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Harmonizing semantic annotations for computational models in biology

View ORCID ProfileML Neal, View ORCID ProfileM König, D Nickerson, G Mısırlı, R Kalbasi, View ORCID ProfileA Dräger, K Atalag, V Chelliah, M Cooling, DL Cook, S Crook, M de Alba, SH Friedman, A Garny, JH Gennari, View ORCID ProfileP Gleeson, M Golebiewski, M Hucka, N Juty, N Le Novère, C Myers, BG Olivier, HM Sauro, M Scharm, JL Snoep, V Touré, A Wipat, O Wolkenhauer, D Waltemath
doi: https://doi.org/10.1101/246470
ML Neal
1Center for Infectious Disease Research, Seattle, WA, USA
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  • For correspondence: max.neal@cidresearch.org
M König
2Department of Biology, Humboldt-University Berlin, Institute for Theoretical Biology, Berlin, Germany
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D Nickerson
3Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
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G Mısırlı
4School of Computing and Mathematics, Keele University, Keele, UK
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R Kalbasi
3Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
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A Dräger
5Applied Bioinformatics Group, Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany
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K Atalag
3Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
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V Chelliah
6European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
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M Cooling
3Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
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DL Cook
7Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
8Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
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S Crook
9School of Mathematical and Statistical Sciences, Arizona State University, Tempe, USA
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M de Alba
10German Federal Institute for Risk Assessment, Berlin, Germany
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SH Friedman
11Opto-Knowledge Systems, Inc. (OKSI), Torrance, CA, USA
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A Garny
3Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
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JH Gennari
8Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
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P Gleeson
12Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
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M Golebiewski
13Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
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M Hucka
14Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
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N Juty
6European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
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N Le Novère
15Babraham Institute, Babraham, Cambridge, UK
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C Myers
16Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA
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BG Olivier
17Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
18Modelling of Biological Processes, BioQUANT/COS, Heidelberg University, Germany
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HM Sauro
19Department of Bioengineering, University of Washington, Seattle, WA, USA
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M Scharm
20Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
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JL Snoep
21Department of Biochemistry, Stellenbosch University, Matieland, South Africa
22Department of Molecular Cell Physiology, Vrije Universiteit, Amsterdam, The Netherlands
23Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
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V Touré
24Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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A Wipat
25School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
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O Wolkenhauer
20Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
26Stellenbosch Institute for Advanced Study (STIAS), Stellenbosch, South Africa
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D Waltemath
20Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
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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 semantic annotation practices among the COmputational Modeling in BIology NEtwork (COMBINE) community and provide a set of recommendations for building a consensus approach to semantic annotation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 23, 2018.
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Harmonizing semantic annotations for computational models in biology
ML Neal, M König, D Nickerson, G Mısırlı, R Kalbasi, A Dräger, K Atalag, V Chelliah, M Cooling, DL Cook, S Crook, M de Alba, SH Friedman, A Garny, JH Gennari, P Gleeson, M Golebiewski, M Hucka, N Juty, N Le Novère, C Myers, BG Olivier, HM Sauro, M Scharm, JL Snoep, V Touré, A Wipat, O Wolkenhauer, D Waltemath
bioRxiv 246470; doi: https://doi.org/10.1101/246470
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Harmonizing semantic annotations for computational models in biology
ML Neal, M König, D Nickerson, G Mısırlı, R Kalbasi, A Dräger, K Atalag, V Chelliah, M Cooling, DL Cook, S Crook, M de Alba, SH Friedman, A Garny, JH Gennari, P Gleeson, M Golebiewski, M Hucka, N Juty, N Le Novère, C Myers, BG Olivier, HM Sauro, M Scharm, JL Snoep, V Touré, A Wipat, O Wolkenhauer, D Waltemath
bioRxiv 246470; doi: https://doi.org/10.1101/246470

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