On Knowledge-Based Representations for Actionable Data …

I bumped into a professional acquaintance last week. After describing briefly a presentation I was about to give, he offered to broker introductions to others who might have an interest in the work I’ve been doing. To initiate the introductions, I crafted a brief description of what I’ve been up to for the past 5 years in this area. I’ve also decided to share it here as follows: 

As always, [name deleted], I enjoyed our conversation at the recent AGU meeting in Toronto. Below, I’ve tried to provide some context for the work I’ve been doing in the area of knowledge representations over the past few years. I’m deeply interested in any introductions you might be able to broker with others at York who might have an interest in applications of the same.

Since 2004, I’ve been interested in expressive representations of data. My investigations started with a representation of geophysical data in the eXtensible Markup Language (XML). Although this was successful, use of the approach underlined the importance of metadata (data about data) as an oversight. To address this oversight, a subsequent effort introduced a relationship-centric representation via the Resource Description Format (RDF). RDF, by the way, forms the underpinnings of the next-generation Web – variously known as the Semantic Web, Web 3.0, etc. In addition to taking care of issues around metadata, use of RDF paved the way for increasingly expressive representations of the same geophysical data. For example, to represent features in and of the geophysical data, an RDF-based scheme for annotation was introduced using XML Pointer Language (XPointer). Somewhere around this point in my research, I placed all of this into a framework.

A data-centric framework for knowledge representation.

 In addition to applying my Semantic Framework to use cases in Internet Protocol (IP) networking, I’ve continued to tease out increasingly expressive representations of data. Most recently, these representations have been articulated in RDFS – i.e., RDF Schema. And although I have not reached the final objective of an ontological representation in the Web Ontology Language (OWL), I am indeed progressing in this direction. (Whereas schemas capture the vocabulary of an application domain in geophysics or IT, for example, ontologies allow for knowledge-centric conceptualizations of the same.)  

From niche areas of geophysics to IP networking, the Semantic Framework is broadly applicable. As a workflow for systematically enhancing the expressivity of data, the Framework is based on open standards emerging largely from the World Wide Web Consortium (W3C). Because there is significant interest in this next-generation Web from numerous parties and angles, implementation platforms allow for increasingly expressive representations of data today. In making data actionable, the ultimate value of the Semantic Framework is in providing a means for integrating data from seemingly incongruous disciplines. For example, such representations are actually responsible for providing new results – derived by querying the representation through a ‘semantified’ version of the Structured Query Language (SQL) known as SPARQL. 

I’ve spoken formally and informally about this research to audiences in the sciences, IT, and elsewhere. With York co-authors spanning academic and non-academic staff, I’ve also published four refereed journal papers on aspects of the Framework, and have an invited book chapter currently under review – interestingly, this chapter has been contributed to a book focusing on data management in the Semantic Web. Of course, I’d be pleased to share any of my publications and discuss aspects of this work with those finding it of interest.

With thanks in advance for any connections you’re able to facilitate, Ian. 

If anything comes of this, I’m sure I’ll write about it here – eventually!

In the meantime, feedback is welcome.

RDF-ization: Is That What I’ve Been Up To?

Recently, on his blog, Kingsley Idehen wrote:

RDF-ization is a term used by the Semantic Web community to describe the process of generating RDF from non RDF Data Sources such as (X)HTML, Weblogs, Shared Bookmark Collections, Photo Galleries, Calendars, Contact Managers, Feed Subscriptions, Wikis, and other information resource collections.

Although Idehen identifies a number of data sources, he does not explicitly identify two data sources I’ve been spending a fair amount of time with over the past few years: 

• One source of data is that generated by scientific instruments. With various colleagues, the semantic framework I’ve built around this data source allows for RDF-ization of scientific data from semi-structured ASCII to XML (specifically ESML) to RDF via GRDDL. (Please see the illustration.) In principle, it should be possible to further transform the RDF representation into OWL thus resulting in what I’ve referred to elsewhere as an informal ontology. (According to Morville as well as Shadbolt et al., the RDF-ization of the data sources Idehen identifies result in folksonomies, rather than informal ontologies.) Again with various colleagues, I’ve also made use of RDF to annotate features inherent in the scientific data via XML Pointer Language (XPointer). 
• Even more recently, with members of my Network Operations team at York University, I’ve been working with a relational database as a source of data on the topology of IP networks. (Please see the illustration.)

Of course, whether the motivation is personal/social-networking or scientific/IT related, the attention to RDF-ization is win-win for all stakeholders. Why? Anything that accelerates the RDF-ization of non-RDF data sources brings us that much closer to realizing the true value of the Semantic Web.

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:

• Its conception dates back to a presentation I gave at the 2006 Fall Meeting of the AGU.
• The paper was submitted as a contribution for Computers
  & Geosciences Special Issue on Geoscience Knowledge Representation in
  Cyberinfrastructure.
• The initial reviews called for major revisions. With tremendous support from my co-authors, the paper was significantly revised, and re-submitted.
• After some additional interactions, I just learned that the paper was finally accepted for publication.

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:

• Ontology Integration: A Pressing Challenge for Earth and Space Science Informatics
• Grid Technologies and Associated Infrastructures
• Putting Ontologies to Work: Real-World Applications in the Earth and Space Sciences

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.

CANARIE’s Network-Enabled Platforms Workshop

Next week, I’ll be attending CANARIE’s Network-Enabled Platforms Workshop: Convergence of Cyber-Infrastructure and the Next-Generation Internet in Ottawa. Although the workshop is described elsewhere, to provide a little context consider that:

The purpose of CANARIE’s Network-Enabled Platforms Workshop is to explore the development of and participation in network-enabled platforms by Canadian researchers and other interested parties. The workshop will be an important step towards the launch of a CANARIE funding program in this area.

Based on the agenda, I expect this will be a highly worthwhile event, and I am looking forward to it.

My contribution to the workshop will be a short presentation described by the following abstract:

Evolving Semantic Frameworks into Network-Enabled Semantic Platforms

Ian Lumb
Manager Network Operations
Computing and Network Services
York University

A semantic framework has been successfuly developed 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 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 sematic platform that (i) facilitates integration of the enabling languages, tools and utilities that already exist, and (ii) identifies the key gaps that need to be addressed to completely implement the platform. After briefly reviewing the semantic framework in a generic way, a J2EE (Java 2 Enterprise Edition) based, work-in-progress proposal for a network-enabled semantic platform is forwarded.

I expect to be sharing more on this thread as it develops …

Data Points on Tim Bray’s Keynote at CANHEIT 2007

As advertized, Tim Bray gave a keynote presentation at CANHEIT 2007 earlier today (May 29, 2007). And even though I would not describe Bray as an overly dynamic speaker, he certainly did suceed in being entertaining, educating, engaging and thought provoking.

Hopefully, Bray’s presentation will be made available online.

Until it is, you may find the following data points of interest:

• Bray spoke very highly of RAILS – RAILS in general, and Ruby on RAILS in particular. As a better way of doing things, he suggested that RAILS might even change the way you think about programming. To whet everyone’s appetite, Bray itemized two of RAILS’ principles:
  • Don’t repeat yourself
  • Emphasize convention over configuration

To substantiate his zeal for RAILS, he shared an example of a project that took four months to develop in J2EE; the same project was developed in five days with RAILS! The momentum behind RAILS is also quantified by book sales and attendance levels (in excess of 1,000) at a recent event.

• Bray also spoke very highly of REST – Even as a Sun employee, Bray was compelled to state that REST may eclipse Java/J2EE in the not-too-distant future. Of course, like many, he suggested that the RESTful approach has already eclipsed Web services. He even shared an image of the WS-DeathStar (Source: Unknown).

• Bray is contributing to the Atom Project – “Atom is a simple way to read and write information on the web, allowing you to easily keep track of more sites in less time, and to seamlessly share your words and ideas by publishing to the web.” Looks interesting!
• Bray made use of Apple’s Keynote presentation software – After seeing how Bray and Al Gore made use of Keynote, I broker down and licensed a copy of the software. In both cases, I was struck by the elegant simplicity of their presentations. After all, the purpose of presentations is to communicate. More on Keynote some other time I expect …
• Bray blogs at http://www.tbray.org/ongoing – Worth reading!

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.