@article{Neal2018,
  author    = {Neal, Maxwell Lewis and K\"onig, Matthias and Nickerson, David and M{\i}s{\i}rl{\i},
    G\"oksel and Kalbasi, Reza and Dr\"ager, Andreas and Atalag, Koray and Chelliah, Vijayalakshmi
    and Cooling, Michael T. and Cook, Daniel L. and Crook, Sharon and {de Alba}, Miguel and Friedman,
    Samuel H. and Garny, Alan and Gennari, John H. and Gleeson, Padraig and Golebiewski, Martin and
    Hucka, Michael and Juty, Nick and Myers, Chris and Olivier, Brett G. and Sauro, Herbert M. and
    Scharm, Martin and Snoep, Jacky L and Tour\'e, Vasundra and Wipat, Anil and Wolkenhauer, Olaf
    and Waltemath, Dagmar},
  title     = {Harmonizing semantic annotations for computational models in biology},
  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  = {semantic annotation, computational modeling, knowledge representation, modeling
    standards, data integration},
  journal   = {Briefings in Bioinformatics},
  volume    = {20},
  number    = {2},
  pages     = {540--550},
  year      = {2018},
  month     = nov,
  issn      = {1477-4054},
  doi       = {10.1093/bib/bby087},
  url       = {https://doi.org/10.1093/bib/bby087},
  eprint    = {https://academic.oup.com/bib/article-pdf/20/2/540/28834058/bby087.pdf},
}