Documentation

Revision as of 15:40, 14 June 2011

This page contains Wandora documentation. Documentation is a work in progress and incomplete. Also note some documentation may be out of date as the application is developed intensely. If you need specific help, leave a note in the discussion forum and we'll answer your request as soon as possible. Additional help may be available on wandoratv.

Preparing Wandora

Wandora is a desktop application written in Java version 6. To run Wandora application you need a Java Runtime Environment (JRE). Wandora application it self can be downloaded from a page addressed below. Wandora application has no installer. Unzip downloaded package and the application is ready to be used. Most common method to run Wandora is to start one of the scripts in bin folder.

• System requirements
• Download Wandora (build date 2016-05-10)
• Installing Wandora
• Running Wandora

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. Association representing hypergraph relationships between topics. And occurrence is an information resource relevant to a particular topic.

• About topic maps
• Topic maps in Wandora

See also Layers section below.

Using Wandora

This section contains some basic tutorials for Wandora. If you are a novice Wandora user, please start here.

• Quickstart
• Opening a topic
• Finding a topic
• Topic shortcuts
• Create new topic
• Delete topic
• Create new association
• Delete association
• Working with topic tables
• Drag and drop topics
• Working with topic trees
• Creating custom topic trees
• View all variant names of a topic
• Transform variant names to topics and associations

See also tutorial videos on wandoratv.

Editing topics

Wandora has a rich set of topic, association and occurrence editing features. Wandora user may edit single topic in a topic panel. Modifying an association takes place in separate dialog window, association editor. Similarly, modifying an occurrence takes place in a separate editor.

• Modifying base name
• Modifying subject locator
• Modifying subject identifiers
• Modifying variant names
• Modifying topic classes
• Modifying associations
• Modifying occurrences

Topic panels

Topic panel is Wandora's UI element to view and edit topics. Wandora supports several different topic panel types. Topic panel type is changed with menu options in View > Topic panels. 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.

• Traditional topic panel
• Tabbed topic panel
• Graph topic panel
• Custom topic panel

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.

• How to save and load project
• How to import existing topic map to Wandora
• How to export topic map in Wandora
• Maiana import and export
• Transferring data with clipboard
• Importing RDF (see also extractors below)
• Importing OBO flat file ontologies
• Gene Ontology Annotation file import
• Importing XML with XSL
• Generic SQL database import
• Exporting WWW site
• Lucene search index export
• SQL Dump Export

Graph and matrix imports

• Adjacency list import
• Adjacency matrix import
• Incidence matrix import

Graph and matrix exports

• Graph Modeling Language export
• GraphML export
• GraphXML export
• GXL graph export
• Export adjacency matrix
• Export incidence matrix

For additional information about Wandora's export capabilities see also Wandora Server and CMS bridges section below. For additional information about Wandora's import capabilities see also Extractors section below.

Extractors

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 WWW browser or Thunderbird email client.

• Drag and drop extractor
• Firefox plugin to extract directly from Firefox WWW browser and Thunderbird email client.

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 to construct basic building blocks for your topic maps. Generators also serve as a nice test suite for Wandora and topic maps in general. Generators locate in Wandora's File > Generate menu. Available generators are

• Random graph generator
• Fully connected graph generator
• Tree graph generator
• Linear list graph generator
• Finite group graph generator
• Platonic solid graph generator
• Hypercube graph generator
• Tiling graph generator (square, triangular, and hexagonal tilings)
• Edge generator
• L-system generator

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, topic map contain several different occurrences, text fragments. Each occurrence has also a type and a language. Wandora supports both Microsoft Translator and Google translate API and can convert both variant names and occurrences to other languages.

• How to add a language to Wandora
• How to add a name type to Wandora
• Translating variant names with Google
• Translating occurrences with Google
• Translating variant names with Microsoft Translator
• Translating occurrences with Microsoft Translator
• View all variant names of a topic

Layers

Wandora supports layered topic maps. Layered topic map contains one or more topic maps stacked into an ordered array. This separation of merged topic maps allows flexible management of topic maps and enables the birth of public knowledge repositories used as a component of other Wandora based knowledge bases. Layer specific options locate in Layers menu.

• Introduction to Layered Topic Maps
• Creating new layers
• Deleting layer
• Layer order and arranging layers
• Merging layers
• Topic's layer distribution

Different layer types

• Layered topic map
• Memory topic map
• Database topic map
• Linked topic map
• Query topic map
• Web service topic map

Analyzing Topic Maps

Generally these tools locate in Layers > Statistics menu. As an exception SOM classifier is found in association table menu.

• Topic map info
• Topic map connection statistics
• Topic map diameter
• Clustering coefficient of topic map
• SOM classifier (Self Organizing Maps classifier)
• Asset weight of a topic

Tools and tool manager

Almost every feature in Wandora is implemented with a tool. Tool packs certain Wandora functionality into a single software component. Wandora's user may customize the available tool set and even add third party tools to Wandora.

• Tool manager
• Available tools
• Writing your own tool
• Installing your own tool
• Tool locks
• Configuring tools
• Additional tool help

Wandora as a server

Wandora application includes an HTTP server. Server can be used to serve topic maps as HTML representations, RSS feeds or a web service. User can also build own representations. As an example, Wandora team has built several modules for Drupal content management system and an extra for Joomla content management system.

• Embedded HTTP server
• Wandora Web Service
• Wandora Drupal extras
• Wandora's Joomla Topic Reader

Wandora Piccolo is a framework to publish topic maps with Wandora and Apache Tomcat. Wandora Piccolo suits well for large scale publishing projects that doesn't require Wandora's UI.

• Setting up Wandora Piccolo server
• Wandora Web Service
• Piccolo XML processor

For additional information, see also Export section above.

Miscellaneous

• Wandora options
• Wandora Javadocs, download