Annotation Modeling: In Press

Our manuscript on annotation modeling is one step closer to publication now, as late last night my co-authors and I received sign-off on the copy-editing phase. The journal, Computers and Geosciences, is now preparing proofs.
For the most part then, as authors, we’re essentially done.
However, we may not be able to resist the urge to include a “Note Added in Proof”. At the very least, this note will allude to:

  • The work being done to refactor Annozilla for use in a Firefox 3 context; and
  • How annotation is figuring in OWL2 (Google “W3C OWL2” for more).

Stay tuned …

Annotation Modeling: To Appear in Comp & Geosci

What a difference a day makes!
Yesterday I learned that my paper on semantic platforms was rejected.
Today, however, the news was better as a manuscript on annotation modeling was
accepted for publication.
It’s been a long road for this paper:

The abstract of the paper is as follows:

Annotation Modeling with Formal Ontologies:
Implications for Informal Ontologies

L. I. Lumb[1], J. R. Freemantle[2], J. I. Lederman[2] & K. D.
Aldridge[2]
[1] Computing and Network Services, York University, 4700 Keele Street,
Toronto, Ontario, M3J 1P3, Canada
[2] Earth & Space Science and Engineering, York University, 4700 Keele
Street, Toronto, Ontario, M3J 1P3, Canada
Knowledge representation is increasingly recognized as an important component of any cyberinfrastructure (CI). In order to expediently address scientific needs, geoscientists continue to leverage the standards and implementations emerging from the World Wide Web Consortium’s (W3C) Semantic Web effort. In an ongoing investigation, previous efforts have been aimed towards the development of a semantic framework for the Global Geodynamics Project (GGP). In contrast to other efforts, the approach taken has emphasized the development of informal ontologies, i.e., ontologies that are derived from the successive extraction of Resource Description Format (RDF) representations from eXtensible Markup Language (XML), and then Web Ontology Language (OWL) from RDF. To better understand the challenges and opportunities for incorporating annotations into the emerging semantic framework, the present effort focuses on knowledge-representation modeling involving formal ontologies. Although OWL’s internal mechanism for annotation is constrained to ensure computational completeness and decidability, externally originating annotations based on the XML Pointer Language (XPointer) can easily violate these constraints. Thus the effort of modeling with formal ontologies allows for recommendations applicable to the case of incorporating annotations into informal ontologies.

I expect the whole paper will be made available in the not-too-distant future …

Evolving Semantic Frameworks into Platforms: Unpublished ms.

I learned yesterday that the manuscript I submitted to HPCS 2008 was not accepted 😦
It may take my co-authors and I some time before this manuscript is revised and re-submitted.
This anticipated re-submission latency, along with the fact that we believe the content needs to be shared in a timely fashion, provides the motivation for sharing the manuscript online.
To whet your appetite, the abstract is as follows:

Evolving a Semantic Framework into a Network-Enabled Semantic Platform
A data-oriented semantic framework has been developed previously for a project involving a network of globally distributed scientific instruments. Through the use of this framework, the semantic expressivity and richness of the project’s ASCII data is systematically enhanced as it is successively represented in XML (eXtensible Markup Language), RDF (Resource Description Formal) and finally as an informal ontology in OWL (Web Ontology Language). In addition to this representational transformation, there is a corresponding transformation from data into information into knowledge. Because this framework is broadly applicable to ASCII and binary data of any origin, it is appropriate to develop a network-enabled semantic platform that identifies the enabling semantic components and interfaces that already exist, as well as the key gaps that need to be addressed to completely implement the platform. After briefly reviewing the semantic framework, a J2EE (Java 2 Enterprise Edition) based implementation for a network-enabled semantic platform is provided. And although the platform is in principle usable, ongoing adoption suggests that strategies aimed at processing XML via parallel I/O techniques are likely an increasingly pressing requirement.

AGU Poster: Relationship-Centric Ontology Integration

Later today in San Francisco, at the 2007 Fall Meeting of the American Geophysical Union (AGU), one of my co-authors will be presenting our poster entitled “Relationship-Centric Ontology Integration” (abstract).

This poster will be in a session for which I was a co-convenor and described elsewhere.

A PDF-version of the poster is available elsewhere (agu07_the_poster_v2.pdf).

Earth and Space Science Informatics at the 2007 Fall Meeting of the American Geophysical Union

In a previous post, I referred to Earth Science Informatics as a discipline-in-the-making.

To support this claim, I cited a number of data points. And of these data points, the 2006 Fall Meeting of the American Geophysical Union (AGU) stands out as a key enabler.

With 22 sessions posted, the 2007 Fall Meeting of the AGU is well primed to further enable the development of this discipline.

Because I’m a passionate advocate of this intersection between the Earth Sciences and Informatics, I’m involved in convening three of the 22 Earth and Space Science Informatics sessions:

I encourage you to take a moment to review the calls for participation for these three, as well as the other 19, sessions in Earth and Space Science Informatics at the 2007 Fall Meeting of the AGU.

Annotation’s Two Solitudes

Most fundamentally, and despite the fact that the term is frequently used, annotation has not been universally defined. Although annotation can be fairly consistently regarded as editorial metadata, or even information about data, there exists considerable latitude regarding the origin/destination scope of annotation. In the language-centric OWL context, annotations originate internal to the ontology and can annotate internally and to some extent externally. Anecdotally, this remains a common usage mode for annotation as evidenced in the online and off-line literature plus most-mature scientific projects. In contrast in the referencing-based case of XPointer, annotations originate external to the formal ontology, and can annotate the ontology itself or make external references. (The figure below attempts to clarify this not entirely subtle distinction.)

The two solitudes with respect to definitions is carried forward in terms of differences in annotation terminology. As a very concrete example, both the OWL and XPointer communities separately define and make use of the same annotation properties or types. There is clearly an opportunity for the W3C to better harmonize the efforts between these distinct communities, their efforts and common interests.

Annotation Location versus Outcome

Annotation Really Is A Big Deal!

My expressed interest in annotation began as a footnote:

An alternative approach has the following two steps: First, extract RDF from the .GGP and .AUX files as before. Second, incorporate data contained in the .LOG file via annotation. Annotation is a well-established practice [45, Chapter 4] involving RDF and the XML Pointer Language (XPointer, [22]) — essentially a URI-centric fragment identifier. This conversion flow is currently under investigation and the corresponding manuscript is in preparation.

This footnote appeared in a paper that was published by the IEEE for HPCS 2006. The alluded-to manuscript will soon be available from the IEEE and will be presented in mid-May at HPCS 2007.

In addition to this manuscript on annotation, along with my co-authors, I’ve recently submitted a broader-based treatment to a special issue (“Geoscience Knowledge Representation for Cyberinfrastructure”) of Computers & Geosciences (C&G). The abstract of the C&G submission is as follows:

Incorporating Annotations into Formal and Informal Ontologies: Experiences and Implications

L. I. Lumb, J. R. Freemantle, J. I. Lederman & K. D. Aldridge

Abstract

Traditionally, and to a first approximation, annotations can be regarded as comments. In the case of the Web Ontology Language (OWL), this perspective is largely accurate, as annotations are internal constructs included with the language. As internal constructs, annotations in OWL Description Logic (DL) are also constrained to ensure, ultimately, that they do not negatively impact on the ontology’s ability to remain computationally complete and decidable. Formal ontologies, however, can also be annotated externally with the XML Pointer Language (XPointer). Because XPointer-based annotations are quite likely to result in violations of the constraints traditionally placed on OWL DL’s built-in annotations, there exist potentially serious consequences for maintaining self-contained formal ontologies. Insight gained in modeling annotations in formal ontologies using top-down strategies can be applied to informal ontologies. In part, the previous practice of incorporating feature-based annotations directly into informal ontologies is regarded differently, as the XPointer-based annotations may require more complex OWL dialects in which computational completeness and decidability cannot be guaranteed. Critical to the development of informal ontologies is Gleaning Resource Descriptions from Dialects of Languages (GRDDL), as it facilitates the extraction of Resource Description Format (RDF) relationships from representations cast in the eXtensible Markup Language (XML). In order to fully enable the creation of informal ontologies, however, an analogous functionality is required to extract OWL classes, properties and individuals from RDF-based representations. Although a strategy for this capability has been specified, hopefully community based efforts will soon target a corresponding implementation.

Key words:
Annotation, Formal Ontology, Informal Ontology, Ontology, Semantic Web, XPointer, Web Ontology Language

In addition to these papers, I’ve blogged a lot about annotation. And the more I delve into annotation, the more I’m taken by it’s applicability. For example, I’ll be making a presentation at CANHEIT 2007 on annotation and wikis.

Annotation really is a big deal!

Googling and Swoogling for Ontologies

Using http://www.google.com/search?q=filetype:owl+owl, you can Google for ontologies.

Currently, Google returns over 53,000 results.

If you prefer, you can Swoogle:

Swoogle (http://swoogle.umbc.edu/) is an specialized web search engine that discovers, analyzes and indexes knowledge encoded in semantic web documents published on the Web. Swoogle reasons about these documents and their constituent parts (e.g., terms, individuals, triples) and records meaningful metadata about them. Swoogle provides webscale semantic web data access service, which helps human users and software systems to find relevant documents, terms and triples, via its search and navigation services. Swoogle also provides a customizable algorithm inspired by Google’s PageRank algorithm but adapted to the semantics and use patterns found in semantic web documents. Swoogle currently has indexed nearly 1.3M Semantic Web documents which contain almost 240M triples. In addition to providing general Semantic Web search services, Swoogle has been used by several projects to maintain and manage specialized collections of RDF data.

Currently, Swoogle searches over 10,000 ontologies – even more if you register.

Swoogle’s stats provide even more meaningful and impressive numbers:

  • Swoogle’s aware of about 1.2 million error-free Semantic Web documents
  • Swoogle was able to parse over 412 million triples from Semantic Web documents

Based on these data points, ontology developers would be wise to consult Google or Swoogle to avoid reinventing that which already exists … !

When using pre-existing ontologies, it’s also important to remember that as developers you have various choices:

Existing ontologies are inherently reusable, extensible and refactorable.

2007 Semantic Technology Conference

This is an event I wish I’d had on my radar … alas, May is already rife with conferences!

Some data (not information!) points:

  • The tutorials/presentations content looks quite good
    • I even recognize or know some of the presenters 🙂
    • The content is bleeding-edge to current to mainstream
    • Much of the content is published
  • Judging by the demographics, e.g., there are a number of vendors involved, the Semantic Web continues to get real – and some of the vendors have cool names (see the sponsors page for more 😉
  • A primer is available for those who are new to the subject
  • San Jose will be a nice place to be in May – it’s close to San Francisco … still one of my favorite places to go!

On the Use of Informal Ontologies in the Delivery of Service Oriented Architectures (SOAs)

In Service-Oriented Architecture: Concepts, Technology and Design, author Thomas Erl frames ontologies (section 10.2) in a top-down strategy for the delivery of a Service Oriented Architecture (SOA) .

As the first step, in a multistep process, what starts with ontologies ultimately results in a Contemporary SOA (Erl, section 3.2.20):

Contemporary SOA represents an open, extensible, federated, composable architecture that promotes service-orientation and is comprised of autonomous, QoS-capable, vendor diverse, interoperable, discoverable, and potentially reuable services, implemented as Web services.

SOA can establish an abstraction of business logic and technology, resulting in a loose coupling between these domains.

SOA is an evolution of past platforms, preserving successful characteristics of traditional architectures, and bringing with it distinct principles that foster service-orientation in support of a service-oriented enterprise.

SOA is ideally standardized throughout an enterprise, but achieving this state requires a planned transition and the support of a still evolving technology set.

In the same chapter, Erl also provides an abridged Contemporary SOA definition:

SOA is a form of technology architecture that adheres to the principles of service-orientation. When realized through the Web services technology platform, SOA establishes the potential to support and promote these principles throughout the business process and automation domains of an enterprise.

In other words, buying into the top-down strategy can ultimately result in a Contemporary SOA and this is a big deal.

Erl also discusses the bottom-up strategy for delivering a SOA (section 10.2).

In striking contrast to the top-down strategy, and as Erl describes it, the bottom-up strategy does not incorporate ontologies. Despite the fact that “… the majority of organizations that are currently building Web services apply the bottom-up approach …” (Erl, pg. 368):

The bottom-up strategy is really not a strategy at all. Nor is it a valid approach to achieving a contemporary SOA. This is a realization that will hit many organizations as they begin to take service-orientation, as an architectural model, more seriously. Although the bottom-up design allows for the creation of Web services as required by applications, implementing an SOA at a later point can result in a great deal of retro-fitting and even the introduction of new standardized service layers positioned over the top of the non-standardized services produced by this approach.

After reading this chapter, one is left with the impression that Erl favors the agile strategy (Erl, section 10.4) as it attempts “… to find an acceptable balance between incorporating service-oriented design principles into business analysis environments without having to wait before introducing Web services technologies into technical environments.”

I would be willing to accept all of this on spec if it weren’t for the fact that it’s possible to create informal ontologies, in non-SOA contexts, during bottom-up processes.

And if this is possible in non-SOA contexts, then it’s reasonable that informal ontologies could be incorporated into the bottom-up strategy for SOA delivery.

I believe this is worth exploring because use of informal ontologies in a bottom-up strategy for SOA delivery may improve the potential for ultimately achieving a Contemporary SOA. (An outcome, you’ll recall from above, Erl stated wasn’t otherwise acheiveable.)

I also believe this is worth exploring as, as Erl states, most organizations are attempting to gravitate towards SOAs from the bottom up.

Because the agile strategy (ideally) combines the best of both the top-down and bottom-up approaches, I also believe it’s worth exploring the potential for informal ontologies in this case as well.

Although further research is required, the figure below extends Erl’s Figure 10.3 (pg. 367) with a first-blush suggestion of how informal ontologies might be incorporated into the bottom-up strategy for SOA delivery.

informal_ontology_soa_delivery

It’s important to note that Erl’s original figure illustrates a five-step process that culminates with “Deploy services”.

Based on work I’ve done elsewhere, in this first-blush depiction, I believe the steps required to make use of informal ontologies would need to include:

  • “Extract service relationships” – In the work I’ve done elsewhere, this extraction has been achieved by Gleaning Resource Descriptions from Dialects of Languages (GRDDL). GRDDL extracts relationships and represents them in RDF from XML via XSLT.
  • “Generate informal ontology” – These days, ontologies are often expressed in the Web Ontology Language (OWL). OWL is a semantically richer and more-expressive variation of XML than is XML. Much like the previous step, the generated informal ontology is expressed in OWL via processing that would likely make use of XSLT. This step might also involve the need to incorporate annotations.
  • “Integrate informal ontologies” – Because each act of modeling through deploying application services will result in an informal ontology, there will eventually be a pressing need a integrate these informal ontologies. This ontology integration, which may also involve top-down or formal ontologies, will provide the best possibilities for ultimately realizing a Contemporary SOA.

Even at this early stage, the use of informal ontologies in the delivery of a SOA appears promising and worth investigating.