Wandora

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This page collects Wandora's documentation. The documentation is a work in progress and incomplete. Also note some documentation may be out of date as the application is developed actively. If you need any specific help, write your question to the discussion forum. Wandora's YouTube channel has several tutorial videos reviewing some application features. Would you like to edit this wiki, send an email to support character.gif wandora.org with your name and information about how you'd like to contribute. Please, remember to add keyword WANDORA to the title of your email. If you just popped in this wiki and don't know Wandora, please see also our landing page at http://wandora.org/ for a general information.

Contents

Introduction

Wandora is a general purpose information management application. The application is written in Java programming language and it's internal data model is based on Topic Maps. Also, Wandora is a desktop application with a graphical user interface, layered data storage, huge collection of data extraction, import and export options and embedded HTTP server. Wandora's license is GNU GPL version 3.

Starting with Wandora

Wandora is a desktop application written in Java version 7. You need a Java Runtime Environment (JRE) to execute the application. Wandora has two distribution packages. A binary distribution package contains a runnable version of the application. Wandora's source code is available as a source code distribution package. Both packages are zip compressed file repositories. Use one of the startup scripts in bin folder to start the Wandora application.

Topic Maps

Wandora's internal datamodel is based on Topic Maps. Wikipedia defines Topic Maps as a standard for the representation and interchange of knowledge, with an emphasis on the findability of information. A topic map represents information using topics, associations and occurrences. Topic represents any concept, from people, countries, and organizations to software modules, individual files, and events. Associations are hypergraph relationships between topics. Occurrence is an information resource relevant to a particular topic. If you are not familiar with Topic Maps, you can think it as a special kind of graph with nodes and edges. Wandora's topic map model is limited. These model limitations are explained in Topic maps in Wandora page.

See also Topic map layers section below. Wandora Team has converted several well known ontologies to Topic Maps format. These ontologies: WordNet, OpenCyc, Gene Ontology, Gellish, and Finnish General Upper Ontology (YSO) are available at Topic map gallery.

Using Wandora

This section contains basic tutorials for Wandora. If you are a novice Wandora user, please start here. See also tutorial videos on wandoratv.

Wandora has a rich set of topic, association and occurrence editing features. Usually a topic is edited in a topic panel one by one. Editing an association takes place in a separate association editor. Similarly, editing an occurrence takes place in an occurrence editor. Next pages discuss about creating and editing topics and associations.

Wandora saves all topic maps in a Wandora project file. Addition to project files, Wandora can read and write topic map serializations. See also chapter Import and Export below.

Next pages discuss some other features of the Wandora application.

Topic panels

Topic panel is Wandora's user interface element to view and edit topics. Wandora supports several different topic panel types. Topic panels are managed with menu options under View. Wandora can view several topic panels simultaneously. Traditional topic panel views all topic elements in a table while tabbed panel views topic details in separate tabs. Graph topic panel is used for graph visualizations. Custom topic panel is based on user specific queries related to the current topic.

Different topic panels are

Topic map layers

Wandora supports layered topic maps. Layered topic map contains one or more topic maps stacked into an ordered array. Any topic in the layered topic map is a superposition of all merging topics in different layers. Wandora views all layered topic maps as a single topic map but allows layer specific operations too. It really matters what layer is active. As user can focus on one layer at a time or replace any layer at any time, the composition of information is flexible. User can easily try different scenarios. Layer specific application options and tools locate in Layers menu. Layered topic maps are very close to the concept of multilayer networks.

Different layer types

Other

Import and Export

Wandora has been designed for easy aggregation of information and features a wide range of import and export tools. Wandora imports not just different Topic Maps formats such as XTM1, XTM2, and LTM but also RDF as XML, N3, and Turtle. Also, Wandora imports bio-ontologies in OBO flat file format. To get an up-to-date overview of Wandora's import options see menu File > Import. Addition to import options, Wandora features a wide range of export options from different Topic Maps formats to different graph formats. See menu options in File > Export. Wandora's native file format is Wandora project, with a file suffix WPR, which is a collection of XTM2 topic maps and a configuration file within a zip package.

Graph and matrix imports

Graph and matrix exports

For additional information about Wandora's export capabilities see also Wandora as a server section below. For additional information about Wandora's import capabilities see also Extractors section below.

Extractors

Wandoras extractors.gif

Wandora is great for information mashups. With Wandora you can easily mashup information from various sources. Extractors are specific Wandora tools used to extract topics and associations out of different file formats and sources. For example, Wandora can extract data from MP3 and JPG files. To see what extractors your Wandora has installed see menu options in File > Extract. To start an extractor select the extractor in the menu or use drag and drop extractor. Wandora also features an add-on for Mozilla Firefox WWW browser. With this add-on you can perform extractions directly in Firefox www browser or in Thunderbird email client.

Search engine extractors

Simple files extractors

Media extractors

Social and Bookmark extractors

Bibliographical extractors

Classifications

Knowledge extractors

HTML structures extractors

News and syndication extractors

Microformat extractors

Wiki extractors

Simple RDF extractors

Language

Databases

Other

See Refining occurrences for some practical examples of how to extract associations and topics out of occurrences.

Generators

Generators are special tools that generate topics and associations algorithmically. Generators help you construct basic building blocks for your topic maps. Generators are also a nice test suite for Wandora and topic maps in general. Generators locate in Wandora's File > Generate menu. Available generators are

Schema

Schema is a collection of specific topics and associations that Wandora uses to construct the user interface of association editor, occurrence editor and topic name panel. Schema eases many topic map operations such as association and occurrence construction. Schema also defines the language support of Wandora application.

  • Schema to ease association and occurrence creation and modification

Language support

Wandora supports only one base name per topic. However, a topic may contain several different variant names. Each variant name has a type and a language. Similarly, a topic may contain several different occurrences, text fragments. Each occurrence has a type and a language also. Wandora supports both Microsoft Translator and Google translate API and can convert both variant names and occurrences to other languages.

Analyzing and querying topic maps

Generally these tools locate in Layers > Statistics menu. As an exception SOM classifier is found in association table menu and topic map comparison in File menu. Wandora provides also a bridge to R language. R language is a comprehensive statistical and graphing environment. With Wandora's R integration, the user can access Wandora's information structures in R environment. This opens up interesting possibilities if used together with information extractors.

See the Extract section and especially the subsection Classifications above also.

Tools and tool manager

A tool packs certain Wandora functionality into a single software component, specifically a Java class. When ever the user performs an action in Wandora, Wandora runs the tool that is responsible for the action. The Tool manager is a specific tool used to manage tools and tool sources. The user can install new tools to the Wandora. To develop a tool for the Wandora, the user writes a Java class source using a Java IDE, preferably Netbeans, and compiles the source using Java JDK.

Wandora as a server

The Wandora application contains an HTTP server. The embedded HTTP server generates various output formats and interactive visualizations out of the information stored in the Wandora. The embedded server hosts service modules. A service module is a software component that serves some information out of the Wandora. For example, HTML service module generates a navigable HTML site out of the topics in the Wandora. D3 graph service module generates an interactive graph out of all topics in the Wandora. More over, XTM topic map service module outputs current topic in the Wandora in an XTM format. It provides a data access point for external applications, or for other instances of the Wandora application. Some service modules rely on extracted information. Such service modules are Timeline service module and Google Maps service module.

Wandora team has also built several service modules for Drupal content management system and an extra for Joomla content management system. These modules can be used to publish Wandora stored information in these CMSes.

Wandora's embedded HTTP server contains a service module for SOAP web service. There is additional information available for Wandora's web service.

Also included is a modular framework for building webapps in Apache Tomcat or similar servlet containers. Topic maps and features of Wandora can be included in the servlet using this framework. The same framework can also be used in the embedded server.

Developing and hacking Wandora

Wandora project is developed with Netbeans IDE. Wandora's source code distribution package contains a Netbeans IDE project. You can download Wandora's source code distribution package from Download page. However, we suggest that you clone Wandora's repository at Github. Perhaps you want to push some fixes or new features back.

See also section Tools and tool manager above.

Papers and presentations

This section lists some papers and presentations related to Wandora and semantic web technologies created by the inner circle of Wandora Team. For a more wider selection of works related to Wandora see Use cases at Wandora forum.

Wandora @ World

See also

As said in the very beginning, the documentation is a work in progress and incomplete. If the available documentation didn't answer your question, please drop a line to Wandora forum and we'll try to find an answer for you.

If you are interested in Topic Maps and information technology related news see Planet Topic Maps and Planet RDF.

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