Showing papers presented at "Semantic Web Applications and Tools for Life Sciences in 2010"

Populous: A tool for populating ontology templates

Abstract: We present Populous, a tool for gathering content with which to populate anontology. Domain experts need to add content, that is often repetitive in itsform, but without having to tackle the underlying ontological representation.Populous presents users with a table based form in which columns areconstrained to take values from particular ontologies; the user can select aconcept from an ontology via its meaningful label to give a value for a givenentity attribute. Populated tables are mapped to patterns that can then be usedto automatically generate the ontology's content. Populous's contribution is inthe knowledge gathering stage of ontology development. It separates knowledgegathering from the conceptualisation and also separates the user from thestandard ontology authoring environments. As a result, Populous can allowknowledge to be gathered in a straight-forward manner that can then be used todo mass production of ontology content.

Linking Open Drug Data to Cheminformatics and Proteochemometrics

Abstract: Semantic Web technologies have made great steps forwardin data exchange in health care and life sciences in the past years. Thework presented here focuses to a some extent on making drug discoveryrelated data available as RDF, and even more so on the integration ofRDF approaches with data analysis of molecular information in drugdiscovery fields like cheminformatics and proteochemometrics. We hereshow how the chem- and bioinformatics workbench Bioclipse and theChemistry Development Kit can be used to this purpose.Abstract. Semantic Web technologies have made great steps forwardin data exchange in health care and life sciences in the past years. Thework presented here focuses to a some extent on making drug discoveryrelated data available as RDF, and even more so on the integration ofRDF approaches with data analysis of molecular information in drugdiscovery fields like cheminformatics and proteochemometrics. We hereshow how the chem- and bioinformatics workbench Bioclipse and theChemistry Development Kit can be used to this purpose.

A study on the relation between linguistics-oriented and domain-specific semantics

Abstract: In this paper we dealt with the comparison and linking between lexical resources with domain knowledge provided by ontologies. It is one of the issues for the combination of the Semantic Web Ontolo ...

Evaluating modelling approaches for medical image annotations

Abstract: Information system designers face many challenges w.r.t. selecting appropriate semantic technologies and deciding on a modelling approach for their system. However, there is no clear methodology yet to evaluate “semantically enriched” information systems. In this paper we present a case study on different modelling approaches for annotating medical images and introduce a conceptual framework that can be used to analyse the fitness of information systems and help designers to spot the strengths and weaknesses of various modelling approaches as well as managing trade-offs between modelling effort and their potential

Argudas: arguing with gene expression information

Abstract: In situ hybridisation gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information are often both incomplete and inconsistent. This paper examines a system, Argudas, designed to help tackle these issues. Argudas is an evolution of an existing system, and so that system is reviewed as a means of both explaining and justifying the behaviour of Argudas. Throughout the discussion of Argudas a number of issues will be raised including the appropriateness of argumentation in biology and the challenges faced when integrating apparently similar online biological databases.