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LexBIG Software User Agreement
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Copyright: (c) 2004-2006 Mayo Foundation for Medical Education and Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the triple-shield Mayo logo are trademarks and service marks of MFMER. Except as contained in the copyright notice above, the trade names, trademarks, service marks, or product names of the copyright holder shall not be used in advertising, promotion or otherwise in connection with this Software without prior written authorization of the copyright holder. Licensed under the Eclipse Public License, Version 1.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.eclipse.org/legal/epl-v10.html Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. |
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Type | Contact |
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Training contact | VKC VocabKC@mayo.edu |
Developer | Division of Biomedical Informatics Mayo Clinic |
Facilities Pertinent to Software Teams
Resource | URL | Description | ||
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Bug Tracking and feature requests | JIRA | |||
Discussion Forums and Project Wiki | This wiki | |||
Architecture and Requirements specifications |
| LexEVS SVN repository |
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Convention | Description | Example | |||||||
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Bold & Capitalized Command | Indicates a Menu command |
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Capitalized command>Capitalized command | Indicates Sequential Menu commands | Admin > Refresh | |||||||
| Used for filenames, directory names, commands, file listings, source code examples and anything that would appear in a Java program, such as methods, variables, and classes. |
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Boldface type | Options that you select in dialog boxes or drop-down menus. Buttons or icons that you click. | Select the file and click the Open button. | |||||||
Italics | Used to reference other documents, sections, figures, and tables. | caCORE Software Development Kit 1.0 Programmer's Guide | |||||||
Italic boldface type | Text that you type | In the New Subset text box, enter Proprietary Proteins. | |||||||
| Highlights a concept of particular interest |
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| Highlights information of which you should be particularly aware. |
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Directory | Description of Content | |||||
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| Installed by default. This directory provides a centralized point for command line scripts that can be executed to perform administrative functions such as the loading, activation/deactivation, and removal of vocabulary resources.
Object code used to carry out these functions is included directly in the LexBIG runtime components. Source code is included in the /source directory in the | |||||
| Optionally installed. This directory provides documentation related to LexBIG services, configuration, and execution. This guide is distributed in the | |||||
| Of special interest to programmers. This directory provides the generated javadoc for model classes and public interfaces available to LexBIG programmers. Also included with each object representation is a UML-based model diagram that shows the object, its attributes and operations, and immediately linked objects. The diagrams work to provide clickable navigation through the javadoc materials. | |||||
| Optionally installed. This directory provides a small number of example programs. | |||||
| Contains sample vocabulary content for reference by the example programs; use the | |||||
| Optionally installed. This folder contains programs and supporting files to launch the LexBIG Graphical User Interface (GUI). The GUI provides convenient centralized access to administrative functions as well as support to test and exercise most of the LexBIG API. The GUI is launched using a platform-specific script file in the /gui directory. The name of the platform (e.g. Windows, OSX, etc) is included in the file name. Program source and related materials are centrally archived under the /source directory in the file | |||||
| Default location for log files, which can be modified by the | |||||
| Installed by default. This directory contains resources referenced and written directly by the LexBIG runtime. It should, in general, be considered off-limits to modify or remove the content of this directory without specific guidance and reason to do so. Files typically stored to this location include the vocabulary registry (tracking certain metadata for installed content) and indexes used to facilitate query over the installed content. One file of particular interest in this directory is the | |||||
| Installed by default. This directory contains a Java archive (.jar) file containing the combined object code of the LexBIG runtime, LexBIG administrative interfaces, and any additional code they are dependent on. All required code for execution of LexBIG administrative and runtime services is installed to this directory.
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| The JDBC drivers used to connect to database repositories are not included in the
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| Optionally installed. Due to license considerations for additional materials (as described by the
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| This subdirectory includes all 3rd party code redistributed with the LexBIG runtime, along with respective license agreements. | |||||
| Archive source directories and files described in further detail in the next table below. | |||||
| Optionally installed. This directory provides an automated test bucket that can be used by System Administrators to verify node installation. Note that the
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| Contains an executable jar that can be invoked by an administrator to uninstall files originally introduced by the LexBIG installation. |
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Example source is provided below for a simple program that lists the available coding schemes (containers for vocabulary concepts and relations) registered to a LexBIG server node:
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import org.LexGrid.LexBIG.DataModel.Collections.CodingSchemeRenderingList;
import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering;
import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl;
import org.LexGrid.LexBIG.LexBIGService.LexBIGService;
import org.LexGrid.LexBIG.Utility.ObjectToString;
public class ListCodeSystems {
public static void main(String[] args) {
try {
LexBIGService lbs = new LexBIGServiceImpl();
CodingSchemeRenderingList schemes = lbs.getSupportedCodingSchemes();
for (CodingSchemeRendering csr
: schemes.getCodingSchemeRendering() )
System.out.printIn(
ObjectToString.toString(csr.getCodingSchemeSummary()));
} catch (Exception e) {
e.printStackTrace();
}
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This section describes architectural detail for services provided by the LexBIG system. These services are geared toward the administration, management, and serving of vocabularies defined to the LexGrid/LexBIG information model. A system overview is provided, followed by a description of key subsystems and components. Each subsystem is described in terms of its overall structure, formal model, and specification of key public interfaces.
Overview
The LexBIG Service is designed to run standalone or as part of a larger network of services. It is comprised of four primary subsystems: Service Management, Service Metadata, Query Operations, and Extensions. The Service Manager provides administration control for loading a vocabulary and activating a service. The Service Metadata provides external clients with information about the vocabulary content (e.g. NCI Thesaurus) and appropriate licensing information. The Query Operations provide numerous functions for querying and traversing vocabulary content. Finally, the extensions component provides a mechanism to extend the specific service functions, such as Loaders, or re-wrap specific query operations into convenience methods. Primary points of interaction for programming include the following classes:
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Finally, the LexBIG architecture provides the underpinnings for LexBIG services to be made accessible through the caGRID environment in the future, where vocabulary services might be deployed and discovered within a caGRID Globus container. However, this portion of the API is preliminary and awaits coordination with caBIG® Architecture WS designees to determine exact recommendations and nature of LexBIG services on the grid.
Query Subsystem
Overview
This subsystem provides the functionality required to fulfill caCORE/EVS and other vocabulary requests. The Query Service is comprised of Lexical Operations, Graph Operations, Metadata, and History Operations.
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Component | Description |
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changeType | Atomic modification actions. Currently populated from a combination of Concordia, SNOMED-CT list and NCI's action list. |
NCIChangeEvent | A change event as documented in ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ReadMe_history.txt  . Note that date and time of the change event is recorded in the containing version. All change events for the same/date and time a recorded in the same version. |
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Linux_64-lbGUI.sh Linux-lbGUI.sh
OSX-lbGUI.command Windows-lbGUI.bat |
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If a Code Set is selected in the lower left, then the lower right section will look like this:
In the lower right section, there are two halves - the top half and the bottom half. The top half is used to apply restrictions. The bottom half provides query options and resolution.
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If you select a Coded Node Graph in the lower left section of the LexBIG GUI, the lower right section will look like this:
Again, there are two halves to the lower right section. The top half allows restrictions to be applied to the selected Code Graph, and it works the same as it does for a Coded Node Set. Please see the section above on applying restrictions to a Coded Node Set.
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Clicking on the Resolve buttons for either a Coded Node Set or a Coded Node Graph will bring up the Result Browser window:
The left side shows a list of all the concept codes returned. When a concept code is selected on the left, the upper right will show a full description of the selected code. The lower right will show a graph view of the neighboring concepts.
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This appendix includes lists and hypertext links, where appropriate, to technical manuals, articles, scientific publications and online resources related to the LexBIG project.
- LexBIG GForge Project - https://gforge.nci.nih.gov/projects/lexevs/project Docs archive, Files archive
- LexBIG Project Administration Materials - https://gforge.nci.nih.gov/docman/?group_id=491
- LexGrid Home Page for this release - LexEVS 4.2.1
- Vocabulary Knowledge Center – https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page
- Sun Java Tools (JDK, JRE, NetBeans) - http://java.sun.com/Eclipse
Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include - Eclipse Project (IDE) - http://www.eclipse.org/eclipse/
Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include
Appendix B Included Materials
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Redistributable components (e.g. those listed below) and associated license terms are also made available. The redistributable components provide equivalent content and function, but require more extensive configuration for program execution. |
| This archive includes the LexBIG runtime code, excluding all dependencies. | ||||||||||||||||
| The LexBIG graphical user interface runtime code, excluding all dependencies. | ||||||||||||||||
| Provided by Sun's reference implementation of the JavaBeans Activation Framework (JAF)
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Grid infrastructure to support the caBIG® community. Contains tools for creating and deploying caBIG®-compliant grid services. | |||||||||||||||||
| Provides a simple API for working with command line arguments, options, option groups, mandatory options and so forth. | ||||||||||||||||
| Provides implementations of common Provides implementations of common encoders and decoders such as Base64, Hex, Phonetic and URLs. | ||||||||||||||||
| Provides a suite of classes that extend or augment the Java Collections Framework. | ||||||||||||||||
| Provides a very common set of utility classes that provide extra functionality for classes in the | ||||||||||||||||
| Provides a bridge between different logging libraries. | ||||||||||||||||
| Provides a generic object pooling interface, a toolkit for creating modular object pools and several general purpose pool implementations. | ||||||||||||||||
| Provides a Java language implementation of Provides a Java language implementation of standard NFA regular expression features. | ||||||||||||||||
| SQL relational database engine written in Java. | ||||||||||||||||
| International components for Unicode processing. | ||||||||||||||||
| Java package for processing regular expressions. | ||||||||||||||||
| Java date chooser bean for graphically picking a date. | ||||||||||||||||
| Java-based solution for accessing, manipulating, and outputting XML data from Java code. | ||||||||||||||||
| Java framework for building Semantic Web
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| Java regression test framework. . | ||||||||||||||||
log4j | Runtime logging services. | ||||||||||||||||
| Text search engine library written in Java. | ||||||||||||||||
| Provided by the Sun JavaMail API
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| JDBC drivers for MySQL database. |
| JDBC drivers for MySQL database. | ||||||||||||||
org.eclipse.* | Used internally by LexBIG load and export extensions to access and manipulate Eclipse Modeling Framework (EMF)
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| JDBC drivers for PostgreSQL database. | ||||||||||||||||
| Used for graph representations in the LexBIG GUI. | ||||||||||||||||
( swt .jar) | Provides the underlying widget toolkit used by the LexBIG GUI. | ||||||||||||||||
| XML parsing services. |
Appendix C Additional Terms and Conditions
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