Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform


Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. Semantic web technologies should be ideal for exploring the complex networks of genes, proteins and metabolites that interact, but much of this data is not natively available to the semantic web. Data is typically collected and stored with free-text annotations in spreadsheets, many of which do not conform to existing metadata standards and are often not publically released. Along with initiatives to promote more data sharing, one of the main challenges is therefore to semantically annotate and extract this data so that it is available to the research community. Data annotation and curation are expensive and undervalued tasks that have enormous benefits to the discipline as a whole, but fewer benefits to the individual data producers. By embedding semantic annotation into spreadsheets, however, and automatically extracting this data into RDF at the time of repository submission, the process of producing standards-compliant data, that is available for semantic web querying, can be achieved without adding additional overheads to laboratory data management. This paper describes these strategies in the context of semantic data management in the SEEK. The SEEK is a web-based resource for sharing and exchanging Systems Biology data and models that is underpinned by the JERM ontology (Just Enough Results Model), which describes the relationships between data, models, protocols and experiments. The SEEK was originally developed for SysMO, a large European Systems Biology consortium studying micro-organisms, but it has since had widespread adoption across European Systems Biology.


DOI: 10.1007/978-3-642-41338-4_14

Projects: SysMO DB

Publication type: Journal

Journal: Advanced Information Systems Engineering

Book Title: Advanced Information Systems Engineering

Editors: David Hutchison and Takeo Kanade and Josef Kittler and Jon M. Kleinberg and Friedemann Mattern and John C. Mitchell and Moni Naor and Oscar Nierstrasz and C. Pandu Rangan and Bernhard Steffen and Madhu Sudan and Demetri Terzopoulos and Doug Tygar and Moshe Y. Vardi and Gerhard Weikum and Camille Salinesi and Moira C. Norrie and Óscar Pastor

Publisher: Springer Berlin Heidelberg

Citation: Advanced Information Systems Engineering 7908:212-227,Springer Berlin Heidelberg

Date Published: 2013

Registered Mode: Not specified

help Submitter
Wolstencroft, K., Owen, S., Krebs, O., Mueller, W., Nguyen, Q., Snoep, J. L., & Goble, C. (2013). Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform. In Advanced Information Systems Engineering (pp. 212–227). Springer Berlin Heidelberg.

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Created: 28th Oct 2013 at 14:57

Last updated: 29th Jul 2020 at 15:47

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