Jana Herwig

SWC’s Matthias Samwald contributes to W3C notes

Early June saw the release of two notes drafted by the Semantic Web Health Care and Life Sciences (HCLS) Interest Group within the W3C. One of the contributors, and editor of one note, is Matthias Samwald, a project coordinator at SWC, who is a member of this SIG and who has worked on several Semantic Web projects for the Yale Center for Medical Informatics (USA), Science Commons (USA) and DERI Galway (Ireland).

A Prototype Knowledge Base for the Life Sciences
W3C Interest Group Note 4 June 2008
Editors: M. Scott Marshall, Eric Prud’hommeaux
Contributors: Alan Ruttenberg, Jonathan Rees, Susie Stephens, Matthias Samwald, Kei-Hoi Cheung
Abstract: The prototype we describe is a biomedical knowledge base, constructed for a demonstration at Banff WWW2007 , that integrates 15 distinct data sources using currently available Semantic Web technologies such as the W3C standard Web Ontology Language [RDF]. This report outlines which resources were integrated, how the knowledge base was constructed using free and open source triple store technology, how it can be queried using the W3C Recommended RDF query language SPARQL [SPARQL], and what resources and inferences are involved in answering complex queries. While the utility of the knowledge base is illustrated by identifying a set of genes involved in Alzheimer’s Disease, the approach described here can be applied to any use case that integrates data from multiple domains.

Experiences with the conversion of SenseLab databases to RDF/OWL
W3C Interest Group Note 4 June 2008
Editors: Matthias Samwald, Kei-Hoi Cheung
Contributors: Alan Ruttenberg, Huajun Chen
Abstract: One of the challenges facing Semantic Web for Health Care and Life Sciences is that of converting relational databases into Semantic Web format. The issues and the steps involved in such a conversion have not been well documented. To this end, we have created this document to describe the process of converting SenseLab databases into OWL. SenseLab is a collection of relational (Oracle) databases for neuroscientific research. The conversion of these databases into RDF/OWL format is an important step towards realizing the benefits of Semantic Web in integrative neuroscience research. This document describes how we represented some of the SenseLab databases in Resource Description Framework (RDF) and Web Ontology Language (OWL), and discusses the advantages and disadvantages of these representations. Our OWL representation is based on the reuse and extension of existing standard OWL ontologies developed in the biomedical ontology communities. The purpose of this document is to share our implementation experience with the community.

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Jana Herwig

And the winner is: The vision of a future where ordinary people publish structured data

Vision CompetitionThe Semantic Web Company is one of the partners of this year’s LinkedData Planet Conference in New York (June 17-18, 2008). As part of this partnership, we launched a competition, asking for your vision of a future with Linked Open Data – and we have a winner!

Aman Shakya, who is a PhD student at the Department of Informatics at The Graduate University for Advanced Studies (SOKENDAI) in Tokyo, developed his vision around the idea of ordinary people being able to publish structured data instead of unstructured text:

The current gigantic network of web documents could be realized by enabling any user to publish any document and link to other documents. If we want to see the network of Linked Open Data explode on a similar scale, we need to enable general users to publish “data” directly on the web and link to other “data”. We need to move the paradigm of web page publishing and hyperlinking towards data publishing and data linking. We should enable people to post structured data about anything rather than just unstructured text. We need the active participation and contribution of the billions of worldwide internet users. Recently, the web has seen enormous user participation with the rise of easy-to-use social software. We should exploit this trend of social web applications, however, for enabling people to create, share and link “data” on the global Linked Data Web.

To endorse his vision, Aman Shakya also introduced his StYLiD application, which I would like to describe as a ‘semantically enhanced tumblelog’, and which “enables people to share a wide variety of structured data with the freedom to define their own structured concepts on the fly.” We have chosen his proposal because it met the criteria of the competition in various ways:

  • The feasibility of the vision is clearly laid out in the proposal, which describes the process of the creation of structured data and the interaction with existing data on the web.
  • The proposal has innovative potential in that it seeks to further and harness the collaborative sharing of structured data, and combines bottom-up and top-down governance for the social semantic web.
  • Sustainability is achieved by its reliance on open standards such as SPARQL.

Read his full proposal here.

We would also like to make an honorary mention of Mike Veytsel’s quadruple-fold approach to a semantic future in which users will be able “to easily and finely tune in to the long tail of knowledge and find content with low friction and high precision.”

Finally, I would also like to give my personal bookworm award to Rob Styles, for his prose account of a life with the semweb which he develops as an antithesis to Orwellian dystopia.

A big ‘Thank you’ to everyone who contributed!

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Jana Herwig

LinkedData Planet – Conference & Expo 2008

Come share your expertise with linked data and semantic technologies and learn from others at LinkedData Planet in New York City (June 17-18, 2008).

In creating the modern generation of enterprise and web applications, we typically integrate information from multiple sources. Relating data from disparate sources presents a challenge of deriving information. However, semantic tools and technologies are evolving that enable us to understand information derived by linking data from different sources, including data from applications, databases, ontologies and content management systems. Semantic technologies and tools support techniques such as tagging online information to make it more readily accessible for data integration. This makes it easier to understand data in relation to other data, even if some of this data is inside your firewall, some is in a business partner’s system, and some is part of the growing collection of useful publicly available data on the web.

LinkedData Planet provides insights into those technologies that enableus to:

  • connect data contained in silos within organizations in a meaningful way
  • extract and correlate data from web sites and databases for purposes such as analyzing trends and decision support, customer and vendor relationship management, and social networking

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Pascal Hitzler

Foundations of the Semantic Web

Semantic Web, Hitzler et. al.It has been half a year now that our German textbook on Foundations of the Semantic Web has appeared [1]. We received very positive feedback and see our book adopted for Semantic Web courses throughout the German speaking countries. We are particularly pleased that our concept seems to have worked out, i.e. our decision to focus on established standards which form the foundation of the Semantic Web instead of giving a shallow overview of the many Semantic Web topics which are not yet mature enough for applications.

In particular, our book introduces RDF, RDF Schema, and OWL in very detail, and does so in an intuitive manner. Separate from this are chapters explaining the formal semantics in terms of logical foundations for these languages in depth, including deduction algorithms. This is accompanied by a discussion of SPARQL and conjunctive queries.

The book is accompanied by a website which contains slides which are ready-to-use for lectures, as well as exercises and selected solutions.

We have received many requests for providing a similar book in the English language, and indeed we are already working on it. This will also include a discussion of the forthcoming revision of the OWL standard, OWL 2, formerly known as OWL 1.1.

Any feedback is very welcome.

[1] Pascal Hitzler, Markus Krötzsch, Sebastian Rudolph, York Sure: Semantic Web. Grundlagen. Springer 2008, ISBN: 978-3-540-33993-9