MEtaData Format for Open Reef Data (MEDFORD)

Polina Shpilker; John Freeman; Hailey McKelvie; Jill Ashey; Jay Miguel Fonticella; Hollie Putnam; Jane Greenberg; Lenore Cowen; Alva Couch; Noah M. Daniels

doi:10.1007/978-3-030-98876-0_18

MEtaData Format for Open Reef Data (MEDFORD)

Polina Shpilker
, John Freeman
, Hailey McKelvie
, Jill Ashey
, Jay Miguel Fonticella
, Hollie Putnam
, Jane Greenberg
, Lenore Cowen
, Alva Couch
, Noah M. Daniels

Workflow and Ecosystem Services

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

3 Scopus citations

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.

Original language	English
Title of host publication	Metadata and Semantic Research - 15th International Conference, MTSR 2021, Revised Selected Papers
Editors	Emmanouel Garoufallou, María-Antonia Ovalle-Perandones, Andreas Vlachidis
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	206-211
Number of pages	6
ISBN (Print)	9783030988753
DOIs	https://doi.org/10.1007/978-3-030-98876-0_18
State	Published - 2022
Event	15th International Conference on Metadata and Semantics Research, MTSR 2021 - Virtual, Online Duration: Nov 29 2021 → Dec 3 2021

Publication series

Name	Communications in Computer and Information Science
Volume	1537 CCIS
ISSN (Print)	1865-0929
ISSN (Electronic)	1865-0937

Conference

Conference	15th International Conference on Metadata and Semantics Research, MTSR 2021
City	Virtual, Online
Period	11/29/21 → 12/3/21

Funding

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.

Keywords

Coral reef data
Metadata
Research accessibility

Access to Document

10.1007/978-3-030-98876-0_18

Cite this

Shpilker, P., Freeman, J., McKelvie, H., Ashey, J., Fonticella, J. M., Putnam, H., Greenberg, J., Cowen, L., Couch, A., & Daniels, N. M. (2022). MEtaData Format for Open Reef Data (MEDFORD). In E. Garoufallou, M.-A. Ovalle-Perandones, & A. Vlachidis (Eds.), Metadata and Semantic Research - 15th International Conference, MTSR 2021, Revised Selected Papers (pp. 206-211). (Communications in Computer and Information Science; Vol. 1537 CCIS). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-030-98876-0_18

Shpilker, Polina ; Freeman, John ; McKelvie, Hailey et al. / MEtaData Format for Open Reef Data (MEDFORD). Metadata and Semantic Research - 15th International Conference, MTSR 2021, Revised Selected Papers. editor / Emmanouel Garoufallou ; María-Antonia Ovalle-Perandones ; Andreas Vlachidis. Springer Science and Business Media Deutschland GmbH, 2022. pp. 206-211 (Communications in Computer and Information Science).

@inproceedings{46b29384dcf7444f9b8ec9db8d67f229,

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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.",

keywords = "Coral reef data, Metadata, Research accessibility",

author = "Polina Shpilker and John Freeman and Hailey McKelvie and Jill Ashey and Fonticella, \{Jay Miguel\} and Hollie Putnam and Jane Greenberg and Lenore Cowen and Alva Couch and Daniels, \{Noah M.\}",

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doi = "10.1007/978-3-030-98876-0\_18",

language = "English",

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Shpilker, P, Freeman, J, McKelvie, H, Ashey, J, Fonticella, JM, Putnam, H, Greenberg, J, Cowen, L, Couch, A & Daniels, NM 2022, MEtaData Format for Open Reef Data (MEDFORD). in E Garoufallou, M-A Ovalle-Perandones & A Vlachidis (eds), Metadata and Semantic Research - 15th International Conference, MTSR 2021, Revised Selected Papers. Communications in Computer and Information Science, vol. 1537 CCIS, Springer Science and Business Media Deutschland GmbH, pp. 206-211, 15th International Conference on Metadata and Semantics Research, MTSR 2021, Virtual, Online, 11/29/21. https://doi.org/10.1007/978-3-030-98876-0_18

MEtaData Format for Open Reef Data (MEDFORD). / Shpilker, Polina; Freeman, John; McKelvie, Hailey et al.
Metadata and Semantic Research - 15th International Conference, MTSR 2021, Revised Selected Papers. ed. / Emmanouel Garoufallou; María-Antonia Ovalle-Perandones; Andreas Vlachidis. Springer Science and Business Media Deutschland GmbH, 2022. p. 206-211 (Communications in Computer and Information Science; Vol. 1537 CCIS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Shpilker, Polina

AU - Freeman, John

AU - McKelvie, Hailey

AU - Ashey, Jill

AU - Fonticella, Jay Miguel

AU - Putnam, Hollie

AU - Greenberg, Jane

AU - Cowen, Lenore

AU - Couch, Alva

AU - Daniels, Noah M.

PY - 2022

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N2 - 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.

AB - 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.

KW - Coral reef data

KW - Metadata

KW - Research accessibility

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M3 - Conference contribution

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SN - 9783030988753

T3 - Communications in Computer and Information Science

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A2 - Garoufallou, Emmanouel

A2 - Ovalle-Perandones, María-Antonia

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PB - Springer Science and Business Media Deutschland GmbH

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Shpilker P, Freeman J, McKelvie H, Ashey J, Fonticella JM, Putnam H et al. MEtaData Format for Open Reef Data (MEDFORD). In Garoufallou E, Ovalle-Perandones MA, Vlachidis A, editors, Metadata and Semantic Research - 15th International Conference, MTSR 2021, Revised Selected Papers. Springer Science and Business Media Deutschland GmbH. 2022. p. 206-211. (Communications in Computer and Information Science). doi: 10.1007/978-3-030-98876-0_18