TY  - JOUR
TI  - Harmonizing semantic annotations for computational models in biology
AU  - Maxwell L. Neal
AU  - Matthias König
AU  - David Nickerson
AU  - Göksel Mısırlı
AU  - Reza Kalbasi
AU  - Andreas Dräger
AU  - Koray Atalağ
AU  - Vijayalakshmi Chelliah
AU  - Michael T. Cooling
AU  - Daniel L. Cook
AU  - Sharon Crook
AU  - Miguel de Alba
AU  - Samuel H. Friedman
AU  - Alan Garny
AU  - John H. Gennari
AU  - Padraig Gleeson
AU  - Martin Golebiewski
AU  - Michael Hucka
AU  - Nick Juty
AU  - Chris J. Myers
AU  - Brett G. Olivier
AU  - Herbert M. Sauro
AU  - Martin Scharm
AU  - Jacky L. Snoep
AU  - Vasundra Touré
AU  - Anil Wipat
AU  - Olaf Wolkenhauer
AU  - Dagmar Waltemath
PY  - 2018
JO  - Briefings in Bioinformatics
DO  - 10.1093/bib/bby087
UR  - https://doi.org/10.1093/bib/bby087
AB  - 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.
ER  -