This is a simple tool designed to facilitate user interaction with controlled vocabularies such as the Enterprise Vocabulary System (EVS) or various ontologies. The tool has two basic components:
This initial version of the VWO tools supports EVS terminology. Future versions will expand support to other controlled vocabularies with a particular focus on the Nanoparticle Ontology.
More information about deployment and use of these tools is provided below.
This tool was developed by (alphabetical order):
This software development effort is part of larger nanomedicine ontology and vocabulary work in the Nathan Baker and Rohit Pappu research groups, supported by the National Cancer Institute (U54 CA119342).
As mentioned above, the primary tool for end-users is a bookmarklet which can be installed in most web browsers and used to highlight recognized terms on a web page. A web page containing the bookmarklet can be visited online at http://vwo.sf.net/EVS_Bookmarklet.html or downloaded here. This bookmarklet works with most major Javascript-enabled web browsers.
The bookmarklet has been tested on several platforms and web browsers, including Firefox, Safari, and Internet Explorer. The bookmarklet is "installed" simply by saving it as a bookmark. On many browsers, this can be done by dragging the "EVS Services..." link at http://vwo.sf.net/EVS_Bookmarklet.html to the bookmarks toolbar of the browser. On other browsers, the bookmarklet is bookmarked by right-clicking on the "EVS Services..." link at http://vwo.sf.net/EVS_Bookmarklet.html and selecting "Bookmark this link..." or "Add to favorites...".
The bookmarklet is extremely easy to use. After installing the bookmarklet, simply visit any web page that contains terms that you would like to look up in the EVS vocabulary (e.g., try a PubMed article.) Once the page is loaded, click on the "EVS Services" bookmarklet bookmark that you just installed. A dialog window will appear asking you if you'd like to highlight recognized terms. Choose your desired option (we would recommend highlighting terms by selecting "OK") and then wait for the bookmarklet to start processing terms on the page. Based on network and server load, term recognition can take a few moments; you can generally monitor its progress through the status bar of your browser. If you selected highlighting for recognized terms, recognized words will start to be colored in a very distinctive green color after a few moments. If you hover your mouse pointer for 2 or more seconds over a recognized word, a tooltip window will appear with links to relevant entries in EVS. Clicking on one of these links will open a new window or tab in your browser. The tooltip will disappear within 4 seconds but can be reinstated by hovering over the desired word again with your mouse pointer.
The default bookmarklet configuration uses a Tomcat server installed in the Baker group at Washington University. However, you may wish to deploy your own installation to reduce network lag or provide site-specific customization.
These instructions assume you are running Tomcat 5.0 or later with the server application connector port assigned to 8080:
webapps directory.WEB-INF/classes/ProxySettings.properties with:
<your proxy server> <your proxy port> (e.g., 8080) <your proxy account user ID> <your proxy account password> Bookmarklet/json_calls.js file in the WAR file (or webapps/EVS_Service after the WAR file has been expanded) to change localhost:8080 to the URI where you installed the EVS web service; e.g., from "http://localhost:8080/EVS_Webservice/" to "http://myURL.edu/EVS_Webservice/" You will also need to configure the bookmarklet for your particular installation. A web page containing the bookmarklet can be visited online at http://vwo.sf.net/EVS_Bookmarklet.html or downloaded here. Using one of these pages as your template, simply modify all instances of "http://ocotillo.wustl.edu:8080" to a URI appropriate to your installation.
For help using, installing, or further developing this tool, please visit our Help Forum.
This software is distributed under an MIT-style open source license:
Vocabulary Webpage Overlay
Nathan A. Baker (baker@biochem.wustl.edu)
Center for Computational Biology
Dept. of Biochemistry and Molecular Biophysics
Washington University in St. LouisCopyright (c) 2008 Washington University in St. Louis
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.