Harmonizing semantic annotations for computational models in biology

Maxwell Lewis Neal¹, Matthias König², David Nickerson³, Göksel Mısırlı⁴, Reza Kalbasi³, Andreas Dräger^{5

6}, Koray Atalag³, Vijayalakshmi Chelliah⁷, Michael T Cooling³, Daniel L Cook^{8

9}, Sharon Crook¹⁰, Miguel de Alba¹¹, Samuel H Friedman¹², Alan Garny³, John H Gennari⁹, Padraig Gleeson¹³, Martin Golebiewski¹⁴, Michael Hucka¹⁵, Nick Juty⁷, Chris Myers¹⁶, Brett G Olivier^{17

18}, Herbert M Sauro¹⁹, Martin Scharm²⁰, Jacky L Snoep^{21

22

23}, Vasundra Touré²⁴, Anil Wipat²⁵, Olaf Wolkenhauer^{20

26}, Dagmar Waltemath²⁰

Affiliations

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.

PMID: 30462164
PMCID: PMC6433895
DOI: 10.1093/bib/bby087

Review

Harmonizing semantic annotations for computational models in biology

Maxwell Lewis Neal et al. Brief Bioinform. 2019.

. 2019 Mar 22;20(2):540-550.

doi: 10.1093/bib/bby087.

Authors

Affiliations

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.

PMID: 30462164
PMCID: PMC6433895
DOI: 10.1093/bib/bby087

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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Figures

**Figure 1**
Example RDF-based annotation from SBML model BIOMD0000000239 [71] in BioModels. The annotation block (indicated by a curly brace) defines the biological meaning of a physical compartment in the model. The RDF block within the *<annotation>* element links the compartment’s metadata identifier ‘metaid_MT_IMS’ to the Gene Ontology term GO:0005758, which represents the mitochondrial intermembrane space. The use of the *bqbiol:is* predicate in this link indicates that the compartment is defined as the mitochondrial intermembrane space.

See this image and copyright information in PMC

References

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1. Neal ML, Cooling MT, Smith LP, et al. A reappraisal of how to build modular, reusable models of biological systems. PLoS Comput Biol 2014;10:e1003849. - PMC - PubMed

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Harmonizing semantic annotations for computational models in biology

Affiliations

Harmonizing semantic annotations for computational models in biology

Authors

Affiliations

Abstract

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References

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