Harmonizing semantic annotations for computational models in biology
Date
2019
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
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.
Description
CITATION: Neal, M. L., et al. 2019. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics, 20(2):540-550, doi:10.1093/bib/bby087.
The original publication is available at https://academic.oup.com/
The original publication is available at https://academic.oup.com/
Keywords
Semantic annotation, Biological systems -- Data processing -- Analysis, Computational modeling, Data integration (Computer science)
Citation
Neal, M. L., et al. 2019. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics, 20(2):540-550, doi:10.1093/bib/bby087