Roman Baum

Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data

Institutions: ZB MED - Information Centre for Life Sciences

https://orcid.org/0000-0001-5246-9351
Niels Zondervan palproject_administrator

Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, WURSynBio

Institutions: Wageningen University & Research

https://orcid.org/0000-0001-7049-5334
Carole Goble

Projects: SysMO DB, FAIRDOM, FAIRDOM user meeting, COVID-19 Disease Map

Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

https://orcid.org/0000-0003-1219-2137
Stuart Owen adminproject_administratorprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting, FAIRDOM Community Workers

Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

https://orcid.org/0000-0003-2130-0865
Katy Wolstencroft adminproject_administratorasset_housekeeperprogramme_administrator

Projects: SysMO DB, HUMET Startup, FAIRDOM, Consensus Hallmark Annotation, NL-Bioimaging FAIR Metadata Templates, FAIR Functional Enrichment

Institutions: University of Leiden, LIACS

https://orcid.org/0000-0002-1279-5133
Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform
SysMO DB

Abstract (Expand)

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.

Editor: 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

Date Published: 2013

Publication Type: Journal

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

Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.

Creators: Stuart Owen, Carole Goble, Katy Wolstencroft, Jacky Snoep, Wolfgang Müller, Olga Krebs, Quyen Nguyen

Submitter: Stuart Owen

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SEEK and RDF
SysMO DB

An overview of the RDF work being done with SEEK, given at the PALs meeting, November 2012. It gives a high level explanation of what RDF is, why its useful and can be used for filtering and finding out information about the data in SEEK. This talk proceeded an interactive session where the PALs came up with 20 questions, to help us refine our model and prioritise what we describe.

Creator: Stuart Owen

Submitter: Stuart Owen

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RightField: Semantic Enrichment of Systems Biology Data using Spreadsheets
SysMO DB

This talk was presented at the IEEE e-Science conference, Chicago, USA (8-12 October 2012). http://www.ci.uchicago.edu/escience2012/ It describes the latest developments in RightField for both semantic data annotation and extraction to RDF.

Creators: Katy Wolstencroft, Stuart Owen, Carole Goble

Submitter: Katy Wolstencroft

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