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MEtaData Format for Open Reef Data (MEDFORD)

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Metadata and Semantic Research (MTSR 2021)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1537))

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Abstract

Reproducibility of research is critical for science. Computational biology research presents a significant challenge, given the need to track critical details, such as software version or genome draft iteration. Metadata research infrastructures, while greatly improved, often assume a level of programming skills in their user community, or rely on expert curators to ensure that key information is not lost. This paper introduces MEDFORD, a new human-readable, easily-editable and templatable metadata language for scientists to collocate all the details relevant to their experiments. We provide an overview of the underlying design principles, language, and current and planned support infrastructure for parsing and translating MEDFORD into other metadata formats. MEDFORD 0.9 has been specifically designed for the coral research community, with initial metadata generated from RNA-Seq analyses of coral transcriptomes and coral photo collections. Notably, the format is generally applicable and useful for many types of scientific metadata generated by non-computer science experts.

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Acknowledgment

The authors thank the anonymous reviewers for their valuable suggestions. This work is supported in part by funds from the National Science Foundation under grants NSF-OAC #1939263, #1939795 and #1940233.

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Authors and Affiliations

  1. Department of Computer Science, Tufts University, Medford, MA, USA

    Polina Shpilker, John Freeman, Hailey McKelvie, Jay-Miguel Fonticella, Lenore Cowen & Alva Couch

  2. Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA

    Jill Ashey & Hollie Putnam

  3. Department of Information Science, Drexel University, Philadelphia, PA, USA

    Jane Greenberg

  4. Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI, USA

    Noah M. Daniels

Authors
  1. Polina Shpilker
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  2. John Freeman
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  3. Hailey McKelvie
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  4. Jill Ashey
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  5. Jay-Miguel Fonticella
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  6. Hollie Putnam
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  7. Jane Greenberg
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  8. Lenore Cowen
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  9. Alva Couch
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  10. Noah M. Daniels
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Corresponding author

Correspondence to Noah M. Daniels .

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Editors and Affiliations

  1. International Hellenic University, Thessaloniki, Greece

    Emmanouel Garoufallou

  2. Complutense University of Madrid, Madrid, Spain

    María-Antonia Ovalle-Perandones

  3. University College London, London, UK

    Andreas Vlachidis

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Shpilker, P. et al. (2022). MEtaData Format for Open Reef Data (MEDFORD). In: Garoufallou, E., Ovalle-Perandones, MA., Vlachidis, A. (eds) Metadata and Semantic Research. MTSR 2021. Communications in Computer and Information Science, vol 1537. Springer, Cham. https://doi.org/10.1007/978-3-030-98876-0_18

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  • DOI: https://doi.org/10.1007/978-3-030-98876-0_18

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-98875-3

  • Online ISBN: 978-3-030-98876-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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