Archive for February, 2012

iKUP wins the Ontologies Come of Age in the Semantic Web grand challenge =

February 12, 2012

The Kidney and urinary Pathway Knowledgebase (KUPKB) (http://www.kupkb.org) its web front-end the iKUP browser has won first prize at the Ontologies come of Age in the Semantic Web grand challenge held at the International Semantic Web Conference in 2012 at Bonn. The KUPKB uses an application ontology make from some OBO ontologies together with extensions and bespoke fragments of ontology to form a schema into which we’ve put annotations on genes, proteins and experiments across various ‘omic levels. The iKUP browser is a GWT built front-end that exposes the KUPKB through a faceted browser that allows users to browse and search the KUPKB’s contents via the various aspects captured in the KUP Ontology.

There are a couple of noteworthy things about our approach:

  1. Julie klein, one of our collaborating biologists in Toulouse, added most of the data from various investigations. We didn’t have her directly adding axioms by hand, but instead used RightField spreadsheets to help her do this task. RightField is a semantic spreadsheet in which menus tied to portions of ontologies can be embedded. This means a standard Excel spreadsheet can be used to add ontology terms to data and have only appropriate terms made available to the user; these marked up spreadsheets are then transformed to KUPKB content by scripts. Julie also added a lot of content to the KUPKB’s ontology (KUPO) with an extension of RightFiel called Populous, a semantic spreadsheet type application for describing entities according to various ontologies and then having the spreadsheet’s contents transformed into axioms via the Ontology Preprocessor Language (OPPL) and put in the KUPKB.
  2. Simon Jupp, who built the KUPKB, also made the iKUP browser. This is a GWT front-end to the KUPKB that allows searching and faceted browsing (based on the KUPO) so that biologists can find genes and proteins together with associated experimental data. The iKUP browser helps construct SPRQL queries against the kUPKB as well as using a bit of OWL reasoning (with HerMiT). The iKUP is the key; it let’s biologists use the KUPKB without necessarily knowing they are using Semantic Web technologies – it is just a Web page.

Our OCAS submission was accompanied by a short paper:

Simon Jupp, Julie Klein, Panagiotis Moulos, Joost Schanstra and Robert Stevens. Ontologies Come of Age with the iKUP Browser. In Alexander Garcia Castro, Ken Baclawski, John Bateman, Kim Viljanen, and Christoph Lange, editors, Proceedings of the Workshop Ontologies Come of Age in the Semantic Web, International Semantic Web Conference, number 809 in CEUR Workshop Proceedings, pages 25-28, Aachen, 2011.

In this paper we outlined some criteria for “coming of age” and how we think KUPKB and iKUP meets them:

  1. When Ontologies / Semantic Web technologies are used outside of their community
  2. When the technology becomes transparent to the user experience
  3. Tools and APIs are mature enough for developers to simply bolt applications together
  4. Questions over performance and scalability go away

The first criterion is analogous to that of the Web; it’s come of age once it’s moved outside those that know how it works and how to write HtML pages by hand (plus when there was something useful on the Web). When my Mum started using the Web to plan days out for herself and my Dad, then the Web had come of age. Similarly, our biology colleagues can come to iKUP, search and browse without knowing that it is an OWL ontology organising some RDF and using SPRQL to get back tables of data. Fulfilling criterion two is helped by criterion one. The iKUP browser makes use of the Semantic Web technologies transparently – it is just a web page in a familiar environment (just as RightField is delivered via a Excel spreadsheet) where keywords are typed in and a faceted browser allows users to both go directly to entities of interest, but also to “just look around”. That the facets are provided by an ontology need not be known (and should not be known) by the user. We can only make the iKUP browser if criterion thre is met – we used a series of standard API and GWT to make the KUPKB available via the iKUP. This really is a sign of “coming of age” – we can “bolt together” applications in fairly short order. Having met our last criterion is harder to justify – KUPKB is relatively small scale, so we don’t have too many performance problems. As RDF gets v big it all gets a bit clunky, but that should change. Anyway, by and large, we feel that the Semantic Web technologies really are coming of age and can do the job (if one’s careful) that they are supposed to do.

As we say in our OCAS paper: “The KUPKB and iKUP show ontologies coming of age by fulfilling some of their promise. The KUPKB has used ontologies to provide a common semantic framework for a broad range of previously semantically heterogeneous data. The use of Semantic Web technologies provides the means to integrate and query these data. The key to the coming of age is the iKUP user interface; without a simple means to access these integrated data, our biologist users would not and could not use the KUPKB; ontologies come of age when they deliver meaningful use to their intended users. This has now happened with the KUPKB, with biologists testing hypotheses generated via the iKUP in laboratories. Though the KUPKB is relatively small, it does what semantic technologies are supposed to do and show what is possible with biology’s rich resource of data once issues of heterogeneity are taken away and the means of delivery to its users is taken into account. “


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