View source for Wandora

This page collects Wandora documentation. 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 Also note some documentation may be out of date as the application is developed actively.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 [http://www.wandora.org/wandora/forum/index.php discussion forum]. Additional help may be available on the [http://www.wandora.org/wandora/tv/ wandoratv] (Flash required). Would you like to edit this wiki, send an email to {{wandora email address}} with your name and information about how you'd like to contribute. Please, remember to add keyword WANDORA to the title of your email.

'''Have you visited Wandora wiki before? As you may notice, we have moved the content from old Documentation page here and removed the old front page of the wiki. From now on the official front page of the Wandora project is the page at http://www.wandora.org/'''.

== Introduction ==

Wandora is a general purpose information management application. Wandora is written in [http://www.oracle.com/technetwork/java/index.html Java programming language]. Wandora's internal data model is based on [[Topic Maps]]. 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 [http://www.gnu.org/licenses/gpl-3.0.txt GNU GPL version 3].

* [[General FAQ]]
* Wandora poster in [http://www.wandora.org/wandora/download/other/poster09.pdf PDF] or [http://www.wandora.org/wandora/download/other/poster09.gif GIF] formats.
* [[Features]]
* [[Screenshots]]
* [http://www.wandora.org/www/news Wandora news]
* [[License of Wandora|License]]

== Starting with Wandora ==

Wandora is a desktop application written in Java version 6. You need Java Runtime Environment (JRE) to execute the application. Wandora has two distribution packages. Binary distribution package contains 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 run Wandora application.

* [[System requirements]]
* [[Download|Download Wandora]] (build date {{build date}})
* [[How to install Wandora|Installing Wandora]]
* [[Running Wandora]]
* [[Tuning Wandora for Mac OS]]
* [[Quickstart]]

== 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. Wandora's topic map model is limited. These model limitations are explained in [[Reduced Topic Maps|Topic maps in Wandora]] page.

* [[Topic Maps|About topic maps]]
* [[Reduced Topic Maps|Topic maps in Wandora]]

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 some basic tutorials for Wandora. If you are a novice Wandora user, please start here. See also tutorial videos on [http://www.wandora.org/wandora/tv/ wandoratv] (Flash required).

* [[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]]
* [[Undo and redo]]

== Editing topics and associations ==

Wandora has a rich set of topic, association and occurrence editing features. Usually a topic is edited in a topic panel but Wandora features a group editions too. Editing an association takes place in a separate association editor. Similarly, modifying an occurrence takes place in an occurrence editor resembling a simple text editor. For editing tips see also tutorial videos on [http://www.wandora.org/wandora/tv/ wandoratv] (Flash required).

* [[Editing topics and associations]]

== 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.

* [[Working with topic panels]]

Different topic panels

* [[Traditional topic panel]]
* [[Tabbed topic panel]]
* [[Graph topic panel]]
* [[Custom topic panel]]
* [[Treemap topic panel]]
* [[R topic panel]]
* [[Processing topic panel]]

== Topic map layers ==

Wandora supports layered topic maps. Layered topic map contains one or more topic maps stacked into an ordered array. 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. 

* [[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]]
<!-- * [[Remote topic map]] -->
* [[Web service topic map]]

'''Other'''
* [[Compare topic maps]]
* [[Topic map patcher]]

== 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)
* [[OBO flat file import|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 as a server''' section below. For additional information about Wandora's import capabilities see also '''Extractors''' section below. <!-- [[Image:import_export_diagram.gif|center]] -->

== Extractors ==

[[Image:Wandoras_extractors.gif|center]]

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.

* [[Drag and drop extractor]]
* [[Wandora Firefox plugin|Firefox plugin]] to extract directly from Firefox WWW browser and Thunderbird email client.

{| cellspacing="0" cellpadding="0" width="100%" background-color="transparent" 
| style="border:none; margin:none; padding:0px;" valign="top" | <!-- LEFT COLUMN -->

'''Search engine extractors'''
* [[Bing extractor]]
* [[Yahoo! BOSS extractor]]
'''Simple files extractors'''
* [[JPG binary metadata extractor]]
* [[PDF extractor]]
* [[File system extractor]]
* [[Simple Text Document Extractor|Convert simple text documents to topic map occurrences]]
* [[Simple CSV association extractor]]
'''Media extractors'''
* [[Europeana extractor]]
* [[MP3 ID3v1 and ID3v2 extractor]]
* [[IMDB extractor]]
* [[FreeDB extractor]]
* [[Last.fm extractors|Convert Last.fm XML feeds to a topic map]]
* [[Flickr extractors]]
* <strike>[[Ovi shared media extractors]]</strike>
* [[YouTube extractor]]s
'''Social and Bookmark extractors'''
* [[Facebook Graph extractor]]
* [[Twitter extractor]]
* [[Digg extractors]]
* [[Delicious extractors]]
* [[Diigo bookmark extractor]]
* [[Twine RDF extractor]]
'''Bibliographical extractors'''
* [[MARCXML extractor]]
* [[Dublin Core XML extractor]]
* [[Bibtex extractor|Convert BibTeX files to a topic map]]
* [[RIS extractor]]
* [[HelMet library data extractor]]
'''Classifications'''
* [[GATE/ANNIE integration|GATE/ANNIE]]
* [[Stanford Named Entity Recognizer integration|Stanford Named Entity Recognizer (NER)]]
* [[OpenCalais classifier]]
* [[AlchemyAPI extractors]]
* [[Yahoo! YQL term extractor]]
* [[Tagthe extractor]]
* [[SemanticHacker classifier]]
* [[Zemanta extractor]]
* [[UClassify integration]]
'''Knowledge extractors'''
* [[OpenCyc extractor]]
* <strike>[[Subj3ct record extractor]]</strike>
* [[DBpedia extractor]]
* [[Freebase extractor]]

| style="border: 1; margin:5; padding-left: 20px;" valign="top"| <!-- RIGHT COLUMN -->

'''HTML structures extractors'''
* [[HTML superclass-subclass list extractor]]
* [[HTML instance list extractor]]
* [[HTML property table extractor]]
* [[HTML association table extractor]]
* [[HTML link extractor]]
'''News and syndication extractors'''
* [[RSS 2.0 Extractor]] and [[RSS 1.0 RDF Extractor]]
* [[Atom extractor]]
* [[New York Times Article Search API extractor]]
* [[New York Times Event API extractor]]
* [[Guardian open platform extractor]]
'''Microformat extractors'''
* [[Any23 extractor]]
* [[Geo microformat extractor|Convert geo microformat snippets to topic maps]]
* [[Adr microformat extractor|Convert adr microformat snippets to topic maps]]
* [[HCalendar microformat extractor|Convert hcalendar microformat snippets to topic maps]]
* [[HCard microformat extractor|Convert hcard microformat snippets to topic maps]]
'''Wiki extractors'''
* [[Wikipedia extractor]]
* More general [[MediaWiki extractor]]
'''Simple RDF extractors'''
* [[SKOS RDF extractor]]
* [[Dublin Core RDF extractor]]
* [[FOAF RDF extractor]]
'''Language'''
* [[Big Huge Thesaurus API extractor]]
* [[VerbOcean extractor]]
* [[Moby thesaurus extractor]]
* [[Stands4 word describer]]
'''Databases'''
* [[Generic SQL database import | Importing SQL database]]
* [[SQL query result set extractor]]
'''Other'''
* [[Email extractor]]
* [[Geonames extractors]]
* [[Gellish ontology extractor]]
* [[GEDCOM extractor]]
* [[SPARQL extractor]]
* [[Oma kaupunki extractor]]
* [[iCal calendar format extractor]]
|}

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

* [[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]]
* [[Cylinder graph generator]]
* [[Lattice graph 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, 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.

* [[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]]

== Analyzing 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.

* [[Topic map info]]
* [[Topic map connection statistics]]
* [[Topic map diameter]]
* [[Merge ratio matrix]]
* [[Export similarity matrix|Topic similarity matrix]]
* [[Clustering coefficient]] of topic map
* [[SOM classifier]] (Self Organizing Maps classifier)
* [[Asset weight of a topic]]
* [[Compare topic maps]]
* [[R in Wandora]]
* [[Query language]]

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

== Tools and tool manager ==

Almost every feature in Wandora is implemented with a tool. A 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]]
* [[:Category:Tools|Available tools]]
* [[Writing your own tool]]
* [[Installing your own tool]]
* [[Tool locks]]
* [[Configuring tools]]
* [[Additional tool help]]
* [[Developing Wandora]]

== Wandora as a server ==

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

* [[Embedded HTTP server]]
** [[HTML service module]] 
** [[Mobile HTML service module]]
** [[RSS feed service module]]
** [[SOAP web service module]] 
** [[Drupal service module]]
** [[Firefox and Thunderbird plugin service module]]
** [[XTM topic map service module]] 
** [[JTM topic map service module]]
** [[RDF service module]]
** [[GRAPHML service module]]
** [[Screencast service module]]
** [[Flash graph service module]]
** [[Timeline service module]]
** [[Google Maps service module]]
** [[D3 graph service module]]
** [[D3 word cloud service module]]
** [[D3 partition service module]]
** [[D3 tree service module]]
** [[D3 matrix service module]]
** [[D3 layer visualization]]

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 Drupal extras]]
* [[Wandora's Joomla Topic Reader]]
* [[JQuery Mobile based topic map browser]]

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

* [[Wandora Web Service]]

For additional information, see also '''Export''' section above.

== Developing and hacking Wandora == 

Wandora project is developed with [http://netbeans.org/ 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.

* [[Change log]]
* [[Download]] (build date {{build date}})
* [[License of Wandora|License]]
* [[Developing Wandora]]
* [http://www.wandora.org/api/ Wandora Javadocs], [http://www.wandora.org/api/wandora-javadoc.zip download]
* [[Wandora's configuration file]]
* [[Upcoming features]]
* [[Open bugs]]

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 [http://www.wandora.org/forum/viewforum.php?f=10&sid=57134deccd5ba47132334f2f1215b520 Use cases at Wandora forum].

* [http://tmra.de/2010/ TMRA 2010] tutorial slides: [http://www.wandora.org/download/other/tmra10/wandora_workshop_tmra2010.pdf Converting information to Topic Maps using Wandora].
* [http://tmra.de/2009/ TMRA 2009] workshop presentation [http://www.slideshare.net/tmra/semantic-mashups-with-wandora Semantic Mashups with Wandora]. [http://www.wandora.org/wandora/download/other/tmra09/wandora_tutorial_leipzig.zip Example data set] is available for brave experimenters.
* Wandora poster in [http://www.wandora.org/wandora/download/other/poster09.pdf PDF] or [http://www.wandora.org/wandora/download/other/poster09.gif GIF] formats.
* Kivelä A.: [http://www.wandora.org/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish). (English Abstract: [http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf Converting OBO ontologies to Topic Maps]).
* Lyytinen O.: [http://www.wandora.org/download/other/gradu_lyytinen.pdf Semanttisen webin tekniikoiden soveltaminen Wikisovelluksissa]. MSc Theses, 2008. (in Finnish) 
* Kivelä A.: [http://www.wandora.org/download/other/wandora_xml_finland.pdf Topic Maps, Wandora ja kourallinen julkaisuprojekteja] (in Finnish). Presentation held in XML Finland meeting November 14th, 2007. 
* Lyytinen O.: [http://www.wandora.net/wandora/download/other/step06.pdf Building Internet Services with Layered Topic Maps]. Presentation held in The Finnish Artificial Intelligence Conference (STeP 2006), 2006-10-26.
* Kivelä A., Lyytinen O.: [http://www.wandora.net/wiki/images/Topic_map_aided_publishing.pdf Topic Map Aided Publishing – A Case Study of Assembly Media Archive]. ''Web Intelligence. STeP 2004 - The 11th Finnish Artificial Intelligence Conference Proceedings - Vol. 2'', 2004.

== Wandora @ World ==

* [http://twitter.com/#!/wandora_app Twitter]
* [http://freecode.com/projects/wandora/ Freecode]
* [http://sourceforge.net/projects/wandora/ SourceForge.net]
* [http://wandora.softpedia.com/ Softpedia]
<!-- * [http://www.garshol.priv.no/tmtools/product.jsp?id=wandora Topic Maps Tools] -->
* [http://www.topicmapslab.de/projects/wandora?locale=en Topic Maps Lab]

== 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. 

* [[General FAQ]]
* [[FAQ for Wandora user]] reveals some nifty details of Wandora application.
* [http://www.wandora.org/tv Wandora tv] (Flash required)
* [http://www.wandora.org/forum/ Wandora forum]
* [[Open bugs]]

If you are interested in Topic Maps and information technology related news see [http://planet.topicmaps.org/ Planet Topic Maps] and [http://planetrdf.com/ Planet RDF].