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Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087.

Harmonizing semantic annotations for computational models in biology.

Author information

1
Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, USA.
2
Department of Biology, Humboldt-University Berlin, Institute for Theoretical Biology, Berlin, Germany.
3
Auckland Bioengineering Institute, University of Auckland, Auckland, NZ.
4
School of Computing and Mathematics, Keele University, Keele, UK.
5
Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany.
6
Department of Computer Science, University of Tübingen, Tübingen, Germany.
7
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
8
Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
9
Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
10
School of Mathematical and Statistical Sciences, Arizona State University, Tempe, USA.
11
German Federal Institute for Risk Assessment, Berlin, Germany.
12
Opto-Knowledge Systems, Inc. (OKSI), Torrance, CA, USA.
13
Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
14
Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany.
15
Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
16
Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA.
17
Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
18
Modelling of Biological Processes, BioQUANT/COS, Heidelberg University, Germany.
19
Department of Bioengineering, University of Washington, Seattle, WA, USA.
20
Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
21
Department of Biochemistry, Stellenbosch University, Matieland, South Africa.
22
Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
23
Manchester Institute for Biotechnology, University of Manchester, Manchester, UK.
24
Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
25
School of Computing Science, Newcastle University, Newcastle upon Tyne, UK.
26
Stellenbosch Institute for Advanced Study (STIAS), Stellenbosch, South Africa.

Abstract

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.

KEYWORDS:

computational modeling; data integration; knowledge representation; modeling standards; semantic annotation

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