A Simple Standard for Sharing Ontological Mappings (SSSOM)
Database, vol. 2022
Abstract
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec.
Authors 41
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Affiliation as printed
Semanticly Ltd, London WC2H 9JQ, UK
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University of North Carolina at Chapel Hill · Renaissance Computing Institute
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RENCI, University of North Carolina, Chapel Hill, NC 27517, USA
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Affiliation as printed
The Jackson Laboratory, Bar Harbor, ME 04609, USA
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University of North Carolina at Chapel Hill · Renaissance Computing Institute
Affiliation as printed
RENCI, University of North Carolina, Chapel Hill, NC 27517, USA
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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Affiliation as printed
Johns Hopkins University, Baltimore, MD 21210, USA
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Lawrence Berkeley National Laboratory
Affiliation as printed
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Affiliation as printed
Maastricht University, Maastricht 6211 LK, The Netherlands
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Affiliation as printed
Johns Hopkins University, Baltimore, MD 21210, USA
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Affiliation as printed
Stanford University, Stanford, CA 94305, USA
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Affiliation as printed
Harvard Medical School, Boston, MA 02115, USA
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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European Bioinformatics Institute
Affiliation as printed
European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
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Lawrence Berkeley National Laboratory
Affiliation as printed
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Affiliation as printed
Pistoia Alliance Inc, USA
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Lawrence Berkeley National Laboratory
Affiliation as printed
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Beth Israel Deaconess Medical Center
Affiliation as printed
Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
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Affiliation as printed
Harvard Medical School, Boston, MA 02115, USA
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Affiliation as printed
Johns Hopkins University, Baltimore, MD 21210, USA
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City, University of London · University of Oslo · City St George's, University of London
Affiliation as printed
City University of London, London EC1V 0HB, UK
University of Oslo, Oslo 0315, Norway
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Affiliation as printed
SciBite Limited, Bio Data Innovation Centre, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1DR, UK
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Affiliation as printed
Robert Bosch LLC, Sunnyvale, CA 94085, USA
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Affiliation as printed
Pistoia Alliance Inc, USA
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Qinqin Long Aachen
Leiden University Medical Center
Affiliation as printed
Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
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Affiliation as printed
BenchSci, 25 York St Suite 1100, Toronto, ON M5J 2V5, Canada
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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Lawrence Berkeley National Laboratory
Affiliation as printed
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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European Bioinformatics Institute
Affiliation as printed
European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
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Affiliation as printed
Knocean Inc., Toronto, ON M6P 2T3, Canada
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La Jolla Institute for Immunology
Affiliation as printed
La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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Núria Queralt-Rosiñach Aachen
Leiden University Medical Center
Affiliation as printed
Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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Affiliation as printed
Johns Hopkins University, Baltimore, MD 21210, USA
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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Affiliation as printed
Independent Scholar
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University of Colorado Anschutz
Affiliation as printed
University of Colorado Anschutz Medical Campus, Aurora, CO 80217, USA
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Nationwide Children's Hospital · The Ohio State University
Affiliation as printed
The Ohio State University College of Medicine, Columbus, OH 43210, USA
The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
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Chris Mungall corresponding
Lawrence Berkeley National Laboratory
Affiliation as printed
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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