Normative Landscape of Ontology Tools

A new generation in ontology development tools is needed. This documentation provides an explication of the landscape under which this new generation of tools is occurring.

Ontologies supply the structure for relating information to other information in the semantic Web or the linked data realm. Because of this structural role, ontologies are pivotal to the coherence and interoperability of interconnected data.

We are just about now concluding the first decade of ontology development tools, especially those geared to the semantic Web and its associated languages of RDFS and OWL. Last year we also saw the release of the major update to the OWL 2 language, with its shift to more expressiveness and a variety of profiles. The upcoming next generation of ontology tools now must also shift.

The current imperative is to shift away from ontology engineering by a priesthood to pragmatic daily use and maintenance by domain practitioners. Market growth demands simpler, task-focused tools with intuitive interfaces. For this change to occur, the general tools architecture needs to shift its center of gravity from IDEs and comprehensive toolkits to APIs and Web services. Not surprisingly, this same shift is what has been occurring across all areas of software.

Methodology Reprise: The Nature of the Landscape
In the previous installment of this series, we presented a new methodological approach to ontology development, geared to lightweight, domain ontologies. One aspect of that design was to separate the operational workflow into two pathways:


 * Instances, and their descriptive characteristics, and
 * Conceptual relationships, or ontologies.

The ontology build methodology concentrated on the upper half of this diagram (blue, with yellow lead-ins and outcomes) with the various steps overviewed in that installment:



The methodology captured in this diagram embraces many different emphases from current practice: re-use of existing structure and information assets; conscious split between instance data (ABox) and the conceptual structure (TBox); incremental design; coherency and other integrity testing; and explicit feedback for scope extension and growth. The methodology also embraces some complementary utility ontologies that also reflect the design of ontology-driven apps.

These are notable changes in emphasis. But they are not the most important one. The most important change is the tools landscape to implement this methodology. This landscape needs to shift to pragmatic daily use and maintenance by domain practitioners. That requires simpler and more task-oriented tools. And that change in tooling needs a still more fundamental shift in tools architecture and design.

A Legacy of Excellent First Generation Tools
In many places throughout this series I use the term "inadequate" to describe the current state of ontology development tools. This characterization is not a criticism of first-generation tools per se. Rather, it is a reflection of their inadequacy to fulfill the realities of the new tooling landscape argued in this series. The fact remains, as initial generation tools, that many of the existing tools are quite remarkable and will play central roles (mostly for the professional ontologist or developer) moving forward.

At the risk of overlooking some important players, let's trace the (partial) legacy of some of the more pivotal tools in today's environment.

As early as a decade ago the ontology standards languages were still in flux and the tools basis was similarly immature. Frame logic, description logics, common logic and many others were competing at that time for primacy and visibility. Most ontology tools such as Protégé, OntoEdit, or OilEd were based on F-logic or the predecessor to OWL, DAML+Oil. But the OWL language was under development by the W3C and in anticipation of its formal release the tools environment was also evolving to meet it. Swoop, for example, was one of the first dedicated OWL browsers. A Protégé plug-in for OWL was also developed by Holger Knublauch. In parallel, the OWL group at the University of Manchester also introduced the OWL API.

With the formal release of OWL 1.0 in 2004, ontology tools continued to migrate to the language. Protégé, up through the version 3x series, became a popular open source system with many visualization and OWL-related plug-ins. Knublauch joined TopQuadrant and brought his OWL experience to TopBraid Composer, which shifted to the Eclipse IDE platform and leveraged the Jena API. In Europe, the NeON (Networked Ontologies) project started in 2006 and by 2008 had an Eclipse-based OWL platform using the OWL API with key language processing capabilities through GATE.

Most recently, Protégé and NeON in open source, and TopBraid Composer on the commercial side, have likely had the largest market share of the comprehensive ontology toolkits. So far, with the release of OWL 2 in late 2009, only Protégé in version 4 and the TwoUse Toolkit have yet fully embraced all aspects of the new specification, doing so by intimately linking with the new OWL API (version 3x has full OWL 2 support). However, most leading reasoners now support OWL 2 and products such as TopBraid Composer and Ontotext's OWLIM support OWL 2 RL as well.

The evolution of Protégé to version 4 (OWL 2) was led by the University of Manchester via its CO-ODE project, now ended, which has also been a source for most existing Protégé 4 plug-ins (because of the switch to OWL 2 and the OWL API most earlier plug-ins are incompatible with Protégé 4). Manchester has also been a leading force in the development of OWL 2 and the alternative Manchester syntax.

Though only recently stable because of the formalization of OWL 2, Protégé 4 and its linkage to the new OWL API provides for a very powerful combination. With Protégé, the system has a familiar ontology editing framework and a mechanism for plug-in migration and growth. With the OWL API, there is now a common API for leading reasoners (Pellet, HermiT, FaCT++, RacerPro, etc.), a solid ontology management and annotation framework, and validators for various OWL 2 profiles (RL, EL and QL). The system is widely embraced by the biology community, probably the most active scientific field in ontologies. However, plug-in support lags the diversity of prior versions of Protégé and there does not appear to be the energy and community standing behind it as in prior years.

A Normative Tools Landscape
These leading frameworks and toolkits have opted to be "ontology engineering" environments. Via plug-ins and complicated interfaces (tabs or Eclipse-style panes) the intent has apparently been to provide "all capabilities in one box." The tools have been IDE-centric.

Unfortunately, one must be a combination of ontologist, developer, programmer and IDE expert in order use the tools effectively. And, as incremental capabilities get added to the systems, these also inherit the same complexity and style of the host environment. It is simply not possible to make complex environments and conventions simple.

Curiously, the existence or use of APIs have also not been adequately leveraged. The usefulness of an API means that subsets of information can be extracted and worked on in very clear and simple ways. This information can then be roundtripped without loss. An API allows a tailored subset abstraction of the underlying data model. In contrast, IDEs such as Protégé or Eclipse in that role forces all interfaces to share their complexity.

With these thoughts in mind, then, we set out to architect a tools suite and work flow that could truly take advantage of a central API. We further wanted to isolate the pieces into distributable Web services in keeping with our standard OSF Web Service Web services framework design.

This approach also allows us to split out simpler, focused tools that domain users and practitioners can use. And, we can do all of this while also enabling the existing professional toolsets and IDEs to also interoperate in the environment.

The resulting tools landscape is shown in the diagram below. This diagram takes the same methodology flow from Figure 1 (blue and yellow boxes) and stretches them out in a more linear fashion. Then, we embed the various tools (brown) and APIs (orange) in relation to that methodology:



This diagram is worth expanding to full size and studying in some detail. Aspects of this diagram that deserve more discussion are presented in the sections below.

OWL API as Center of Gravity
As noted in the preceding methodology installment, the working ontology is the central object being managed and extended for a given deployment. Because that ontology will evolve and grow over time, it is important the complete ontology specification itself be managed by some form of version control system (green). This is the one independent tool in the landscape.

Access to and from the working ontology is mediated by the OWL API. The API allows all or portions of the ontology specification to be manipulated separately, with a variety of serializations. Changes made to the ontology can also be tested for validity. Most leading reasoners can interact directly with the API. Protégé 4 also interacts directly with the API, as can various rules engines. Additionally, other existing APIs, notably the Alignment API with its own mapping tools and links to other tools such as S-Match can interact with the OWL API. It is reasonable to expect more APIs to emerge over time that also interoperate.

The OWL API is the best current choice because of its native capabilities and because Jena does not yet support OWL 2. However, because of the basic design with OSF Web Service (see next), it is also possible to swap out with different APIs at a later time should developments warrant.

In short, having the API play the central management role in the system means that any and all tools can be designed to interact effectively with the working ontology(ies) without any loss in information due to roundtripping.

Web Services (OSF Web Service) as Canonical Access Layer
The same rationale that governed our development of OSF Web Service applies here: to abstract basic services and functionality through a platform-independent Web services layer. This Web services layer has canonical (standard) ways to interact with other services and is generally RESTful in design to support distributed deployments. The design conforms to proper separation of view from logic and structure. Morever, because of the design, changes can be made on either side of the layer in terms of user interface or functionality.

Use of the OSF Web Service layer also means that tools and functionality can be distributed anywhere on the Web. Specialized server-side functions can be supported as well as dedicated specialty hardware. Text indexing or disambiguation services can fit within this design.

The ultimate value of piggybacking on the OSF Web Service framework is that all other extant services also become available. Thus, a wealth of converters, data managers, and semantic components (or display widgets) can be invoked depending on the needs of the specific tool.

Simpler, Task-specific Tools
The objective, of course, of this design is to promote more and simpler tools useful to domain users. Some of these are shown under the Use & Maintain box in the diagram above; others are listed by category in the table below.

The RESTful interface and parameter calls of the OSF Web Service layer further simplify the ontology management and annotation abstractions arising from the OWL API. The number of simple tools available to users under this design is virtually limitless. These tools are also fast to develop and test.

Combining These New Thrusts and Moving Forward
This landscape is not yet a reality. It is a vision of adaptive and simpler tools, working with a common API, and accessible via platform-independent Web services. It also preserves many of the existing tools and IDEs familiar to present ontology engineers.

However, pieces of this landscape do presently exist and more are on the way. The next section briefly overviews some of the major application areas where these tools might contribute.

Individual Tools within the Landscape
If one inspects the earlier listing of 185 ontology tools it is clear that there is a diversity of tools both in terms of scope and function across the entire ontology development stack. It is also clear that nearly all of those 185 tools listed do not communicate with one another. That is a tremendous waste.

Via shared APIs and some degree of consistent design it should be possible to migrate these capabilities into a more-or-less interoperating whole. We have thus tried to categorize some important tool types and exemplar tools from that listing to show the potential that exists. (Please note that the Example Tools are links to the tools and categories from the earlier 185 tools listing.)

This correlation of types and example tools is not meant to be exhaustive nor a recommendation of specific tools. But, this tabulation is illustrative of the potential that exists to both simplify and extend tool support across the entire ontology development workflow:

The beauty of this approach is that most of the tools listed are open source and potentially amenable to the minor modifications necessary to conform with this proposed landscape.

Key Gaps in the Landscape
Contrasting the normative tools landscape above with the existing listing of ontology tools points out some key gaps or areas deserving more development attention. Some of these are:


 * Vocabulary managers -- easy inspection and editing environments for concepts and predicates are lacking. Though standard editors allow direct ontology language edits (OWL or RDFS), these are not presently navigable or editable by non-ontologists. Intuitive browsing structures with more "infobox"-like editing environments could be helpful here
 * Graph API -- it would be wonderful to have a graph API (including analysis options) that could communicate with the OWL API. Failing that, it would be helpful to have a graph API that communicated well with RDF and ontology structures; extant options are few
 * Large-graph visualizer -- while we have earlier reviewed large-scale graph visualization software, the alternatives are neither easy to set up nor use. Being able to readily select layout options with quick zooms and scaling options are important
 * Graphical editor -- some browsers or editors (e.g, FlexViz) provide nice graph-based displays of ontologies and their properties and annotations. However, there appear to be few environments where the ontology graph can be directly edited or visually used for design or expansion.

Finally, it does appear that the effort and focus behind Protégé seems to be slowing somewhat. With Protégé 4 the future has clearly shifted to OWL 2, but besides the admirable CO-ODE project (now ended), tools and plug-in support seems to have slowed. Many of the admirable plug-ins for Protégé 3x do not appear to be under active development for upgrades to Protégé 4. While Protégé's future (and similar IDEs) seems assured, its prominence possibly will (and should) shift to a simpler kit of tools useful to users and practitioners.