wishes.  Note that this should be done every time the HDD Access content is updated.  There was a minor bug fix to HyperSearch, and the browser now shows the version of the terminology content it is accessing.  Lastly, the information shown for each concept has been enhanced.

For October 2012, the browser remains at v1.2 with no changes.

The HDD Access browser has been tested with Mozilla Firefox 14, Google Chrome 21, and Internet Explorer 8 and 9.  Javascript is required by the HDD Access browser.

HDD Access Web Services Application Programming Interface Version 1.1

The HDD Access Web Services API v1.1, released in September 2012, is designed to make it easier to interface the HDD Access terminology service with other client applications. The API supports the following functions:

  • HL7 CTS v1.2 Web Services API

HL7 CTS is a standard that specifies functions supported by terminology services.  The current version of the HDD Access Web Services API supports a subset of HL7 CTS v1.2 functions, as described in the help documentation.

  • 3M Web Services API

3M Web Services API is designed to complement the functionality provided by the HL7 CTS Web Services API.  The 3M services are designed to support functionality specific to HDD Access and to improve performance.  They are described in the help documentation.

For October 2012, the API remains at v1.1 with no changes.

Supported Technologies

The HDD Access database supports the following technologies and has been tested with the following application servers:

  • Apache Tomcat 7.0.27 (or later).

System Requirements

Operating System

The current version of HDD Access installer installs the HDD Access software to run on any of the following operating systems:

  • Microsoft  Windows 7 32-bit
  • Microsoft Windows Server 2008 R2 64-bit
  • CentOS Linux 6.3 32-bit or 64-bit

The software may also work on the following operating systems, but was not tested extensively: Microsoft Windows Server 2012 64-bit, Windows XP 32-bit, Windows 7 64-bit and other Linux distributions.

Advanced users may deploy the WAR file distribution of HDD Access software on Apache Tomcat on Microsoft Windows, Linux or other operating systems.

Hardware

Minimum hardware requirements for HDD Access are:

  • Processor: 2 GHz
  • Memory (RAM): 3 GB
  • Disk space: 6 GB of free disk space

Software

HDD Access requires the software listed below:

  • Oracle Java (JDK or JRE) 1.6 (or later)
  • Database:
    • Oracle  11g (or later)
    • MySQL 5.1 (or later)
    • H2 version 1.3 (or later) – this will be installed for you if you choose “simple installation”
    • Java application server:
      • Apache Tomcat 7.0.27 (or later) – this will be installed for you if you choose “simple installation”

Network resources

‘Simple installation’ in the installer configures the installed Apache Tomcat server software to use network ports 8080 and 8005 by default.  Note that the September 2012 release notes also included port 8009; that is incorrect.  These ports can be changed by the user during installation through the installer program, or after installation manually in the configuration file.

Installation and upgrade

Installation

HDD Access is released as a graphical installer for Windows and Linux, a command-line installer for Linux, and a binary (WAR file) distribution that can be installed on Windows or Linux.  For the current release, the HDD Access content v2 (from the September 2012 release) is included in all these distributions, and also as separate CSV (comma-separated values) files.  The October 2012 v3 content is provided in CSV and zipped XML format – the latter, “HDD Access terminology content v3 (UPDATE)”, is used to update the content of the installed HDD Access database (see the section on Installer Version 1.2).

The graphical and the command line installers provide step-by-step installation instructions.

Installation instructions for the binary (WAR file) distribution are provided in the INSTALL.txt file within the archive file, and are also included in the HDD Access documentation library.

The CSV files are provided so that the users may open and use the terminology content with any application that can open these files (text editors, Microsoft Excel or Access, statistical analysis software, etc.).  Please read the HDD Access Documentation Library to understand the four core terminology tables and how to use them.

Upgrade

Users on the September 2012 release do not need to upgrade;please follow the “Update Content” instructions in the section on Installer Version 1.2 to bring your content up to v3.  Users on the August 2012 release should uninstall the August 2012 release and install the current release then also follow the “Update Content” instructions in the section on Installer Version 1.2 to bring your content up to v3.  If you are on the August 2012 release and proceed to install the current release without uninstalling the August 2012 release, and you choose to install the files in the same directory, the previous version will be overwritten. Note that if you installed using MySQL or Oracle the database will not be overwritten by the installer.  You must manually remove the old database tables before installing the current version, or provide a new database or schema location during the installation.  Please note that all the local content modifications will be lost if you choose to replace the previous installation with the current version.

Compatibility with Earlier Releases

The current release of the software depends on terminology content which is v2 and above. It is not compatible with content v1.Installing the current content will involve overwriting of the previous content versions.Any local content modifications in a previously installed version will be lost.

Known Issues

  1. If you choose ‘simple install’ and network ports 8080 and 8005 are not available, the Apache Tomcat server will fail to start.  You may make these ports available or manually change the port numbers used by Apache Tomcat to overcome this issue. This can be done when you run the installer, or after the installation. If the port numbers are modified, you will need to modify the tomcatPort variable in the following “.bat” files in Windows or “.sh” files in Linux:  hddBrowser, hddLoad, hddCreateIndex, and hddUpdate in the [HDDAccess]\hddServer\bin directory to add the new port to the URL and then manually start Tomcat.  Open a web browser and visit http://domain:port/load (the default is http://localhost:8080/load) to load the terminology content into your database.
  2. Text search in the HDD Access Browser uses HyperSearch. The time it takes for HyperSearch searches increases exponentially with the number of words (tokens) in the input string. This is a known limitation of HyperSearch.
  3. A new issue has surfaced since the September 2012 release:
    If you have installed the software on Linux and attempt to start Tomcat from one of the shortcuts (sym links), the page may remain blank with no action occurring. This is in order to allow you to place the hddFiles directory in a location other than the Tomcat bin directory. In order to avoid this problem, you must either start the Tomcat server only from the bin directory (not using the shortcut), or setup the environment variable i.e. export HDD_FILE_DIR="<install_directory>/HDDAccess/hddServer/bin/hddFiles/" (where install_directory is the absolute path to the installation directory).

Documentation

Documentation for HDD Access software and terminology content is available athttp://www.hddaccess.com.

Support

HDD Access terminology content and software are published as-is without warranties or support.  Community support may be available through the HDD Access discussion forums athttp://www.hddaccess.com.

Content Integrity

All the downloadable packages (installer, binary, source, content files and documentation) have their MD5 checksum published on the HDD Access website. Users may verify the integrity of the downloaded files by calculating their MD5 checksums using a checksum application and comparing them with the checksums published on the website.

Users may validate the number of rows that were loaded into the four core tables in their database by comparing them against the row counts published at the beginning of this document.

Users may also use the web-based HDD Access online browser athttp://search.hddaccess.com/to manually browse and search against the read-only master version. The HDD Access Browser provides read-only access to HDD Access content, and can be used for comparing content in your local database against the master version.

Licenses

HDD Access software is open source under the Apache License, version 2.0.  Source code is available fromhttp://www.hddaccess.com.

HDD Access terminology content is published under the HDD Content Download License (you can view it athttp://www.hddaccess.com/content_license/).  You will need to accept the license during the download process for the HDD Access installer to create the database and load the terminology content on your system.

Third-party software files included in the HDD Access software are released under their respective licenses by their authors.  They are listed below.  You can also view the list of third-party software files and their respective licenses during the installation process.

The JAR files listed below are included in the [Web_application_root]/WEB-INF/lib directory in the binary builds. They may be located in other appropriate directories in the source distribution. Other files may be in other relevant directories.

1.      Public Domain

Third Party File Copyright Notice
antlr-2.7.6.jar http://www.antlr2.org/license.html
aopalliance-1.0.jar http://aopalliance.sourceforge.net/

 2.      Apache 2.0

http://www.apache.org/licenses/LICENSE-2.0.txt

Third Party File Copyright Notice
cglib-nodep-2.2.2.jar ASM: a very small and fast Java bytecode manipulation frameworkCopyright (c) 2000,2002,2003 INRIA, France TelecomAll rights reserved.
gson-1.7.1.jar http://code.google.com/p/google-gson/
commons-beanutils-1.8.3.jar Apache Commons BeanUtilsCopyright 2000-2010 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-codec-1.5.jar Apache Commons CodecCopyright 2002-2011 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).src/test/org/apache/commons/codec/language/DoubleMetaphoneTest.java contains test data from http://aspell.sourceforge.net/test/batch0.tab.Copyright (C) 2002 Kevin Atkinson (This email address is being protected from spambots. You need JavaScript enabled to view it.). Verbatim copying and distribution of this entire article is permitted in any medium, provided this notice is preserved.
commons-collections-3.2.1.jar Apache Commons CollectionsCopyright 2001-2008 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-dbcp-1.3.jar Apache Commons DBCPCopyright 2001-2010 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-digester-2.1.jar Apache Commons DigesterCopyright 2001-2010 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-fileupload-1.2.2.jar Apache Commons FileUploadCopyright 2002-2010 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-io-2.1.jar Apache Commons IOCopyright 2002-2011 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-lang-2.4.jar Apache Commons LangCopyright 2001-2008 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
commons-pool-1.5.6.jar Apache Commons PoolCopyright 2001-2011 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
joda-time-1.6.jar NOTICE file corresponding to section 4d of the Apache License Version 2.0This product includes software developed by Joda.org (http://www.joda.org/).
log4j-1.2.16.jar Apache log4jCopyright 2007 The Apache Software FoundationThis product includes software developed atThe Apache Software Foundation (http://www.apache.org/).
flexjson-2.1.jar http://flexjson.sourceforge.net/
commons-lang3-3.1.jar Apache Commons LangCopyright 2001-2011 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).This product includes software from the Spring Framework,under the Apache License 2.0 (see: StringUtils.containsWhitespace())
Apache Lucene Copyright © 2011-2012 The Apache Software Foundation, Licensed under the Apache License, Version 2.0.http://lucene.apache.org/core/
lucene-core-3.6.0.jar Apache LuceneCopyright 2012 The Apache Software FoundationThis product includes software developed byThe Apache Software Foundation (http://www.apache.org/).
tiles-template-2.2.2.jar Tiles - Template Technologies SupportCopyright 2001-2010 Apache Software FoundationThis product includes software developed atThe Apache Software Foundation (http://www.apache.org/).
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Third Party Files:org.springframework.roo.annotations-1.2.1.RELEASE.jarspring-aop-3.0.0.RC3.jarspring-asm-3.1.0.RELEASE.jarspring-context-3.1.0.RELEASE.jarspring-context-support-3.1.0.RELEASE.jarspring-js-resources-2.2.1.RELEASE.jar http://www.springsource.com/© Copyright 2012 SpringSource, a division of VMware.  All Rights Reserved.
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3.      Berkeley Software Distribution (BSD) 2-Clause

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Third Party File:hamcrest-core-1.1.jar
http://code.google.com/p/hamcrest/source/browse/trunk/hamcrest-java/LICENSE.txt
Copyright (c) 2000-2006, www.hamcrest.org
All rights reserved.Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of Hamcrest nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

4.      Berkeley Software Distribution (BSD) 3-Clause

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Third Party Files:asm-3.3.1.jarasm-commons-3.3.1.jarasm-tree-3.3.1.jarhttp://asm.ow2.org/license.htmlCopyright (c) 2000-2011 INRIA, France TelecomAll rights reserved.Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.3. Neither the name of the copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESSINTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Third Party Files:jquery.dataTables.min-1.9.1.jsjquery.dataTables-1.8.2.jsjquery.dataTables-1.9.1.jshttp://datatables.net/license_bsdCopyright (c) 2008-2012, Allan Jardine
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  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of Allan Jardine nor SpryMedia may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

5.      Berkeley Software Distribution (BSD) Variant

Third Party File:dom4j-1.6.1.jarhttp://dom4j.sourceforge.net/dom4j-1.6.1/license.htmlRedistribution and use of this software and associated documentation ("Software"), with or without modification, are permitted provided that the following conditions are met:
  1. Redistributions of source code must retain copyright statements and notices. Redistributions must also contain a copy of this document.
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THIS SOFTWARE IS PROVIDED BY METASTUFF, LTD. AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL METASTUFF, LTD. OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.Copyright 2001-2005 (C) MetaStuff, Ltd. All Rights Reserved.

6.      Common Development and Distribution License (CDDL) 1.0

http://opensource.org/comment/983

Third Party File:jstl-impl-1.2.jarhttp://glassfish.java.net/public/CDDL+GPL.htmlHDD Access elects to include this software in this distribution under the CDDL licensehttp://repo1.maven.org/maven2/org/glassfish/web/jstl-impl/1.2/jstl-impl-1.2.pomCopyright (c) 1997-2011 Oracle and/or its affiliates. All rights reserved.The contents of this file are subject to the terms of either the GNU General Public License Version 2 only ("GPL") or the Common Development and Distribution License("CDDL") (collectively, the "License").  You may not use this file except in compliance with the License.  You can obtain a copy of the License at https://glassfish.dev.java.net/public/CDDL+GPL_1_1.html or packager/legal/LICENSE.txt.  See the License for the specific language governing permissions and limitations under the License.When distributing the software, include this License Header Notice in each file and include the License file at packager/legal/LICENSE.txt.GPL Classpath Exception:Oracle designates this particular file as subject to the "Classpath" exception as provided by Oracle in the GPL Version 2 section of the License file that accompanied this code.Modifications:If applicable, add the following below the License Header, with the fields enclosed by brackets [] replaced by your own identifying information:"Portions Copyright [year] [name of copyright owner]"Contributor(s):If you wish your version of this file to be governed by only the CDDL or only the GPL Version 2, indicate your decision by adding "[Contributor]elects to include this software in this distribution under the [CDDL or GPL Version 2] license."  If you don't indicate a single choice of license, a recipient has the option to distribute your version of this file under either the CDDL, the GPL Version 2 or to extend the choice of license to its licensees as provided above.  However, if you add GPL Version 2 code and therefore, elected the GPL Version 2 license, then the option applies only if the new code is made subject to such option by the copyright holder.

7.      Common Development and Distribution License (CDDL) 1.1

http://glassfish.java.net/public/CDDL+GPL_1_1.html

Third Party Files:jersey-spring-1.12.jarjersey-core-1.12.jarjersey-server-1.12.jarjersey-servlet-1.12.jarhttp://glassfish.java.net/public/CDDL+GPL_1_1.htmlHDD Access elects to include this software in this distribution under the CDDL licensehttp://repo1.maven.org/maven2/com/sun/jersey/contribs/jersey-spring/1.12-b01/jersey-spring-1.12-b01.pomhttp://repo1.maven.org/maven2/com/sun/jersey/jersey-core/1.12/jersey-core-1.12.pomhttp://repo1.maven.org/maven2/com/sun/jersey/jersey-server/1.12/jersey-server-1.12.pomhttp://repo1.maven.org/maven2/com/sun/jersey/jersey-servlet/1.12/jersey-servlet-1.12.pomCopyright (c) 1997-2011 Oracle and/or its affiliates. All rights reserved.The contents of this file are subject to the terms of either the GNU General Public License Version 2 only ("GPL") or the Common Development and Distribution License("CDDL") (collectively, the "License").  You may not use this file except in compliance with the License.  You can obtain a copy of the License at https://glassfish.dev.java.net/public/CDDL+GPL_1_1.html or packager/legal/LICENSE.txt.  See the License for the specific language governing permissions and limitations under the License.When distributing the software, include this License Header Notice in each file and include the License file at packager/legal/LICENSE.txt.GPL Classpath Exception:Oracle designates this particular file as subject to the "Classpath" exception as provided by Oracle in the GPL Version 2 section of the License file that accompanied this code.Modifications:If applicable, add the following below the License Header, with the fields enclosed by brackets [] replaced by your own identifying information:"Portions Copyright [year] [name of copyright owner]"Contributor(s):If you wish your version of this file to be governed by only the CDDL or only the GPL Version 2, indicate your decision by adding "[Contributor]elects to include this software in this distribution under the [CDDL or GPL Version 2] license."  If you don't indicate a single choice of license, a recipient has the option to distribute your version of this file under either the CDDL, the GPL Version 2 or to extend the choice of license to its licensees as provided above.  However, if you add GPL Version 2 code and therefore, elected the GPL Version 2 license, then the option applies only if the new code is made subject to such option by the copyright holder.

8.      Eclipse Public License (EPL) 1.0

http://opensource.org/licenses/eclipse-1.0.php

Third Party Files:aspectjrt-1.6.12.jaraspectjweaver-1.6.12.jarThe Eclipse Foundation makes available all content in this distribution ("Content"). Unless otherwise indicated below, the Content is provided to you under the terms and conditions of the Eclipse Public License Version 1.0 ("EPL"). A copy of the EPL is available at http://www.eclipse.org/legal/epl-v10.html. For purposes of the EPL, "Program" will mean the Content.If you did not receive this Content directly from the Eclipse Foundation, the Content is being redistributed by another party ("Redistributor") and different terms and conditions may apply to your use of any object code in the Content. Check the Redistributor's license that was provided with the Content. If no such license exists, contact the Redistributor. Unless otherwise indicated below, the terms and conditions of the EPL still apply to any source code in the Content and such source code may be obtained at http://www.eclipse.org.
Third Party File:h2-1.3.168.jarhttp://www.h2database.com/html/license.htmlHDD Access elects to include this software in this distribution under the EPL licenseH2 is dual licensed and available under a modified version of the MPL 1.1 (Mozilla Public License) or under the (unmodified) EPL 1.0 (Eclipse Public License). The changes to the MPL areunderlined. There is a license FAQ for both the MPL and the EPL, most of that is applicable to the H2 license as well.
  • You can use H2 for free. You can integrate it into your applications (including in commercial applications), and you can distribute it.
  • Files containing only your code are not covered by this license (it is 'commercial friendly').
  • Modifications to the H2 source code must be published.
  • You don't need to provide the source code of H2 if you did not modify anything.
  • If you distribute a binary that includes H2, you need to add a disclaimer of liability - see the example below.
However, nobody is allowed to rename H2, modify it a little, and sell it as a database engine without telling the customers it is in fact H2. This happened to HSQLDB: a company called 'bungisoft' copied HSQLDB, renamed it to 'RedBase', and tried to sell it, hiding the fact that it was in fact just HSQLDB. It seems 'bungisoft' does not exist any more, but you can use theWayback Machineand visit old web pages ofhttp://www.bungisoft.com.About porting the source code to another language (for example C# or C++): converted source code (even if done manually) stays under the same copyright and license as the original code. The copyright of the ported source code does not (automatically) go to the person who ported the code.If you distribute a binary that includes H2, you need to add the license and a disclaimer of liability (as you should do for your own code). You should add a disclaimer for each open source libraries you use. For example, add a file3rdparty_license.txtin the directory where the jar files are, and list all open source libraries, each one with its license and disclaimer. For H2, a simple solution is to copy the following text below. You may also include a copy of the complete license.
This software contains unmodified binary redistributions for H2 database engine (http://www.h2database.com/),
which is dual licensed and available under a modified version of the MPL 1.1 (Mozilla Public License)
or under the (unmodified) EPL 1.0 (Eclipse Public License).
An original copy of the license agreement can be found at: http://www.h2database.com/html/license.html

9.      GNU Lesser General Public License (LGPL) 2.1

http://www.gnu.org/licenses/lgpl-2.1.html

Third Party Files:jackson-core-lgpl-1.9.0.jarjackson-mapper-lgpl-1.9.0.jarThis product currently only contains code developed by authors of specific components, as identified by the source code files; if such notes are missing files have been created by Tatu Saloranta.For additional credits (generally to people who reported problems) see CREDITS file.
Third Party Files:Hibernatehibernate-core-4.1.5SP1.jarhibernate-entitymanager-4.1.5SP1.jarhibernate-validator-4.3.0.Final.jarhibernate-commons-annotations-3.2.0.Final.jarhibernate-jpa-2.0-api-1.0.1.Final.jarjboss-logging-3.1.0.GA.jarjboss-transaction-api_1.1_spec-1.0.0.Final.jarhttp://www.hibernate.org/license

Free, as in Speech

Hibernate is Free Software.Hibernate is licensed under theLGPL v2.1. The LGPL is sufficiently flexible to allow the use of Hibernate in both open source and commercial projects. The LGPL guarantees that Hibernate and any modifications made to Hibernate will stay open source, protecting our and your work. Anyone who wanted to release Hibernate under a different license would have to obtain permission from hundreds of people who have contributed code to Hibernate, which would be impractical. Hibernate is and will be open source distributed under the LGPL.The use of the unmodified Hibernate binary of course never affects the license of your application or distribution. You will never have to pay money to any commercial entity for using or integrating Hibernate.If you modify Hibernate and redistribute your modifications, the LGPL applies. Please submit any modifications to our issue tracking system for review and possible inclusion in the upstream Hibernate project(s).

10.  Massachusetts Institute of Technology

http://opensource.org/licenses/mit-license.php/

Third Party File Copyright Notice
jquery.cookie.js HDD Access elects to include this software in this distribution under the MIT licenseCopyright (c) 2006 Klaus Hartl (stilbuero.de)Dual licensed under the MIT and GPL licenses:http://www.opensource.org/licenses/mit-license.phphttp://www.gnu.org/licenses/gpl.html
jquery.jstree.js HDD Access elects to include this software in this distribution under the MIT licensejsTree 1.0-rc3http://jstree.com/Copyright (c) 2010 Ivan Bozhanov (vakata.com)Licensed same as jquery - under the terms of either the MIT License or the GPL Version 2 Licensehttp://www.opensource.org/licenses/mit-license.phphttp://www.gnu.org/licenses/gpl.html
jquery-ui-1.8.16.custom.min.js HDD Access elects to include this software in this distribution under the MIT licensejQuery UI 1.8.16Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)Dual licensed under the MIT or GPL Version 2 licenses.http://jquery.org/licensehttp://docs.jquery.com/UI
Third Party Files:slf4j-api-1.6.4.jarslf4j-log4j12-1.6.4.jarjcl-over-slf4j-1.6.4.jarhttp://www.slf4j.org/license.htmlSLF4J source code and binaries are distributed under the MIT license.Copyright (c) 2004-2011 QOS.ch All rights reserved.Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Third Party Files:jQueryjquery-1.7.2.js HDD Access elects to include this software in this distribution under the MIT licensejQuery JavaScript Library v1.7.2http://jquery.com/Copyright 2011, John ResigDual licensed under the MIT or GPL Version 2 licenses.http://jquery.org/licenseIncludes Sizzle.jshttp://sizzlejs.com/Copyright 2011, The Dojo FoundationReleased under the MIT, BSD, and GPL Licenses.Date: Wed Mar 21 12:46:34 2012 -0700

11.  Mozilla Public License (MPL) 1.1

http://opensource.org/licenses/mozilla1.1

Third Party File:javassist-3.15.0.GA.jarCopyright (C) 1999-2010 by Shigeru Chiba, All rights reserved.

12.  SPECIALIST NLP Tools

http://lexsrv3.nlm.nih.gov/LexSysGroup/Docs/termsAndConditions.html

Third Party File:lvg-2012.jarLexical Tools, 2012 Release. 12/01/2011.Terms and Conditions for Use of the SPECIALIST NLP Tools1. IntroductionThe following Terms and Conditions apply for use of the SPECIALIST NLP Tools. Using the SPECIALIST NLP Tools indicates your acceptance of the following Terms and Conditions. These Terms and Conditions apply to all SPECIALIST NLP Tools, independent of format and method of acquisition.2. The SPECIALIST NLP ToolsThe Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, has developed the SPECIALIST NLP Tools to investigate the contributions that natural language processing techniques can make to the task of mediating between the language of users and the language of online biomedical information resources. The SPECIALIST NLP Tools facilitate natural language processing by helping application developers with lexical variation and text analysis tasks in the biomedical domain.3. AvailabilityThe SPECIALIST NLP Tools are available to all requesters, both within and outside the United States, at no charge.4. Use of the SPECIALIST NLP Toolsa. Redistributions of the SPECIALIST NLP Tools in source or binary form must include this list of conditions in the documentation and/or other materials provided with the distribution.b. In any publication or distribution of all or any portion of the SPECIALIST NLP Tools (1) you must attribute the source of the tools as the SPECIALIST NLP Tools with the release number and date; (2) you must state any modifications made to the SPECIALIST NLP Tools along with a complete description of the modifications, which may be in the form of patch files.c. You shall not assert any proprietary rights to any portion of the SPECIALIST NLP Tools, nor represent the SPECIALIST NLP Tools or any part thereof to anyone as other than a United States Government product.d. The name of the U.S. Department of Health and Human Services, National Institutes of Health, National Library of Medicine, Lister Hill National Center for Biomedical Communications may not be used to endorse or promote products derived from the SPECIALIST NLP Tools without specific prior written permission.e. Neither the United States Government, U.S. Department of Health and Human Services, National Institutes of Health, National Library of Medicine, Lister Hill National Center for Biomedical Communications, nor any of its agencies, contractors, subcontractors or employees of the United States Government make any warranties, expressed or implied, with respect to the SPECIALIST NLP Tools, and, furthermore, assume no liability for any party's use, or the results of such use, of any part of these tools.These terms and conditions are in effect as long as the user retains any part of the SPECIALIST NLP Tools.