Download Ontology Viewer

Ontology Viewer
Installation and User Manual
OntoReason, LLC
OntoReason, LLC  7292 Shady Woods Circle  Midvale, UT 84047  Phone: 801.260.1502  http://www.ontoreason.com
Overview
The Ontology Viewer consists of two components: a Protégé plug-in and a web
application. Both components provide the same capabilities:

A view of the ontology specific to the NND data set

A search function to easily locate specific information

Export of selected data to an Excel file
Installation – Protégé Plug-in
The Protégé plug-in was developed for Protégé 4.1 Release Candidate 1. All testing was
performed on a PC using the MS Windows operating system.
To install the plug-in:
1. Download and install Protégé 4.1: http://protege.stanford.edu/. Ensure that
Protégé can run properly.
2. The Protégé installation directory will contain a sub-directory named plugins.
Add to this directory the file com.otrllc.excelexport.jar. This file is part of the
Ontology Viewer distribution.
3. Re-start Protégé.
Installation – Web Application
The web application has been tested on a MS Windows PC using the Apache Tomcat 6.0
web application server.
To install the web application:
1. Download and install Apache Tomcat: http://tomcat.apache.org/
2. The Tomcat installation directory will contain a sub-directory named webapps.
Add to this directory the file ophpr.war. This file is part of the Ontology Viewer
distribution.
3. Re-start the Tomcat server.
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Viewing the Ontology with the Protégé Plug-in
Launch Protégé and make the plug-in active:
1. Launch Protégé. On the Protégé welcome screen, click Open OWL ontology.
2. From the file selector, choose the root ontology file, currently named
V2.5.1_ORU_R01.owl. This ontology is part of the Ontology Viewer
distribution.
3. The ontology may be split into several related ontologies. While opening the
main ontology Protégé may ask you to locate the other ontologies. They will be
part of the Ontology Viewer distribution
4. After Protégé is launched, the Excel Export tab must be enabled. From the
Window menu, choose Tabs→Excel Export. A new tab will appear in the user
interface. Select this tab.
Figure 1 Protégé Ontology Viewer
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Viewing the Ontology with the Web Application
All testing of the web based Ontology Viewer was performed with MS Internet Explorer
8.
The URL of the web application will be dependent upon your specific setup. In general,
the web application can be launched by accessing a URL of the following format in your
web browser:
http://www.yourhost.com/ophpr/ OphprViewer.html
The web application will appear in your browser.
Figure 2 Web Ontology Viewer
Navigating the Ontology
A fully specified condition will have four levels in the tree labeled Disease. Double click
on the condition to drill down to the deepest level as shown in Figure 1 and Figure 2.
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Select the deepest level item. The second column will then be populated with the
possible Observation Values and Observation Identifiers for that test.
Select an Observation Value or Observation Identifier. The properties for the selected
item, including code, will be displayed in the Data Properties column.
Searching and Filtering
To search for specific terms, type the term into the search box and press Search. The
results will be displayed in the right-most list box ranked by a best-match algorithm.
Clicking on a search result item will filter the information shown in the Ontology
Viewer’s left-most Disease pane. The drill-down procedure on these filtered results
remains the same as the non-filtered case.
Remove the filter by pressing the Clear button. The Ontology Viewer once again
displays the full data set.
Some general syntax for using the search system:
Wildcard Searches
Search supports single and multiple character wildcard searches within single terms (not
within phrase queries).
To perform a single character wildcard search use the "?" symbol.
To perform a multiple character wildcard search use the "*" symbol.
The single character wildcard search looks for terms that match that with the single
character replaced. For example, to search for "text" or "test" you can use the search:
te?t
Multiple character wildcard searches looks for 0 or more characters. For example, to
search for test, tests or tester, you can use the search:
test*
You can also use the wildcard searches in the middle of a term.
te*t
Note: You cannot use a * or ? symbol as the first character of a search.
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Boosting a Term
The search provides the relevance level of matching objects based on the terms found. To
boost a term use the caret, "^", symbol with a boost factor (a number) at the end of the
term you are searching. The higher the boost factor, the more relevant the term will be.
Boosting allows you to control the relevance of an object by boosting its term. For
example, if you are searching for
botulinumtoxin
and you want the term "botulinum" to be more relevant boost it using the ^ symbol along
with the boost factor next to the term. You would type:
botulinum^4 toxin
This will make objects with the term botulinum appear more relevant. You can also boost
Phrase Terms as in the example:
"botulinum toxin"^4 "toxin assay"
By default, the boost factor is 1. Although the boost factor must be positive, it can be less
than 1 (e.g. 0.2)
Boolean Operators
Boolean operators allow terms to be combined through logic operators. Search supports
AND, "+", OR, NOT and "-" as Boolean operators(Note: Boolean operators must be ALL
CAPS).
OR
The OR operator is the default conjunction operator. This means that if there is no
Boolean operator between two terms, the OR operator is used. The OR operator links two
terms and finds a matching object if either of the terms exist in an object. This is
equivalent to a union using sets. The symbol || can be used in place of the word OR.
To search for objects that contain either " botulinumtoxin" or just "botulinum" use the
query:
"botulinumtoxin" botulinum
or
"botulinumtoxin" OR botulinum
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AND
The AND operator matches objects where both terms exist anywhere in the text of a
single object property. This is equivalent to an intersection using sets. The symbol &&
can be used in place of the word AND.
To search for objects that contain "botulinumtoxin" and "Apachetoxin Luceneassay" use
the query:
"botulinumtoxin" AND "Apachetoxin Luceneassay"
+
The "+" or required operator requires that the term after the "+" symbol exist somewhere
in a field of a single object.
To search for objects that must contain "botulinum" and may contain "assay" use the
query:
+botulinum luceneassay
NOT
The NOT operator excludes objects that contain the term after NOT. This is equivalent to
a difference using sets. The symbol ! can be used in place of the word NOT.
To search for objects that contain "botulinumtoxin" but not "Toxin Assay" use the query:
"botulinumtoxin" NOT "Toxin Assay"
Note: The NOT operator cannot be used with just one term. For example, the following
search will return no results:
NOT "botulinumtoxin"
The "-" or prohibit operator excludes objects that contain the term after the "-" symbol.
To search for objects that contain "botulinumbotulinum toxin" but not "Toxin Assay" use
the query:
"botulinumbotulinum toxin" -"Toxin Assay"
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Grouping
Search supports using parentheses to group clauses to form sub queries. This can be very
useful if you want to control the boolean logic for a query.
To search for either "botulinum" or "toxin" and "website" use the query:
(botulinum OR toxin) AND website
This eliminates any confusion and makes sure you that website must exist and either term
botulinum or toxin may exist.
Escaping Special Characters
Searching supports escaping special characters that are part of the query syntax. The
current list special characters are
+ - && || ! ( ) { } [ ] ^ " ~ * ? : \
To escape these character use the \ before the character. For example to search for
(1+1):2 use the query:
\(1\+1\)\:2
Export to Excel
Data can be exported to an Excel ’97 formatted file by pressing the Export to Excel
button in the lower right corner. In Protégé, the user will be presented with a “Save
As…” dialog. In the web application, the user will be given the choice to save the file or
to open directly into Excel.
When the viewer has been filtered by clicking on a search result, the exported data will
be restricted to the filtered data.
Changing Ontologies
From time to time the ontologies may be updated. When using the Protégé browser,
changing the ontology is simply a matter of opening the new file.
For the web application, there are a few more steps:
1. The Tomcat installation directory will contain the following directory:
/webapps/ophpr/WEB-INF/ontologies
Remove the old ontology files and add the new ontology files.
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2. The ontology directory will also contain a file prefs.xml. This file is used by the
web application to determine which ontologies to open and which ontology is the root
(or main) file.
If no ontology file name or URI changed, no changes need to be made to the
prefs.xml file.
If some file name or URI was changed, the prefs.xml file will need to be edited.
Open the file with a text editor. Modify such that each file has an entry of the
following format:
<entry key=”uri of file”>filename</entry>
For example:
<entry key="http://www.OntoReason.com/ontologies/V2.5.1_ORU_R01.owl">V2.5.1_ROU_R01.owl</entry>
3. The main ontology (corresponding to the file that a user would open first in
Protégé) needs to have an additional entry in the prefs.xml file:
<entry key=”primary”>filename</entry>
For example:
<entry key="primary">V2.5.1_ROU_R01.owl</entry>
4. Re-start the Tomcat server.
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