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Title: FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

Abstract

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true ‘machine-actionable interoperability’, which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.

Authors:
 [1];  [1];  [2];  [1];  [1]
+ Show Author Affiliations
  1. La Jolla Inst. for Allergy and Immunology, La Jolla, CA (United States). Center for Emerging Diseases and Biodefense. Division of Vaccine Discovery
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Division of Environmental Genomics and Systems Biology
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH)
OSTI Identifier:
1625309
Grant/Contract Number:  
AC02-05CH11231 HHSN272201200010C; 1R24HG010032-01
Resource Type:
Accepted Manuscript
Journal Name:
Database
Additional Journal Information:
Journal Volume: 2018; Journal ID: ISSN 1758-0463
Publisher:
Oxford University Press - International Society for Biocuration
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; Mathematical & Computational Biology

Citation Formats

Vita, Randi, Overton, James A., Mungall, Christopher J., Sette, Alessandro, and Peters, Bjoern. FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. United States: N. p., 2018. Web. doi:10.1093/database/bax105.
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Vita, Randi, Overton, James A., Mungall, Christopher J., Sette, Alessandro, & Peters, Bjoern. FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. United States. https://doi.org/10.1093/database/bax105
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Vita, Randi, Overton, James A., Mungall, Christopher J., Sette, Alessandro, and Peters, Bjoern. Mon . "FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability". United States. https://doi.org/10.1093/database/bax105. https://www.osti.gov/servlets/purl/1625309.
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@article{osti_1625309,
title = {FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability},
author = {Vita, Randi and Overton, James A. and Mungall, Christopher J. and Sette, Alessandro and Peters, Bjoern},
abstractNote = {The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true ‘machine-actionable interoperability’, which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.},
doi = {10.1093/database/bax105},
journal = {Database},
number = ,
volume = 2018,
place = {United States},
year = {Mon Feb 19 00:00:00 EST 2018},
month = {Mon Feb 19 00:00:00 EST 2018}
}
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Publisher's Version of Record
https://doi.org/10.1093/database/bax105
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  • Nucleic Acids Research, Vol. 43, Issue D1
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journal, January 2013

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bioCADDIE white paper - Data Discovery Index
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bioCADDIE white paper - Data Discovery Index
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    Cyberinfrastructure and resources to enable an integrative approach to studying forest trees
    journal, June 2019

    • Wegrzyn, Jill L.; Falk, Taylor; Grau, Emily
    • Evolutionary Applications, Vol. 13, Issue 1
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    The Immune Epitope Database (IEDB): 2018 update
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    • Vita, Randi; Mahajan, Swapnil; Overton, James A.
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    • DOI: 10.1093/nar/gky1006

    The Immune Epitope Database and Analysis Resource Program 2003–2018: reflections and outlook
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    Noncoding regions are the main source of targetable tumor-specific antigens
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    The Immune Epitope Database (IEDB): 2018 update
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    • Vita, Randi; Mahajan, Swapnil; Overton, James A.
    • Nucleic Acids Research, Vol. 47, Issue D1
    • DOI: 10.1093/nar/gky1006
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