Posted:August 8, 2011

Geshi NetworkVisualization + Analysis Pushes Aside Cytoscape

Though I never intended it, some posts of mine from a few years back dealing with 26 tools for large-scale graph visualization have been some of the most popular on this site. Indeed, my recommendation for Cytoscape for viewing large-scale graphs ranks within the top 5 posts all time on this site.

When that analysis was done in January 2008 my company was in the midst of needing to process the large UMBEL vocabulary, which now consists of 28,000 concepts. Like anything else, need drives research and demand, and after reviewing many graphing programs, we chose Cytoscape, then provided some ongoing guidelines in its use for semantic Web purposes. We have continued to use it productively in the intervening years.

Like for any tool, one reviews and picks the best at the time of need. Most recently, however, with growing customer usage of large ontologies and the development of our own structOntology editing and managing framework, we have begun to butt up against the limitations of large-scale graph and network analysis. With this post, we announce our new favorite tool for semantic Web network and graph analysis — Gephi — and explain its use and showcase a current example.

The Cytoscape Baseline and Limitations

Three and one-half years ago when I first wrote about Cytoscape, it was at version 2.5. Today, it is at version 2.8, and many aspects have seen improvement (including its Web site). However, in other respects, development has slowed. For example, version 3.x was first discussed more than three years ago; it is still not available today.

Though the system is open source, Cytoscape has also largely been developed with external grant funds. Like other similarly funded projects, once and when grant funds slow, development slows as well. While there has clearly been an active community behind Cytoscape, it is beginning to feel tired and a bit long in the tooth. From a semantic Web standpoint, some of the limitations of the current Cytoscape include:

  • Difficult conversion of existing ontologies — Cytoscape requires creating a CSV input; there was an earlier RDFscape plug-in that held great promise to bridge the software into the RDF and semantic Web sphere, but it has not remained active
  • Network analysis — one of the early and valuable generalized network analysis plug-ins was NetworkAnalyzer; however, that component has not seen active development in three years, and dynamic new generalized modules suitable for social network analysis (SNA) and small-world networks have not been apparent
  • Slow performance and too-frequent crashes — Cytoscape has always had a quirky interface and frequent crashes; later versions are a bit more stable, but usability remains a challenge
  • Largely supported by the biomedical community — from the beginning, Cytoscape was a project of the biomedical community. Most plug-ins still pertain to that space. Because of support for OBO (Open Biomedical and Biological Ontologies) formats and a lack of uptake by the broader semantic Web community, RDF- and OWL-based development has been keenly lacking
  • Aside from PDFs, poor ability to output large graphs in a viewable manner
  • Limited layout support — and poor performance for many of those included with the standard package.

Undoubtedly, were we doing semantic technologies in the biomedical space, we might well develop our own plug-ins and contribute to the Cytoscape project to help overcome some of these limitations. But, because I am a tools geek (see my Sweet Tools listing with nearly 1000 semantic Web and -related tools), I decided to check out the current state of large-scale visualization tools and see if any had made progress on some of our outstanding objectives.

Choosing Gephi and Using It

There are three classes of graph tools in the semantic technology space:

  1. Ontology navigation and discovery, to which the Relation Browser and RelFinder are notable examples
  2. Ontology structure visualization (and sometimes editing), such as the GraphViz (OWLViz) or OntoGraf tools used in Protégé (or the nice FlexViz, again used by the OBO community), and
  3. Large-scale graph visualization in order to gain a complete picture and macro relationships in the ontology.

One could argue that the first two categories have received the most current development attention. But, I would also argue that the third class is one of the most critical:  to understand where one is in a large knowledge space, much better larger-scale visualization and navigation tools are needed. Unfortunately, this third category is also the one that appears to be receiving the least development attention. (To be sure, large-scale graphs pose computational and performance challenges.)

In the nearly four years since my last major survey of 26 tools in this category, the new entrants appear quite limited. I’ve surely overlooked some, but the most notable are Gruff, NAViGaTOR, NetworkX and Gephi [1]. Gruff actually appears to belong most in Category #2; I could find no examples of graphs on the scale of thousands of nodes. NAViGaTOR is biomedical only. NetworkX has no direct semantic graph importing and — while apparently some RDF libraries can be used for manipulating imports — alternative workflows were too complex for me to tackle for initial evaluation. This leaves Gephi as the only potential new candidate.

From a clean Web site to well-designed intro tutorials, first impressions of Gephi are strongly positive. The real proof, of course, was getting it to perform against my real use case tests. For that, I used a “big” ontology for a current client that captures about 3000 different concepts and their relationships and more than 100 properties. What I recount here — from first installing the program and plug-ins and then setting up, analyzing, defining display parameters, and then publishing the results — took me less than a day from a totally cold start. The Gephi program and environment is surprisingly easy to learn, aided by some great tutorials and online info (see concluding section).

The critical enabler for being able to use Gephi for this source and for my purposes is the SemanticWebImport plug-in, recently developed by Fabien Gandon and his team at Inria as part of the Edelweiss project [2]. Once the plug-in is installed, you need only open up the SemanticWebImport tab, give it the URL of your source ontology, and pick the Start button (middle panel):

SemWeb Plug-in for GephiNote the SemanticWebImport tool also has the ability (middle panel) to issue queries to a SPARQL endpoint, the results of which return a results graph (partial) from the source ontology. (This feature is not further discussed herein.) This ontology load and display capability worked without error for the five or six OWL 2 ontologies I initially tested against the system.

Once loaded, an ontology (graph) can be manipulated with a conventional IDE-like interface of tabs and views. In the right-hand panels above we are selecting various network analysis routines to run, in this case Average Degrees. Once one or more of these analysis options is run, we can use the results to then cluster or visualize the graph; the upper left panel shows highlighting the Modularity Class, which is how I did the community (clustering) analysis of our big test ontology. (When run you can also assign different colors to the cluster families.) I also did some filtering of extraneous nodes and properties at this stage and also instructed the system via the ranking analysis to show nodes with more link connections as larger than those nodes with fewer links.

At this juncture, you can also set the scale for varying such display options as linear or some power function. You can also select different graph layout options (lower left panel). There are many layout plug-in options for Gephi. The layout plugin called OpenOrd, for instance, is reported to be able to scale to millions of nodes.

At this point I played extensively with the combination of filters, analysis, clusters, partitions and rankings (as may be separately applied to nodes and edges) to: 1) begin to understand the gross structure and characteristics of the big graph; and 2) refine the ultimate look I wanted my published graph to have.

In our example, I ultimately chose the standard Yifan Hu layout in order to get the communities (clusters) to aggregate close to one another on the graph. I then applied the Parallel Force Atlas layout to organize the nodes and make the spacings more uniform. The parallel aspect of this force-based layout allows these intense calculations to run faster. The result of these two layouts in sequence is then what was used for the results displays.

Upon completion of this analysis, I was ready to publish the graph. One of the best aspects of Gephi is its flexibility and control over outputs. Via the main Preview tab, I was able to do my final configurations for the published graph:

Publication Options for GephiThe graph results from the earlier-worked out filters and clusters and colors are shown in the right-hand Preview pane. On the left-hand side, many aspects of the final display are set, such as labels on or off, font sizes, colors, etc. It is worth looking at the figure above in full size to see some of the options available.

Standard output options include either SVG (vector image) or PDFs, as shown at the lower left, with output size scaling via slider bar. Also, it is possible to do standard saves under a variety of file formats or to do targeted exports.

One really excellent publication option is to create a dynamically zoomable display using the Seadragon technology via a separate Seadragon Web Export plug-in. (However, because of cross-site scripting limitations due to security concerns, I only use that option for specific sites. See next section for the Zoom It option — based on Seadragon — to workaround that limitation.)

Outputs Speak for Themselves

I am very pleased with the advances in display and analysis provided by Gephi. Using the Zoom It alternative [3] to embedded Seadragon, we can see our big ontology example with:

  • All 3000 nodes labeled, with connections shown (though you must must zoom to see) and
  • When zooming (use scroll wheel or + icon) or panning (via mouse down moves), wait a couple of seconds to get the clearest image refresh:

Note: at standard resolution, if this graph were to be rendered in actual size, it would be larger than 7 feet by 7 feet square at full zoom !!!

To compare output options, you may also;

Still, Some Improvements Would be Welcomed

It is notable that Gephi still only versions itself as an “alpha”. There is already a robust user community with promise for much more technology to come.

As an alpha, Gephi is remarkably stable and well-developed. Though clearly useful as is, I measure the state of Gephi against my complete list of desired functionality, with these items still missing:

  • Real-time and interactive navigation — the ability to move through the graph interactively and to issue queries and discover relationships
  • Huge node numbers — perhaps the OpenOrd plug-in somewhat addresses this need. We will be testing Gephi against UMBEL, which is an order of magnitude larger than our test big ontology
  • More node and edge control — Cytoscape still retains the advantage in the degree to which nodes and edges can be graphically styled
  • Full round-tripping — being able to use Gephi in an edit mode would be fantastic; the edit functionality is fairly straightforward, but the ability to round-trip in appropriate formats (OWL, RDF or otherwise) may be the greater sticking point.

Ultimately, of course, as I explained in an earlier presentation on a Normative Landscape for Ontology Tools, we would like to see a full-blown graphical program tie in directly with the OWL API. Some initial attempts toward that have been made with the non-Gephi GLOW visualization approach, but it is still in very early phases with ongoing commitments unknown. Optimally, it would be great to see a Gephi plug-in that ties directly to the OWL API.

In any event, while perhaps Cytoscape development has stalled a bit for semantic technology purposes, Gephi and its SemanticWebImport plug-in have come roaring into the lead. This is a fine toolset that promises usefulness for many years to come.

Some Further Gephi Links

To learn more about Gephi, also see the:

Also, for future developments across the graph visualization spectrum, check out the Wikipedia general visualization tools listing on a periodic basis.


[1] The R open source math and statistics package is very rich with apparently some graph visualization capabilities, such as the dedicated network analysis and visualization project statnet. rrdf may also provide an interesting path for RDF imports. R and its family of tools may indeed be quite promising, but the commitment necessary to R appears quite daunting. Longer-term, R may represent a more powerful upgrade path for our general toolsets. Neo4j is also a rising star in graph databases, with its own visualization components. However, since we did not want to convert our underlying data stores, we also did not test this option.
[2] Erwan Demairy is the lead developer and committer for SemanticWebImport. The first version was released in mid-April 2011.
[3] For presentations like this blog post, the Seadragon JavaScript enforces some security restrictions against cross-site scripting. To overcome that, the option I followed was to:
  • Use Gephi’s SVG export option
  • Open the SVG in Inkscape
  • Expand the size of the diagram as needed (with locked dimensions to prevent distortion)
  • Save As a PNG
  • Go to Zoom It and submit the image file
  • Choose the embed function, and
  • Embed the link provided, which is what is shown above.
(Though Zoom.it also accepts SVG files directly, I found performance to be spotty, with many graphical elements dropped in the final rendering.)

Posted by AI3's author, Mike Bergman Posted on August 8, 2011 at 3:27 am in Ontologies, Open Source, Semantic Web Tools, UMBEL | Comments (0)
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Posted:January 26, 2010

AI3's Ontologies category
140 Tools: 20 Must Haves, 70 Possible Usefuls, and 50 Has Beens and Marginals

Well, for another client and another purpose, I was goaded into screening my Sweet Tools listing of semantic Web and -related tools and to assemble stuff from every other nook and cranny I could find. The net result is this enclosed listing of some 140 or so tools — most open source — related to semantic Web ontology building in one way or another.

Ever since I wrote my Intrepid Guide to Ontologies nearly three years ago (and one of the more popular articles of this site, though it is now perhaps a bit long in the tooth), I have been intrigued with how these semantic structures are built and maintained. That interest, in no small measure, is why I continue to maintain the Sweet Tools listing.

As far as I know, the following is the largest and most comprehensive listing of ontology building tools available. I broadly interpret the classification of ‘ontology building’; I include, for example, vocabulary extraction and prompting tools, as well as ontology visualization and mapping.

There are some 140 tools, perhaps 90 or so are still in active use. (Given the scope, not every tool could be inspected in detail. Some listed as being perhaps inactive may not be so, and others not in that category perhaps should be.) Of the entire roster of tools, somewhere on the order of 12 to 20 are quite impressive and deserving of local installation, test runs, and close inspection.

There are relatively few tools useful to non-specialists (or useful to engaging knowledgeable publics in the ontology-building exercise). There appear to be key gaps in the entire workflow from domain scoping and initial ontology definition and vocabulary candidates, to longer-term maintenance and revision. For example, spreadsheets would appear to be a possible useful first step in any workflow process (which is why irON is listed), but the spreadsheet tool per se is not listed herein (nor are text editors).

I surely have missed some tools and likely improperly assigned others. Please drop me an email or comment on this post with any revisions or suggestions.

Some Worth A Closer Look

In my own view, there are some tools that definitely deserve a closer look. My favorite candidates — for very different reasons and for very different places in the workflow — are (in no particular order): Apelon DTS, irON, FlexViz, Knoodl, Protégé, diagramic.com, BooWa, COE, ontopia, Anzo, PoolParty, Vine (and voc2rdf), Erca, Graphl, and GrOWL. Each one of these links is more fully described below. Also, all tools in the Vocabulary Prompting Tools category (which also includes extraction) are worth reviewing since all or nearly all have online demos.

Other tools may also be deserving, depending on use case. Some of the more specific analysis and conversion tools, for example, are in the Miscellaneous category.

Also, some purists may quibble with why some tools are listed here (such as inclusion of some stuff related to Topic Maps). Well, my answer to that is there are no real complete solutions, and whatever we can pragmatically do today requires glueing together many disparate parts.

Comprehensive Ontology Tools

  • Altova SemanticWorks is a visual RDF and OWL editor that auto-generates RDF/XML or nTriples based on visual ontology design. No open source version available
  • Amine is a rather comprehensive, open source platform for the development of intelligent and multi-agent systems written in Java. As one of its components, it has an ontology GUI with text- and tree-based editing modes, with some graph visualization
  • The Apelon DTS (Distributed Terminology System) is an integrated set of open source components that provides comprehensive terminology services in distributed application environments. DTS supports national and international data standards, which are a necessary foundation for comparable and interoperable health information, as well as local vocabularies. Typical applications for DTS include clinical data entry, administrative review, problem-list and code-set management, guideline creation, decision support and information retrieval.. Though not strictly an ontology management system, Apelon DTS has plug-ins that provide visualization of concept graphs and related functionality that make it close to a complete solution
  • DOME is a programmable XML editor which is being used in a knowledge extraction role to transform Web pages into RDF, and available as Eclipse plug-ins. DOME stands for DERI Ontology Management Environment
  • FlexViz is a Flex-based, Protégé-like client-side ontology creation, management and viewing tool; very impressive. The code is distributed from Sourceforge; there is a nice online demo available; there is a nice explanatory paper on the system, and the developer, Chris Callendar, has a useful blog with Flex development tips
  • Knoodl facilitates community-oriented development of OWL based ontologies and RDF knowledge bases. It also serves as a semantic technology platform, offering a Java service-based interface or a SPARQL-based interface so that communities can build their own semantic applications using their ontologies and knowledgebases. It is hosted in the Amazon EC2 cloud and is available for free; private versions may also be obtained. See especially the screencast for a quick introduction
  • The NeOn toolkit is a state-of-the-art, open source multi-platform ontology engineering environment, which provides comprehensive support for the ontology engineering life-cycle. The v2.3.0 toolkit is based on the Eclipse platform, a leading development environment, and provides an extensive set of plug-ins covering a variety of ontology engineering activities. You can add these plug-ins or get a current listing from the built-in updating mechanism
  • ontopia is a relative complete suite of tools for building, maintaining, and deploying Topic Maps-based applications; open source, and written in Java. Could not find online demos, but there are screenshots and there is visualization of topic relationships
  • Protégé is a free, open source visual ontology editor and knowledge-base framework. The Protégé platform supports two main ways of modeling ontologies via the Protégé-Frames and Protégé-OWL editors. Protégé ontologies can be exported into a variety of formats including RDF(S), OWL, and XML Schema. There are a large number of third-party plugins that extends the platform’s functionality
    • Protégé Plugin Library – frequently consult this page to review new additions to the Protégé editor; presently there are dozens of specific plugins, most related to the semantic Web and most open source
    • Collaborative Protégé is a plug-in extension of the existing Protégé system that supports collaborative ontology editing as well as annotation of both ontology components and ontology changes. In addition to the common ontology editing operations, it enables annotation of both ontology components and ontology changes. It supports the searching and filtering of user annotations, also known as notes, based on different criteria. There is also an online demo
  • TopBraid Composer is an enterprise-class modeling environment for developing Semantic Web ontologies and building semantic applications. Fully compliant with W3C standards, Composer offers comprehensive support for developing, managing and testing configurations of knowledge models and their instance knowledge bases. It is based on the Eclipse IDE. There is a free version (after registration) for small ontologies.

Not Apparently in Active Use

  • Adaptiva is a user-centred ontology building environment, based on using multiple strategies to construct an ontology, minimising user input by using adaptive information extraction
  • Exteca is an ontology-based technology written in Java for high-quality knowledge management and document categorisation, including entity extraction. Though code is still available, no updates have been provided since 2006. It can be used in conjunction with search engines
  • IODT is IBM’s toolkit for ontology-driven development. The toolkit includes EMF Ontolgy Definition Metamodel (EODM), EODM workbench, and an OWL Ontology Repository (named Minerva)
  • KAON is an open-source ontology management infrastructure targeted for business applications. It includes a comprehensive tool suite allowing easy ontology creation and management and provides a framework for building ontology-based applications. An important focus of KAON is scalable and efficient reasoning with ontologies
  • Ontolingua provides a distributed collaborative environment to browse, create, edit, modify, and use ontologies. The server supports over 150 active users, some of whom have provided us with descriptions of their projects. Provided as an online service; software availability not known.

Vocabulary Prompting Tools

  • AlchemyAPI from Orchestr8 provides an API based application that uses statistical and natural language processing methods. Applicable to webpages, text files and any input text in several languages
  • BooWa is a set expander for any language (formerly known as SEALS); developed by RC Wang of Carnegie Mellon
  • Google Keywords allows you to enter a few descriptive words or phrases or a site URL to generate keyword ideas
  • Google Sets for automatically creating sets of items from a few examples
  • Open Calais is free limited API web service to automatically attach semantic metadata to content, based on either entities (people, places, organizations, etc.), facts (person ‘x’ works for company ‘y’), or events (person ‘z’ was appointed chairman of company ‘y’ on date ‘x’). The metadata results are stored centrally and returned to you as industry-standard RDF constructs accompanied by a Globally Unique Identifier (GUID)
  • Query-by-document from BlogScope has a nice phrase extraction service, with a choice of ranking methods. Can also be used in a Firefox plug-in (not texted with 3.5+)
  • SemanticHacker (from Textwise) is an API that does a number of different things, including categorization, search, etc. By using ‘concept tags’, the API can be leveraged to generate metadata or tags for content
  • TagFinder is a Web service that automatically extracts tags from a piece of text. The tags are chosen based on both statistical and linguistic analysis of the original text
  • Tagthe.net has a demo and an API for automatic tagging of web documents and texts. Tags can be single words only. The tool also recognizes named entities such as people names and locations
  • TermExtractor extracts terminology consensually referred in a specific application domain. The software takes as input a corpus of domain documents, parses the documents, and extracts a list of “syntactically plausible” terms (e.g. compounds, adjective-nouns, etc.)
  • TermFinder uses Poisson statistics, the Maximum Likelihood Estimation and Inverse Document Frequency between the frequency of words in a given document and a generic corpus of 100 million words per language; available for English, French and Italian
  • TerMine is an online and batch term extractor that emphasizes part of speech (POS) and n-gram (phrase extraction). TerMine is the terminological management system with the C-Value term extraction and AcroMine acronym recognition integrated
  • Topia term extractor is a part-of-speech and frequency based term extraction tool implemented in python. Here is a term extraction demo based on this tool
  • Topicalizer is a service which automatically analyses a document specified by a URL or a plain text regarding its word, phrase and text structure. It provides a variety of useful information on a given text including the following: Word, sentence and paragraph count, collocations, syllable structure, lexical density, keywords, readability and a short abstract on what the given text is about
  • TrMExtractor does glossary extraction on pure text files for either English or Hungarian
  • Wikify! is a system to automatically “wikify” a text by adding Wikipedia-like tags throughout the document. The system extracts keywords and then disambiguates and matches them to their corresponding Wikipedia definition
  • Yahoo! Placemaker is a freely available geoparsing Web service. It helps developers make their applications location-aware by identifying places in unstructured and atomic content – feeds, web pages, news, status updates – and returning geographic metadata for geographic indexing and markup
  • Yahoo! Term Extraction Service is an API to Yahoo’s term extraction service, as well as many other APIs and services in a variety of languages and for a variety of tasks; good general resource. The service has been reported to be shut down numerous times, but apparently is kept alive due to popular demand.

Initial Ontology Development

  • COE COE (CmapTools Ontology Editor) is a specialized version of the CmapTools from IMHC. COE — and its CmapTools parent — is based on the idea of concept maps. A concept map is a graph diagram that shows the relationships among concepts. Concepts are connected with labeled arrows, with the relations manifesting in a downward-branching hierarchical structure. COE is an integrated suite of software tools for constructing, sharing and viewing OWL encoded ontologies based on these constructs
  • Conzilla2 is a second generation concept browser and knowledge management tool with many purposes. It can be used as a visual designer and manager of RDF classes and ontologies, since its native storage is in RDF. It also has an online collaboration server
  • http://diagramic.com/ has an online Flex network graph demo, which also has a neat facility for quick entry and visualization of relationships; mostly small scale; pretty cool. Does not appear to be code available anywhere
  • DogmaModeler is a free and open source, ontology modeling tool based on ORM. The philosophy of DogmaModeler is to enable non-IT experts to model ontologies with a little or no involvement of an ontology engineer; project is quite old, but the software is still available and it may provide some insight into naive ontology development
  • Erca is a framework that eases the use of Formal and Relational Concept Analysis, a neat clustering technique. Though not strictly an ontology tool, Erca could be implemented in a work flow that allows easy import of formal contexts from CSV files, then algorithms that computes the concept lattice of the formal contexts that can be exported as dot graphs (or in JPG, PNG, EPS and SVG formats). Erca is provided as an Eclipse plug-in
  • GraphMind is a mindmap editor for Drupal. It has the basic mindmap features and some Drupal specific enhancements. There is a quick screencast about how GraphMind looks like and what is does. The Flex source is also available from Github
  • GrOWL is the software framework to provide graphical, intuitive browsing and editing of knowledge maps. GrOWL is open source and is used in several projects worldwide. None of the online demos apparently work, but the screenshots look interesting and the code is still available
  • irON using spreadsheets, via its notation and specification. Spreadsheets can be used for initial authoring, esp if the irON guidelines are followed. See further this case study of Sweet Tools in a spreadsheet using irON (commON)
  • ITM T3 stands for Terminology, Thesaurus, Taxonomy, Metadata dictionary. ITM T3 includes a range of functions for managing enterprise shareable multilingual domain-specific taxonomies, thesaurus, terminologies in a unified way. It uses XML, SKOS and RDF standards. Commercial; from Mondeca
  • MindRaider is Semantic Web outliner. It aims to connect the tradition of outline editors with emerging technologies. MindRaider mission is to organize not only the content of your hard drive but also your cognitive base and social relationships in a way that enables quick navigation, concise representation and inferencing
  • Topincs is a Topic Map authoring software that allows groups to share their knowledge over the web. It makes use of a variety of modern technologies. The most important are Topic Maps, REST and Ajax. It consists of three components: the Wiki, the Editor, and the Server. The servier requires AMP; the Editor and Wiki are based on browser plug-ins.

Ontology Editing

  • First, see all of the Comprehensive Tools listing above
  • Anzo for Excel includes an (RDFS and OWL-based) ontology editor that can be used directly within Excel. In addition to that, Anzo for Excel includes the capability to automatically generate an ontology from existing spreadsheet data, which is very useful for quick bootstrapping of an ontology.
  • Hozo is an ontology visualization and development tool that brings version control constructs to group ontology development; limited to a prototype, with no online demo
  • Lexaurus Editor is for off-line creation and editing of vocabularies, taxonomies and thesauri. It supports import and export in Zthes and SKOS XML formats, and allows hierarchical / poly-hierarchical structures to be loaded for editing, or even multiple vocabularies to be loaded simultaneously, so that terms from one taxonomy can be re-used in another, using drag and drop. Not available in open source
  • Model Futures OWL Editor combines simple OWL tools, featuring UML (XMI), ErWin, thesaurus and imports. The editor is tree-based and has a “navigator” tool for traversing property and class-instance relationships. It can import XMI (the interchange format for UML) and Thesaurus Descriptor (BT-NT XML), and EXPRESS XML files. It can export to MS Word.
  • OntoTrack is a browsing and editing ontology authoring tool for OWL Lite. It combines a sophisticated graphical layout with mouse enabled editing features optimized for efficient navigation and manipulation of large ontologies
  • OWLViz is an attractive visual editor for OWL and is available as a Protégé plug-in
  • PoolParty is a triple store-based thesaurus management environment which uses SKOS and text extraction for tag recommendations. See further this manual, which describes more fully the system’s functionality. Also, there is a PoolParty Web service that enables a Zthes thesaurus in XML format to be uploaded and converted to SKOS (via skos:Concepts)
  • SKOSEd is a plugin for Protege 4 that allows you to create and edit thesauri (or similar artefacts) represented in the Simple Knowledge Organisation System (SKOS).
  • TemaTres is a Web application to manage controlled vocabularies, taxonomies and thesaurus. The vocabularies may be exported in Zthes, Skos, TopicMap, etc.
  • ThManager is a tool for creating and visualizing SKOS RDF vocabularies. ThManager facilitates the management of thesauri and other types of controlled vocabularies, such as taxonomies or classification schemes
  • Vitro is a general-purpose web-based ontology and instance editor with customizable public browsing. Vitro is a Java web application that runs in a Tomcat servlet container. With Vitro, you can: 1) create or load ontologies in OWL format; 2) edit instances and relationships; 3) build a public web site to display your data; and 4) search your data with Lucene. Still in somewhat early phases, with no online demos and with minimal interfaces.

Not Apparently in Active Use

  • Omnigator The Omnigator is a form-based manipulaton tool centered on Topic Maps, though it enables the loading and navigation of any conforming topic map in XTM, HyTM, LTM or RDF formats. There is a free evaluation version.
  • OntoGen is a semi-automatic and data-driven ontology editor focusing on editing of topic ontologies (a set of topics connected with different types of relations). The system combines text-mining techniques with an efficient user interface. It requires .Net.
  • OWL-S-editor is an editor for the development of services in OWL-S, with graphical, WSDL and import/export support
  • ReTAX+ is an aide to help a taxonomist create a consistent taxonomy and in particular provides suggestions as to where a new entity could be placed in the taxonomy whilst retaining the integrity of the revised taxonomy (c.f., problems in ontology modelling)
  • SWOOP is a lightweight ontology editor. (Swoop is no longer under active development at mindswap. Continuing development can be found on SWOOP’s Google Code homepage at http://code.google.com/p/swoop/)
  • WebOnto supports the browsing, creation and editing of ontologies through coarse grained and fine grained visualizations and direct manipulation.

Ontology Mapping

  • COMA++ is a schema and ontology matching tool with a comprehensive infrastructure. Its graphical interface supports a variety of interaction
  • ConcepTool is a system to model, analyse, verify, validate, share, combine, and reuse domain knowledge bases and ontologies, reasoning about their implication
  • MatchIT automates and facilitates schema matching and semantic mapping between different Web vocabularies. MatchIT runs as a stand-alone or plug-in Eclipse application and can be integrated with popular third party applications. MatchIT’s uses Adaptive Lexicon™ as an ontology-driven dictionary and thesaurus of English language terminology to quantify and ank the semantic similarity of concepts. It apparently is not available in open source
  • myOntology is used to produce the theoretical foundations, and deployable technology for the Wiki-based, collaborative and community-driven development and maintenance of ontologies instance data and mappings
  • OLA/OLA2 (OWL-Lite Alignment) matches ontologies written in OWL. It relies on a similarity combining all the knowledge used in entity descriptions. It also deal with one-to-many relationships and circularity in entity descriptions through a fixpoint algorithm
  • Potluck is a Web-based user interface that lets casual users—those without programming skills and data modeling expertise—mash up data themselves. Potluck is novel in its use of drag and drop for merging fields, its integration and extension of the faceted browsing paradigm for focusing on subsets of data to align, and its application of simultaneous editing for cleaning up data syntactically. Potluck also lets the user construct rich visualizations of data in-place as the user aligns and cleans up the data.
  • PRIOR+ is a generic and automatic ontology mapping tool, based on propagation theory, information retrieval technique and artificial intelligence model. The approach utilizes both linguistic and structural information of ontologies, and measures the profile similarity and structure similarity of different elements of ontologies in a vector space model (VSM).
  • Vine is a tool that allows users to perform fast mappings of terms across ontologies. It performs smart searches, can search using regular expressions, requires a minimum number of clicks to perform mappings, can be plugged into arbitrary mapping framework, is non-intrusive with mappings stored in an external file, has export to text files, and adds metadata to any mapping. See also http://sourceforge.net/projects/vine/.

Not Apparently in Active Use

  • ASMOV (Automated Semantic Mapping of Ontologies with Validation) is an automatic ontology matching tool which has been designed in order to facilitate the integration of heterogeneous systems, using their data source ontologies
  • Chimaera is a software system that supports users in creating and maintaining distributed ontologies on the web. Two major functions it supports are merging multiple ontologies together and diagnosing individual or multiple ontologies
  • CMS (CROSI Mapping System) is a structure matching system that capitalizes on the rich semantics of the OWL constructs found in source ontologies and on its modular architecture that allows the system to consult external linguistic resources
  • ConRef is a service discovery system which uses ontology mapping techniques to support different user vocabularies
  • DRAGO reasons across multiple distributed ontologies interrelated by pairwise semantic mappings, with a vision of peer-to-peer mapping of many distributed ontologies on the Web. It is implemented as an extension to an open source Pellet OWL Reasoner
  • Falcon-AO (Finding, aligning and learning ontologies) is an automatic ontology matching tool that includes the three elementary matchers of String, V-Doc and GMO. In addition, it integrates a partitioner PBM to cope with large-scale ontologies
  • FOAM is the Framework for ontology alignment and mapping. It is based on heuristics (similarity) of the individual entities (concepts, relations, and instances)
  • hMAFRA (Harmonize Mapping Framework) is a set of tools supporting semantic mapping definition and data reconciliation between ontologies. The targeted formats are XSD, RDFS and KAON
  • IF-Map is an Information Flow based ontology mapping method. It is based on the theoretical grounds of logic of distributed systems and provides an automated streamlined process for generating mappings between ontologies of the same domain
  • LILY is a system matching heterogeneous ontologies. LILY extracts a semantic subgraph for each entity, then it uses both linguistic and structural information in semantic subgraphs to generate initial alignments. The system is presently in a demo version only
  • MAFRA Toolkit – the Ontology MApping FRAmework Toolkit allows users to create semantic relations between two (source and target) ontologies, and apply such relations in translating source ontology instances into target ontology instances
  • OntoEngine is a step toward allowing agents to communicate even though they use different formal languages (i.e., different ontologies). It translates data from a “source” ontology to a “target”
  • OWLS-MX is a hybrid semantic Web service matchmaker. OWLS-MX 1.0 utilizes both description logic reasoning, and token based IR similarity measures. It applies different filters to retrieve OWL-S services that are most relevant to a given query
  • RiMOM (Risk Minimization based Ontology Mapping) integrates different alignment strategies: edit-distance based strategy, vector-similarity based strategy, path-similarity based strategy, background-knowledge based strategy, and three similarity-propagation based strategies
  • semMF is a flexible framework for calculating semantic similarity between objects that are represented as arbitrary RDF graphs. The framework allows taxonomic and non-taxonomic concept matching techniques to be applied to selected object properties
  • Snoggle is a graphical, SWRL-based ontology mapper. Snoggle attempts to solve the ontology mapping problem by providing a graphical user interface (similar to which of the Microsoft Visio) to guide the process of ontology vocabulary alignment. In Snoggle, user-defined mappings can be serialized into rules, which is expressed using SWRL
  • Terminator is a tool for creating term to ontology resource mappings (documentation in Finnish).

Ontology Visualization/Analysis

Though all are not relevant, see my post from a couple of years back on large-scale RDF graph software.

  • Social network graphing tools (many covered elsewhere)
  • Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data; I have also written specifically about Cytoscape’s use in UMBEL
    • RDFScape is a project that brings Semantic Web “features” to the popular Systems Biology software Cytoscape
    • NetworkAnalyzer performs analysis of biological networks and calculates network topology parameters including the diameter of a network, the average number of neighbors, and the number of connected pairs of nodes. It also computes the distributions of more complex network parameters such as node degrees, average clustering coefficients, topological coefficients, and shortest path lengths. It displays the results in diagrams, which can be saved as images or text files; used by SD
  • Graphl is a tool for collaborative editing and visualisation of graphs, representing relationships between resources or concepts of the real world. Graphl may be thought of as a visual wiki, a place where everybody can contribute to a shared repository of knowledge
  • igraph is a free software package for creating and manipulating undirected and directed graphs
  • Network Workbench is a very complex, comprehensive; Swiss Army Knife
  • NetworkX – Python; very clean
  • Stanford Network Analysis Package (SNAP) is a general purpose network analysis and graph mining library. It is written in C++ and easily scales to massive networks with hundreds of millions of nodes
  • Social Networks Visualizer (SocNetV) is a flexible and user-friendly tool for the analysis and visualization of Social Networks. It lets you construct networks (mathematical graphs) with a few clicks on a virtual canvas or load networks of various formats (GraphViz, GraphML, Adjacency, Pajek, UCINET, etc) and modify them to suit your needs. SocNetV also offers a built-in web crawler, allowing you to automatically create networks from all links found in a given initial URL
  • Tulip may be incredibly strong
  • Springgraph component for Flex
  • VizierFX is a Flex library for drawing network graphs. The graphs are laid out using GraphViz on the server side, then passed to VizierFX to perform the rendering. The library also provides the ability to run ActionScript code in response to events on the graph, such as mousing over a node or clicking on it.

Miscellaneous Ontology Tools

  • Apolda (Automated Processing of Ontologies with Lexical Denotations for Annotation) is a plugin (processing resource) for GATE (http://gate.ac.uk/). The Apolda processing resource (PR) annotates a document like a gazetteer, but takes the terms from an (OWL) ontology rather than from a list
  • DL-Learner is a tool for learning complex classes from examples and background knowledge. It extends Inductive Logic Programming to Description Logics and the Semantic Web. DL-Learner now has a flexible component based design, which allows to extend it easily with new learning algorithms, learning problems, reasoners, and supported background knowledge sources. A new type of supported knowledge sources are SPARQL endpoints, where DL-Learner can extract knowledge fragments, which enables learning classes even on large knowledge sources like DBpedia, and includes an OWL API reasoner interface and Web service interface.
  • LexiLink is a tool for building, curating and managing multiple lexicons and ontologies in one enterprise-wide Web-based application. The core of the technology is based on RDF and OWL
  • mopy is the Music Ontology Python library, designed to provide easy to use python bindings for ontology terms for the creation and manipulation of music ontology data. mopy can handle information from several ontologies, including the Music Ontology, full FOAF vocab, and the timeline and chord ontologies.
  • OBDA (Ontology Based Data Access) is a plugin for Protégé aimed to be a full-fledged OBDA ontology and component editor. It provides data source and mapping editors, as well as querying facilities that, in sum, allow you to design and test every aspect of an OBDA system. It supports relational data sources (RDBMS) and GLAV-like mappings. In its current beta form, it requires Protege 3.3.1, a reasoner implementing the OBDA extensions to DIG 1.1 (e.g., the DIG server for QuOnto) and Jena 2.5.5
  • OntoComP is a Protégé 4 plugin for completing OWL ontologies. It enables the user to check whether an OWL ontology contains “all relevant information” about the application domain, and extend the ontology appropriately if this is not the case
  • Ontology Browser is a browser created as part of the CO-ODE (http://www.co-ode.org/) project; rather simple interface and use
  • Ontology Metrics is a web-based tool that displays statistics about a given ontology, including the expressivity of the language it is written in
  • OntoSpec is a SWI-Prolog module, aiming at automatically generating XHTML specification from RDF-Schema or OWL ontologies
  • OWL API is a Java interface and implementation for the W3C Web Ontology Language (OWL), used to represent Semantic Web ontologies. The API is focused towards OWL Lite and OWL DL and offers an interface to inference engines and validation functionality
  • OWL Module Extractor is a Web service that extracts a module for a given set of terms from an ontology. It is based on an implementation of locality-based modules that is part of the OWL API.
  • OWL Syntax Converter is an online tool for converting ontologies between different formats, including several OWL syntaxes, RDF/XML, KRSS
  • OWL Verbalizer is an on-line tool that verbalizes OWL ontologies in (controlled) English
  • OwlSight is an OWL ontology browser that runs in any modern web browser; it’s developed with Google Web Toolkit and uses Gwt-Ext, as well as OWL-API. OwlSight is the client component and uses Pellet as its OWL reasoner
  • Pellint is an open source lint tool for Pellet which flags and (optionally) repairs modeling constructs that are known to cause performance problems. Pellint recognizes several patterns at both the axiom and ontology level.
  • PROMPT is a tab plug-in for Protégé is for managing multiple ontologies by comparing versions of the same ontology, moving frames between included and including project, merging two ontologies into one, or extracting a part of an ontology.
  • SegmentationApp is a Java application that segments a given ontology according to the approach described in “Web Ontology Segmentation: Analysis, Classification and Use” (http://www.co-ode.org/resources/papers/seidenberg-www2006.pdf)
  • SETH is a software effort to deeply integrate Python with Web Ontology Language (OWL-DL dialect). The idea is to import ontologies directly into the programming context so that its classes are usable alongside standard Python classes
  • SKOS2GenTax is an online tool that converts hierarchical classifications available in the W3C SKOS (Simple Knowledge Organization Systems) format into RDF-S or OWL ontologies
  • SpecGen (v5) is an ontology specification generator tool. It’s written in Python using Redland RDF library and licensed under the MIT license
  • Text2Onto is a framework for ontology learning from textual resources that extends and re-engineers an earlier framework developed by the same group (TextToOnto). Text2Onto offers three main features: it represents the learned knowledge at a metalevel by instantiating the modelling primitives of a Probabilistic Ontology Model (POM), thus remaining independent from a specific target language while allowing the translation of the instantiated primitives
  • Thea is a Prolog library for generating and manipulating OWL (Web Ontology Language) content. Thea OWL parser uses SWI-Prolog’s Semantic Web library for parsing RDF/XML serialisations of OWL documents into RDF triples and then it builds a representation of the OWL ontology
  • TONES Ontology Repository is primarily designed to be a central location for ontologies that might be of use to tools developers for testing purposes; it is part of the TONES project
  • Visual Ontology Manager (VOM) is a family of tools enables UML-based visual construction of component-based ontologies for use in collaborative applications and interoperability solutions.
  • Web Ontology Manager is a lightweight, Web-based tool using J2EE for managing ontologies expressed in Web Ontology Language (OWL). It enables developers to browse or search the ontologies registered with the system by class or property names. In addition, they can submit a new ontology file
  • RDF evoc (external vocabulary importer) is an RDF external vocabulary importer module (evoc) for Drupal caches any external RDF vocabulary and provides properties to be mapped to CCK fields, node title and body. This module requires the RDF and the SPARQL modules.

Not Apparently in Active Use

  • Almo is an ontology-based workflow engine in Java supporting the ARTEMIS project; part of the OntoWare initiative
  • ClassAKT is a text classification web service for classifying documents according to the ACM Computing Classification System
  • Elmo provides a simple API to access ontology oriented data inside a Sesame RDF repository. The domain model is simplified into independent concerns that are composed together for multi-dimensional, inter-operating, or integrated applications
  • ExtrAKT is a tool for extracting ontologies from Prolog knowledge bases.
  • F-Life is a tool for analysing and maintaining life-cycle patterns in ontology development.
  • Foxtrot is a recommender system which represents user profiles in ontological terms, allowing inference, bootstrapping and profile visualization.
  • HyperDAML creates an HTML representation of OWL content to enable hyperlinking to specific objects, properties, etc.
  • LinKFactory is an ontology management tool, it provides an effective and user-friendly way to create, maintain and extend extensive multilingual terminology systems and ontologies (English, Spanish, French, etc.). It is designed to build, manage and maintain large, complex, language independent ontologies.
  • LSW – the Lisp semantic Web toolkit enables OWL ontologies to be visualized. It was written by Alan Ruttenberg
  • Ontodella is a Prolog HTTP server for category projection and semantic linking
  • OntoWeaver is an ontology-based approach to Web sites, which provides high level support for web site design and development
  • OWLLib is a PHP library for accessing OWL files. OWL is w3.org standard for storing semantic information
  • pOWL is a Semantic Web development platform for ontologies in PHP. pOWL consists of a number of components, including RAP
  • ROWL is the Rule Extension of OWL; it is from the Mobile Commerce Lab in the School of Computer Science at Carnegie Mellon University
  • Semantic Net Generator is a utlity for generating Topic Maps automatically from different data sources by using rules definitions specified with Jelly XML syntax. This Java library provides Jelly tags to access and modify data sources (also RDF) to create a semantic network
  • SMORE is OWL markup for HTML pages. SMORE integrates the SWOOP ontology browser, providing a clear and consistent way to find and view Classes and Properties, complete with search functionality
  • SOBOLEO is a system for Web-based collaboration to create SKOS taxonomies and ontologies and to annotate various Web resources using them
  • SOFA is a Java API for modeling ontologies and Knowledge Bases in ontology and Semantic Web applications. It provides a simple, abstract and language neutral ontology object model, inferencing mechanism and representation of the model with OWL, DAML+OIL and RDFS languages; from java.dev
  • WebScripter is a tool that enables ordinary users to easily and quickly assemble reports extracting and fusing information from multiple, heterogeneous DAMLized Web sources.