WandoraWiki - User contributions [en]

IoT Pinger

2015-05-04T08:56:32Z

Eero: Created page with "'''This is an upcoming feature and is not included yet in the public release.''' thumb The IoT ([http://en.wikipedia.org/wiki/Internet_of_Things Internet o..."

'''This is an upcoming feature and is not included yet in the public release.'''

[[File:iot_7.png|thumb]] The IoT ([http://en.wikipedia.org/wiki/Internet_of_Things Internet of Things]) pinger is a general purpose API consumer intended to aggregate data from several different sources providing data via HTTP. The IoT Panel is found in the Wandora menu bar and presents most of the pinger's configuration options. The Pinger searches the current Topic Map for topics with an occurrence with '''Source Occurrence Type'''. Those topics are expected to correspond to an API endpoint defined by corresponding occurrence data. The pinger queries each endpoint every specified time interval and saves the response as an occurrence with '''Target Occurrence Type'''. The pinger process can be configured to stop at a set time using the '''Expires''' toggle. '''Save on tick''' saves the current Topic Map in the specified folder after each tick of the pinger in the form <code>iot_yyyy_mm_dd_hh_mm_ss.jtm</code>.

[[File:iot_1.png|400px|center]]

The log window lists starts, stops, runs and any errors the pinger might encounter.

[[File:iot_2.png|400px|center]]

In addition to ordinary web APIs the pinger supports several special local endpoints with special sources

; Time
:<code>http://wandora.org/si/iot/time</code>
: Return the current time. The time is formatted using the parameter <code>format</code>.
; Stats
: <code>http://wandora.org/si/iot/tm-stats</code>
: Return the topic and association counts for the current Topic Map in the format
{
"num_topics": <num_topics>,
"num_associations": <num_associations>;
}
; Geolocation
: <code>http://wandora.org/si/iot/geolocation</code>
: Return the current location in the form <code><latitude>, <longitude></code>

All these special endpoints implement <code>org.wandora.application.tools.iot.IoTSource</code> and are listed in <code>org.wandora.application.tools.iot.SourceMapping.sources</code>. You can add your own by simply implementing the interface and appending the source to the sources list.

== Example ==

A prepared sample Topic Map with appropriate occurrence type and endpoint topics is useful in demonstrating the functionality of the IoT Pinger.

[[Media:iot_sample.wpr]]

The IoT Source Type and IoT Target Type topics are general occurrence type topics used to signal the pinger that the topic is an endpoint. The time topic simply uses the special time endpoint to fetch the current timestamp. The date topic uses the same service to fetch the current date. The stats and geolocation topics in turn use the respective services to fetch data.

To separate text and binary data, two separate pinger instances are used. The first one fetches text data for the before-mentioned topics. The second instance is used to fetch binary image data for the Wandora logo. Note the selected "is binary" toggle for the binary pinger instance.

[[File:iot_3.png|400px|center]]

[[File:iot_4.png|400px|center]]

The first pinger will process each topic containing a HTTP source occurrence with the appropriate source type. The pinger will then load text data from the given topics to their respective target occurrence fields.

[[File:iot_5.png|600px|center]]

The binary pinger operates in a similar fashion. However, the source is now defined to be binary and the pinger treats it as such. The image data is handled appropriately and presented as an image in the appropriate occurrence field.

[[File:iot_6.png|600px|center]]

The pinger also saves a snapshot of the current Topic Map on each tick if the "save on tick" option has been selected. Each snapshot is timestamped in the format of <code>yyyy_mm_dd_hh_mm_ss</code>.

[[File:iot_8.png|400px|center]]

Wandora

2015-05-04T08:53:04Z

Eero: /* Import and Export */

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 [http://wandora.org/forum/ discussion forum]. [https://www.youtube.com/channel/UClJoFDmiThA02RmAUT5YEcw Wandora's YouTube channel] has several tutorial videos reviewing some application features. 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. 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.

== Introduction ==

Wandora is a general purpose information management application. The application is written in [http://www.oracle.com/technetwork/java/index.html 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 [http://www.gnu.org/licenses/gpl-3.0.txt GNU GPL version 3].

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

== 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.

* [[System requirements]]
* [[Change log]]
* [[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. [http://en.wikipedia.org/wiki/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 [[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 basic tutorials for Wandora. If you are a novice Wandora user, please start here. See also tutorial videos on [http://wandora.org/wandora/tv/ wandoratv].

* [[Quickstart]]
* [[Opening a topic]]

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.

* [[Create new topic]]
* [[Delete topic]]
* [[Create new association]]
* [[Delete association]]
* [[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.

* [[How to save and load project]]
* [[How to import existing topic map to Wandora]]
* [[How to export topic map in Wandora]]

Next pages discuss some other features of the Wandora application.

* [[Finding a topic]]
* [[Topic shortcuts]]
* [[Working with topic tables]]
* [[Working with topic trees]]
* [[Drag and drop topics]]
* [[Creating custom topic trees]]
* [[View all variant names of a topic]]
* [[Transform variant names to topics and associations]]
* [[Undo and redo]]

== 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 are

* [[Traditional topic panel]]
* [[Tabbed topic panel]]
* [[Graph topic panel]]
* [[Custom topic panel]]
* [[Treemap topic panel]]
* [[R topic panel]]
* [[Processing topic panel]]
* [[Sketch grid]]
* [[Webview]]
* [[Tree panel]]
* [[Search panel]]
* [[Layer info panel]]
* [[Query editor topic panel]]

== 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.

* [[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]]

'''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]]
* [[Waiana import and export]]
** [[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]]
* [[IoT Pinger]]

'''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]]
* See also page [[Graph topic panel]] and it's chapter Export options.

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 ==

[[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" | 

'''Search engine extractors'''
* [[Bing extractor]]
* [[Yahoo! BOSS extractor]]
* [[DuckDuckGo 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]]
* [[OCR 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
* [[Rekognition extractor]]
'''Social and Bookmark extractors'''
* [[Facebook Graph extractor]]
* [[Twitter extractor]]
* [[Twitter JSON extractor]]
* [[Reddit extractor]]
* [[Digg extractors]]
* <strike>[[Delicious extractors]]</strike>
* <strike>[[Diigo bookmark extractor]]</strike>
* <strike>[[Twine RDF extractor]]</strike>
'''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]]
* <strike>[[Tagthe extractor]]</strike>
* <strike>[[SemanticHacker classifier]]</strike>
* [[Zemanta extractor]]
* [[UClassify integration]]
* [[Simple Word Matching Extractor]]
* [[Similarity Word Extractor]]

'''Knowledge extractors'''
* [[OpenCyc extractor]]
* <strike>[[Subj3ct record extractor]]</strike>
* [[DBpedia extractor]]
* [[Freebase extractor]]
* [[Umbel extractors]]

| style="border: 1; margin:5; padding-left: 20px;" valign="top"| 

'''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]]
* [[MediaWiki Content 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]]
* [[Excel extractors]]
'''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 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.

* [[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]]
** [[Statistical analysis of Topic Maps in R]]
* [[Query language]]
* [[TMQL]]

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.

* [[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 ==

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'''.

* [[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]]
** [[Waiana service module]]
** [[SameAs 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 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]]

Also included is a [[Wandora modules framework|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 [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. However, we suggest that you clone [https://github.com/wandora-team/wandora Wandora's repository] at Github. Perhaps you want to push some fixes or new features back.

* [[Change log]]
* [https://github.com/wandora-team/wandora Wandora @ Github]
* [[Download]] (build date {{build date}})
* [[License of Wandora|License]]
* [[Developing Wandora]]
* [http://wandora.org/api/ Wandora Javadocs], [http://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://wandora.org/forum/viewforum.php?f=10&sid=57134deccd5ba47132334f2f1215b520 Use cases at Wandora forum].

* [http://tmra.de/2010/ TMRA 2010] tutorial slides: [http://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://wandora.org/wandora/download/other/tmra09/wandora_tutorial_leipzig.zip Example data set] is available for brave experimenters.
* Wandora poster in [http://wandora.org/wandora/download/other/poster09.pdf PDF] or [http://wandora.org/wandora/download/other/poster09.gif GIF] formats.
* Kivelä A.: [http://wandora.org/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish). (English Abstract: [http://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://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://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 ==

* [https://github.com/wandora-team/wandora Github]
* [http://twitter.com/#!/wandora_app Twitter]
* [https://www.youtube.com/channel/UClJoFDmiThA02RmAUT5YEcw YouTube]
* [http://freecode.com/projects/wandora/ Freecode]
* [http://sourceforge.net/projects/wandora/ SourceForge.net]

* [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://wandora.org/tv Wandora tv]
* [http://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].

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Twitter extractor

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Eero:

Wandora's Twitter extractor performs a [http://www.twitter.com Twitter] search and converts the result set to topics and associations. Extracted topics and associations can then be visualized as a graph, for example. Also, it is possible to merge information from other source into the graph generated by Twitter extractor. Wandora's Twitter extractor starts with a menu option '''File > Extract > Social > Twitter extractor...'''. Choosing the menu option opens up a dialog window used to specify a search word and search options. Twitter search and extraction starts by pressing '''Extract''' button.

== Twitter extraction example ==

In this set of screen captures, Wandora user performs Twitter extraction with a hashtag '''#topicmaps'''. Then Wandora user browses created topics and associations in [[Traditional topic panel]]. Finally user switches to [[Processing topic panel]] and loads Processing script '''TopicRing.sketch''' and visualizes Twitter topics and associations by running the script.

[[Image:twitter_extractor_01.gif|center]]

[[Image:twitter_extractor_02.gif|center]]

[[Image:twitter_extractor_03.gif|center]]

[[Image:twitter_extractor_04.gif|center]]

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[[Image:twitter_extractor_09.gif|center]]

[[Image:twitter_extractor_10.gif|center]]

[[Image:twitter_extractor_11.gif|center]]

[[Image:twitter_extractor_12.gif|center]]

[[Image:twitter_extractor_14.gif|center]]

[[Image:twitter_extractor_15.gif|center]]

==See also==
*[[Twitter JSON extractor]]

File:Twitter json 3.png

2015-04-27T13:08:14Z

Eero: Eero uploaded a new version of "File:Twitter json 3.png"

Similarity Word Extractor

2015-04-27T13:04:37Z

Eero: Created page with "The word similarity extractor uses a given similarity metric to associate words with sufficiently similar topic data. The configuration dialog for the extractor allows setting..."

The word similarity extractor uses a given similarity metric to associate words
with sufficiently similar topic data. The configuration dialog for the extractor
allows setting the metric, similarity threshold as well as a few other settings
controlling the association process:

; Similarity metric
: Which similarity metric to use. The implementation relies on [https://github.com/Simmetrics/simmetrics SimMetrics].
; Threshold
: The level of similarity required in order to consider data similar. Level of 0 corresponds to everything being considered similar and 1 corresponds to only identical data being considered similar.
; Case sensitive
: Whether to match words in a case sensitive manner.
; Variant Name
: Whether to consider the variant name of the topic when determining a match
; Base Name
: Whether to consider the base name of the topic when determining a match
; Instance Data
: Whether to consider instance data of the topic when determining a match

The extractor is found in '''File > Classification > Word Similarity Extractor'''.

== Example ==

The extractor's operations is demonstrated using the current description of
Wandora found on [http://wandora.org wandora.org]:

<blockquote>
Wandora is a tool for people who collect and process information, especially networked knowledge and knowledge about WWW resources. With Wandora you can aggregate and combine information from various different sources. You can manipulate the collected knowledge flexible and efficiently, and without programming skills. More generally speaking Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora suits well for constructing and maintaining vocabularies, ontologies and information mashups. Application areas include linked data, open data, data integration, business intelligence, digital preservation and data journalism. Wandora's license is GNU GPL. Wandora application is developed actively by a small number of experienced software developers. We call ourselves as the Wandora Team.
</blockquote>

First create a topic to contain this text data via '''Topics > New topic'''.

[[File:word_similarity_1.png]]

Open the topic and add the text as English occurrence data. Use the default occurrence type by pressing '''Use default'''.

[[File:word_similarity_2.png]]
[[File:word_similarity_3.png]]

The default configuration options are as listed in the configuration dialog.

[[File:word_similarity_4.png]]

Open the extractor via '''File > Extract > Classification > Word Similarity extractor'''. In the '''raw''' panel specify words that are similar to what appear in the description text

[[File:word_similarity_5.png]]

The extractor then associates the description topic with the words according to the given extraction parameters.

[[File:word_similarity_6.png]]

The generated associations contain three players describing the topic, word as well as the similarity score given by the specified metric. Here '''preserve''' was considered to have a similarity score of 0.875 to the word '''preservation''' found in the description text.

[[File:word_similarity_7.png]]

==See also==
*[[Simple Word Matching Extractor]]

Simple Word Matching Extractor

2015-04-27T13:04:27Z

Eero: Created page with "The simple word extractor associates a list of keywords with topics with corresponding data. Several configuration options control how this association is made. See [[Configur..."

The simple word extractor associates a list of keywords with topics with
corresponding data. Several configuration options control how this association
is made. See [[Configuring tools]] for instructions on how to configure tools.

; Regex
: Whether to treat each word a regular expression instead of a substring.
; Case sensitive
: Whether to match words in a case sensitive manner.
; Match word
: Whether to require the word to match completely (in terms of whitespace), i.e. if disabled, "white" would not match "whitespace".
; Base Name
: Whether to consider the base name of the topic when determining a match
; Variant Name
: Whether to consider the variant name of the topic when determining a match
; Instance Data
: Whether to consider instance data of the topic when determining a match

The extractor is found in '''File > Classification > Word Extractor'''.

== Example ==

The extractor's operations is demonstrated using the current description of
Wandora found on [http://wandora.org wandora.org]:

<blockquote>
Wandora is a tool for people who collect and process information, especially networked knowledge and knowledge about WWW resources. With Wandora you can aggregate and combine information from various different sources. You can manipulate the collected knowledge flexible and efficiently, and without programming skills. More generally speaking Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora suits well for constructing and maintaining vocabularies, ontologies and information mashups. Application areas include linked data, open data, data integration, business intelligence, digital preservation and data journalism. Wandora's license is GNU GPL. Wandora application is developed actively by a small number of experienced software developers. We call ourselves as the Wandora Team.
</blockquote>

First create a topic to contain this text data via '''Topics > New topic'''.

[[File:simple_word_1.png]]

Open the topic and add the text as English occurrence data. Use the default occurrence type by pressing '''Use default'''.

[[File:simple_word_2.png]]
[[File:simple_word_3.png]]

Open the extractor via '''File > Extract > Classification > Word extractor'''

[[File:simple_word_4.png]]

In the '''raw''' panel specify words Java and GNU, which we expect to find in
the description.

[[File:simple_word_5.png]]

The extractor reports two associations with the given words.

[[File:simple_word_6.png]]

These associations are then listed in the previously created topic.

[[File:simple_word_7.png]]

==See also==
*[[Similarity Word Extractor]]

Twitter JSON extractor

2015-04-27T13:04:07Z

Eero:

The Twitter JSON extractor is a simple extractor that forms topic data from a given JSON response from the [https://dev.twitter.com/rest/public Twitter REST APIs]. The underlying implementation uses the [http://twitter4j.org/ Twitter4j] library like the [[Twitter extractor]].

The extractor is found in '''File > Social > Twitter JSON Extractor'''.

== Example ==

We first use [https://github.com/twitter/twurl Twurl] to fetch the timeline of
[https://twitter.com/wandora_app @wandora_app] and save it to disk. Then open
the extractor in Wandora and point it to the file containing the JSON response.

[[File:twitter_json_1.png]]
[[File:twitter_json_2.png]]

The extraction then yields a topic structure similar to that which is generated with the [[Twitter extractor]].

[[File:twitter_json_3.png]]

==See also==
*[[Twitter extractor]]

Twitter JSON extractor

2015-04-27T13:03:30Z

Eero: Created page with "The Twitter JSON extractor is a simple extractor that forms topic data from a given JSON response from the [https://dev.twitter.com/rest/public Twitter REST APIs]. The underly..."

Wandora

2015-04-27T13:03:14Z

Eero:

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 [http://wandora.org/forum/ discussion forum]. [https://www.youtube.com/channel/UClJoFDmiThA02RmAUT5YEcw Wandora's YouTube channel] has several tutorial videos reviewing some application features. 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. 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.

== Introduction ==

Wandora is a general purpose information management application. The application is written in [http://www.oracle.com/technetwork/java/index.html 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 [http://www.gnu.org/licenses/gpl-3.0.txt GNU GPL version 3].

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

== 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.

* [[System requirements]]
* [[Change log]]
* [[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. [http://en.wikipedia.org/wiki/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 [[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 basic tutorials for Wandora. If you are a novice Wandora user, please start here. See also tutorial videos on [http://wandora.org/wandora/tv/ wandoratv].

* [[Quickstart]]
* [[Opening a topic]]

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.

* [[Create new topic]]
* [[Delete topic]]
* [[Create new association]]
* [[Delete association]]
* [[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.

* [[How to save and load project]]
* [[How to import existing topic map to Wandora]]
* [[How to export topic map in Wandora]]

Next pages discuss some other features of the Wandora application.

* [[Finding a topic]]
* [[Topic shortcuts]]
* [[Working with topic tables]]
* [[Working with topic trees]]
* [[Drag and drop topics]]
* [[Creating custom topic trees]]
* [[View all variant names of a topic]]
* [[Transform variant names to topics and associations]]
* [[Undo and redo]]

== 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 are

* [[Traditional topic panel]]
* [[Tabbed topic panel]]
* [[Graph topic panel]]
* [[Custom topic panel]]
* [[Treemap topic panel]]
* [[R topic panel]]
* [[Processing topic panel]]
* [[Sketch grid]]
* [[Webview]]
* [[Tree panel]]
* [[Search panel]]
* [[Layer info panel]]
* [[Query editor topic panel]]

== 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.

* [[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]]

'''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]]
* [[Waiana import and export]]
** [[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]]
* See also page [[Graph topic panel]] and it's chapter Export options.

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 ==

[[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" | 

'''Search engine extractors'''
* [[Bing extractor]]
* [[Yahoo! BOSS extractor]]
* [[DuckDuckGo 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]]
* [[OCR 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
* [[Rekognition extractor]]
'''Social and Bookmark extractors'''
* [[Facebook Graph extractor]]
* [[Twitter extractor]]
* [[Twitter JSON extractor]]
* [[Reddit extractor]]
* [[Digg extractors]]
* <strike>[[Delicious extractors]]</strike>
* <strike>[[Diigo bookmark extractor]]</strike>
* <strike>[[Twine RDF extractor]]</strike>
'''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]]
* <strike>[[Tagthe extractor]]</strike>
* <strike>[[SemanticHacker classifier]]</strike>
* [[Zemanta extractor]]
* [[UClassify integration]]
* [[Simple Word Matching Extractor]]
* [[Similarity Word Extractor]]

'''Knowledge extractors'''
* [[OpenCyc extractor]]
* <strike>[[Subj3ct record extractor]]</strike>
* [[DBpedia extractor]]
* [[Freebase extractor]]
* [[Umbel extractors]]

| style="border: 1; margin:5; padding-left: 20px;" valign="top"| 

'''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]]
* [[MediaWiki Content 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]]
* [[Excel extractors]]
'''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 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.

* [[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]]
** [[Statistical analysis of Topic Maps in R]]
* [[Query language]]
* [[TMQL]]

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.

* [[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 ==

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'''.

* [[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]]
** [[Waiana service module]]
** [[SameAs 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 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]]

Also included is a [[Wandora modules framework|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 [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. However, we suggest that you clone [https://github.com/wandora-team/wandora Wandora's repository] at Github. Perhaps you want to push some fixes or new features back.

* [[Change log]]
* [https://github.com/wandora-team/wandora Wandora @ Github]
* [[Download]] (build date {{build date}})
* [[License of Wandora|License]]
* [[Developing Wandora]]
* [http://wandora.org/api/ Wandora Javadocs], [http://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://wandora.org/forum/viewforum.php?f=10&sid=57134deccd5ba47132334f2f1215b520 Use cases at Wandora forum].

* [http://tmra.de/2010/ TMRA 2010] tutorial slides: [http://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://wandora.org/wandora/download/other/tmra09/wandora_tutorial_leipzig.zip Example data set] is available for brave experimenters.
* Wandora poster in [http://wandora.org/wandora/download/other/poster09.pdf PDF] or [http://wandora.org/wandora/download/other/poster09.gif GIF] formats.
* Kivelä A.: [http://wandora.org/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish). (English Abstract: [http://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://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://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 ==

* [https://github.com/wandora-team/wandora Github]
* [http://twitter.com/#!/wandora_app Twitter]
* [https://www.youtube.com/channel/UClJoFDmiThA02RmAUT5YEcw YouTube]
* [http://freecode.com/projects/wandora/ Freecode]
* [http://sourceforge.net/projects/wandora/ SourceForge.net]

* [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://wandora.org/tv Wandora tv]
* [http://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].

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New York Times Article Search API extractor

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The New York Times API Extractor is used to parse articles from the [http://developer.nytimes.com/docs/read/article_search_api_v2 New York Times Article Search service] into Topic Map data. The service requires credentials for access. API keys for the article search as well as other NYT end points can be requested on the NYT [http://developer.nytimes.com/ Developer Pages]. In Wandora, the API key is not saved between sessions.

== Example ==

As an example, the service is queried for articles related to Barack Obama. Extractors using NYT services are found in '''File > Extract > News > New York Times API Extractor'''

[[File:nyt_article_1.png]]

The Article Search dialog mirrors options available in the Article Search service. In addition to a search query, the service allows selecting a subset of fields to return for each article. The results may also be restricted to a certain date range, offset with a page number (i.e. a multiple of 10 articles) or sorted newest or oldest first.

[[File:nyt_article_2.png]]

If an API key isn't already stored it is requested.

[[File:nyt_article_3.png]]

Often the query returns more than one page, or 10 articles, and the extractor prompts for further action. The pagination options allow for either

* Stopping and not retrieving additional articles
* Extracting one more page and stopping
* Extracting one more page and prompting again
* Extract 10 more pages and prompting again
* Extracting all remaining pages

The NYT article database is large, and vague queries might return results sets in the order of thousands of articles. Review the API rate limits before running excessive queries in order to avoid exhausting available quota.

[[File:nyt_article_4.png]]

The fetched articles are then parsed into topics and associations representing relations between articles, keywords etc.

[[File:nyt_article_5.png]]

In particular the keyword structure used by the service is parsed into a topic structure associating articles with common keywords.

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Rekognition extractor

2014-08-18T11:04:33Z

Eero: Created page with "The ReKognition Face Detection extractor uses the [http://rekognition.com/ ReKognition Face Detection API] to construct Topic Map data from image data containing faces. Most o..."

The ReKognition Face Detection extractor uses the [http://rekognition.com/ ReKognition Face Detection API] to construct Topic Map data from image data containing faces. Most of the API features are supported and are available. The API and hence the extractor both require an API key available after registeration [http://rekognition.com/user/create here].

The extractor is located in '''File > Extract > Media > ReKognition extractor...'''

Most of the qustomization options available are listed in a configuration dialog for the tool. Most of the face detection features are represented as either occurrance data of a detection topic or as separate topics associated with the detection and possibly a confidence value topic. The extractor also makes use of the celebrity naming functionality of the API. An attempt is made to name celebrities in a given image so that the best match in terms of confidence is selected given that the confidence is larger than the treshold specified in the configuration dialog. Other matches are also added as associated topics to the detection.

It should be noted that large scale usage of the API is paid and more detailed searches in terms details queried contribute more to the usage count and thus the cost of usage. Therefore one should expect higher costs for detailed and large scale usage of the API also within Wandora.

== Example 1 ==

A simple use case where an [http://upload.wikimedia.org/wikipedia/commons/8/8b/Jim_Carrey_2008.jpg image of Jim Carrey] is subjected to detection is detailed here.

First we check all the detection jobs and celebrity naming functionality to demonstrate the results we obtain.

[[Image:rekognition_extractor_01.png|center]]

Confirming the configuration we are asked to input the API key and secret.

[[Image:rekognition_extractor_02.png|center]]

We can then open the extractor dialog and give the URL for the image we want to work with.

[[Image:rekognition_extractor_03.png|center]]

The API is then contacted and the response is parsed into TopicMap data. Here we find a highly confident match to Jim Carrey as expected. Also a long list of features as well as possible emotions and other celebrity matches are listed.

[[Image:rekognition_extractor_04.png|center]]

== Example 2 ==

For a more complex use case we use the [[Reddit extractor]] to find the top posts currently in [http://www.reddit.com/r/photoshopbattles r/photoshopbattles] and attempt to name possible celebrities. The reddit API extraction returns a list of links including at least of few cases where we expect a celebrity to be matched.

[[Image:rekognition_extractor_05.png|center]]

Finding the destination associations for those links we are able to select a list of corresponding image URLs.

[[Image:rekognition_extractor_06.png|center]]

We then navigate through a context menu to '''Topics > Subject locators > Extract with subject locator > Media > ReKognition face detection extractor''' to run an extraction on each of the image URLs.

[[Image:rekognition_extractor_07.png|center]]

Looking through the results we find a lot of detections where in addition to Jim Carrey before the API was able to detect Kate Upton in one of the pictures. The link description leads us to believe that the detection is valid.

[[Image:rekognition_extractor_08.png|center]]

On the other hand a [http://i.imgur.com/7uCWdjw.jpg "Man with ice cream"] is mistaken for a happy [http://en.wikipedia.org/wiki/Gianluigi_Buffon Gianluigi Buffon] known for his long career as the first choice goalkeeper for Juventus and the Italy national team.

[[Image:rekognition_extractor_09.png|center]]

Wandora

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Eero:

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 [http://wandora.org/forum/ discussion forum]. [https://www.youtube.com/channel/UClJoFDmiThA02RmAUT5YEcw Wandora's YouTube channel] has several tutorial videos reviewing some application features. 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. 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.

== Introduction ==

Wandora is a general purpose information management application. The application is written in [http://www.oracle.com/technetwork/java/index.html 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 [http://www.gnu.org/licenses/gpl-3.0.txt GNU GPL version 3].

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

== 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.

* [[System requirements]]
* [[Change log]]
* [[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. [http://en.wikipedia.org/wiki/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 [[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 basic tutorials for Wandora. If you are a novice Wandora user, please start here. See also tutorial videos on [http://wandora.org/wandora/tv/ wandoratv].

* [[Quickstart]]
* [[Opening a topic]]

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.

* [[Create new topic]]
* [[Delete topic]]
* [[Create new association]]
* [[Delete association]]
* [[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.

* [[How to save and load project]]
* [[How to import existing topic map to Wandora]]
* [[How to export topic map in Wandora]]

Next pages discuss some other features of the Wandora application.

* [[Finding a topic]]
* [[Topic shortcuts]]
* [[Working with topic tables]]
* [[Working with topic trees]]
* [[Drag and drop topics]]
* [[Creating custom topic trees]]
* [[View all variant names of a topic]]
* [[Transform variant names to topics and associations]]
* [[Undo and redo]]

== 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 are

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

== 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]]

* [[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]]
* [[Waiana 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]]
* See also page [[Graph topic panel]] and it's chapter Export options.

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 ==

[[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" | 

'''Search engine extractors'''
* [[Bing extractor]]
* [[Yahoo! BOSS extractor]]
* [[DuckDuckGo 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]]
* [[OCR 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
* [[Rekognition extractor]]
'''Social and Bookmark extractors'''
* [[Facebook Graph extractor]]
* [[Twitter extractor]]
* [[Reddit extractor]]
* [[Digg extractors]]
* <strike>[[Delicious extractors]]</strike>
* <strike>[[Diigo bookmark extractor]]</strike>
* <strike>[[Twine RDF extractor]]</strike>
'''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]]
* <strike>[[Tagthe extractor]]</strike>
* <strike>[[SemanticHacker classifier]]</strike>
* [[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"| 

'''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]]
* [[MediaWiki Content 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]]
* [[Excel extractors]]
'''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 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.

* [[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]]
** [[Statistical analysis of Topic Maps in R]]
* [[Query language]]
* [[TMQL]]

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.

* [[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 ==

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'''.

* [[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]]
** [[Waiana service module]]
** [[SameAs 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 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]]

Also included is a [[Wandora modules framework|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 [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. However, we suggest that you clone [https://github.com/wandora-team/wandora Wandora's repository] at Github. Perhaps you want to push some fixes or new features back.

* [[Change log]]
* [https://github.com/wandora-team/wandora Wandora @ Github]
* [[Download]] (build date {{build date}})
* [[License of Wandora|License]]
* [[Developing Wandora]]
* [http://wandora.org/api/ Wandora Javadocs], [http://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://wandora.org/forum/viewforum.php?f=10&sid=57134deccd5ba47132334f2f1215b520 Use cases at Wandora forum].

* [http://tmra.de/2010/ TMRA 2010] tutorial slides: [http://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://wandora.org/wandora/download/other/tmra09/wandora_tutorial_leipzig.zip Example data set] is available for brave experimenters.
* Wandora poster in [http://wandora.org/wandora/download/other/poster09.pdf PDF] or [http://wandora.org/wandora/download/other/poster09.gif GIF] formats.
* Kivelä A.: [http://wandora.org/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish). (English Abstract: [http://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://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://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 ==

* [https://github.com/wandora-team/wandora Github]
* [http://twitter.com/#!/wandora_app Twitter]
* [https://www.youtube.com/channel/UClJoFDmiThA02RmAUT5YEcw YouTube]
* [http://freecode.com/projects/wandora/ Freecode]
* [http://sourceforge.net/projects/wandora/ SourceForge.net]

* [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://wandora.org/tv Wandora tv]
* [http://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].

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