Harmonizing semantic annotations for computational models in biology

Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon Crook, Miguel De Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers & 8 others Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

Research output: Contribution to JournalArticleAcademicpeer-review

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.

LanguageEnglish
Pages540-550
Number of pages11
JournalBriefings in bioinformatics
Volume20
Issue number2
DOIs
Publication statusPublished - 22 Mar 2019

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Semantics
Research Personnel
Biota
Biological Science Disciplines
Theoretical Models
Reusability
Biological systems
Parameterization
Interoperability
Chemical analysis

Keywords

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

Cite this

Neal, M. L., König, M., Nickerson, D., Misirli, G., Kalbasi, R., Dräger, A., ... Waltemath, D. (2019). Harmonizing semantic annotations for computational models in biology. Briefings in bioinformatics, 20(2), 540-550. https://doi.org/10.1093/bib/bby087
Neal, Maxwell Lewis ; König, Matthias ; Nickerson, David ; Misirli, Göksel ; Kalbasi, Reza ; Dräger, Andreas ; Atalag, Koray ; Chelliah, Vijayalakshmi ; Cooling, Michael T. ; Cook, Daniel L. ; Crook, Sharon ; De Alba, Miguel ; Friedman, Samuel H. ; Garny, Alan ; Gennari, John H. ; Gleeson, Padraig ; Golebiewski, Martin ; Hucka, Michael ; Juty, Nick ; Myers, Chris ; Olivier, Brett G. ; Sauro, Herbert M. ; Scharm, Martin ; Snoep, Jacky L. ; Touré, Vasundra ; Wipat, Anil ; Wolkenhauer, Olaf ; Waltemath, Dagmar. / Harmonizing semantic annotations for computational models in biology. In: Briefings in bioinformatics. 2019 ; Vol. 20, No. 2. pp. 540-550.
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Neal, ML, König, M, Nickerson, D, Misirli, G, Kalbasi, R, Dräger, A, Atalag, K, Chelliah, V, Cooling, MT, Cook, DL, Crook, S, De Alba, M, Friedman, SH, Garny, A, Gennari, JH, Gleeson, P, Golebiewski, M, Hucka, M, Juty, N, Myers, C, Olivier, BG, Sauro, HM, Scharm, M, Snoep, JL, Touré, V, Wipat, A, Wolkenhauer, O & Waltemath, D 2019, 'Harmonizing semantic annotations for computational models in biology', Briefings in bioinformatics, vol. 20, no. 2, pp. 540-550. https://doi.org/10.1093/bib/bby087

Harmonizing semantic annotations for computational models in biology. / Neal, Maxwell Lewis; König, Matthias; Nickerson, David; Misirli, Göksel; Kalbasi, Reza; Dräger, Andreas; Atalag, Koray; Chelliah, Vijayalakshmi; Cooling, Michael T.; Cook, Daniel L.; Crook, Sharon; De Alba, Miguel; Friedman, Samuel H.; Garny, Alan; Gennari, John H.; Gleeson, Padraig; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Myers, Chris; Olivier, Brett G.; Sauro, Herbert M.; Scharm, Martin; Snoep, Jacky L.; Touré, Vasundra; Wipat, Anil; Wolkenhauer, Olaf; Waltemath, Dagmar.

In: Briefings in bioinformatics, Vol. 20, No. 2, 22.03.2019, p. 540-550.

Research output: Contribution to JournalArticleAcademicpeer-review

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Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A et al. Harmonizing semantic annotations for computational models in biology. Briefings in bioinformatics. 2019 Mar 22;20(2):540-550. https://doi.org/10.1093/bib/bby087