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FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

View ORCID ProfileDaniel J. B. Clarke, Lily Wang, Alex Jones, View ORCID ProfileMegan L. Wojciechowicz, Denis Torre, View ORCID ProfileKathleen M. Jagodnik, View ORCID ProfileSherry L. Jenkins, View ORCID ProfilePeter McQuilton, Zachary Flamholz, Moshe C. Silverstein, View ORCID ProfileBrian M. Schilder, View ORCID ProfileKimberly Robasky, Claris Castillo, Ray Idaszak, Stanley C. Ahalt, View ORCID ProfileJason Williams, View ORCID ProfileStephan Schurer, View ORCID ProfileDaniel J. Cooper, View ORCID ProfileRicardo de Miranda Azevedo, View ORCID ProfileJuergen A. Klenk, Melissa A. Haendel, View ORCID ProfileJared Nedzel, Paul Avillach, View ORCID ProfileMary E. Shimoyama, Rayna M. Harris, Meredith Gamble, Rudy Poten, Amanda L. Charbonneau, View ORCID ProfileJennie Larkin, View ORCID ProfileC. Titus Brown, View ORCID ProfileVivien R. Bonazzi, View ORCID ProfileMichel J. Dumontier, View ORCID ProfileSusanna-Assunta Sansone, View ORCID ProfileAvi Ma’ayan
doi: https://doi.org/10.1101/657676
Daniel J. B. Clarke
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Lily Wang
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Alex Jones
2Deloitte Consulting LLP, 1919 N Lynn St, Arlington, VA 22209, USA
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Megan L. Wojciechowicz
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Denis Torre
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Kathleen M. Jagodnik
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Sherry L. Jenkins
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Peter McQuilton
3Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
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Zachary Flamholz
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Moshe C. Silverstein
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Brian M. Schilder
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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Kimberly Robasky
4Renaissance Computing Institute, University of North Carolina, Chapel Hill, USA
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Claris Castillo
4Renaissance Computing Institute, University of North Carolina, Chapel Hill, USA
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Ray Idaszak
4Renaissance Computing Institute, University of North Carolina, Chapel Hill, USA
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Stanley C. Ahalt
4Renaissance Computing Institute, University of North Carolina, Chapel Hill, USA
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Jason Williams
5Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
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Stephan Schurer
6University of Miami, Pharmacology, 1600 NW 10th Avenue, Miami, FL 33136, USA
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Daniel J. Cooper
6University of Miami, Pharmacology, 1600 NW 10th Avenue, Miami, FL 33136, USA
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Ricardo de Miranda Azevedo
7Institute of Data Science Maastricht University, Universiteitssingel 60, 6229 ER, Maastricht, The Netherlands
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Juergen A. Klenk
2Deloitte Consulting LLP, 1919 N Lynn St, Arlington, VA 22209, USA
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Melissa A. Haendel
8Oregon State University, 307 Linus Pauling Science Center, 2900 SW Campus Way, Corvallis, OR 9733, USA
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Jared Nedzel
9The Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
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Paul Avillach
10Harvard Medical School, Department of Biomedical Informatics, 10 Shattuck St, Boston, MA 02115, USA
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Mary E. Shimoyama
11Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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Rayna M. Harris
12Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, CA 95616, USA
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Meredith Gamble
13Curoverse, Inc. Somerville, MA 02144, USA
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Rudy Poten
13Curoverse, Inc. Somerville, MA 02144, USA
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Amanda L. Charbonneau
12Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, CA 95616, USA
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Jennie Larkin
14National Institute of Diabetes, Digestive, and Kidney Diseases (NIDDK), National Institutes of Health (NIH), 6707 Democracy Blvd, Bethesda, MD 20817, USA
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C. Titus Brown
12Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, CA 95616, USA
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Vivien R. Bonazzi
15Office of the Director, National Institutes of Health, 8600 Rockville Pike, Rm 2S-20, Bethesda, MD, 20894, USA
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Michel J. Dumontier
7Institute of Data Science Maastricht University, Universiteitssingel 60, 6229 ER, Maastricht, The Netherlands
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Susanna-Assunta Sansone
3Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
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Avi Ma’ayan
1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA
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  • For correspondence: avi.maayan@mssm.edu
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Abstract

As more datasets, tools, workflows, APIs, and other digital resources are produced by the research community, it is becoming increasingly difficult to harmonize and organize these efforts for maximal synergistic integrated utilization. The Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge by making these digital resources follow common standards and best practices so that they can become more integrated and organized. Faced with the question of how to make digital resources more FAIR, it has become imperative to measure what it means to be FAIR. The diversity of resources, communities, and stakeholders have different goals and use cases and this makes assessment of FAIRness particularly challenging. To begin resolving this challenge, the FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual, semi- and fully-automated FAIR assessment capabilities. The FAIRshake toolkit contains a database that lists registered digital resources, with their associated metrics, rubrics, and assessments. The FAIRshake toolkit also has a browser extension and a bookmarklet that enables viewing and submitting assessments from any website. The FAIR assessment results are visualized as an insignia that can be viewed on the FAIRshake website, or embedded within hosting websites. Using FAIRshake, a variety of bioinformatics tools, datasets listed on dbGaP, APIs registered in SmartAPI, workflows in Dockstore, and other biomedical digital resources were manually and automatically assessed for FAIRness. In each case, the assessments revealed room for improvement, which prompted enhancements that significantly upgraded FAIRness scores of several digital resources.

Footnotes

  • https://www.fairshake.cloud

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources
Daniel J. B. Clarke, Lily Wang, Alex Jones, Megan L. Wojciechowicz, Denis Torre, Kathleen M. Jagodnik, Sherry L. Jenkins, Peter McQuilton, Zachary Flamholz, Moshe C. Silverstein, Brian M. Schilder, Kimberly Robasky, Claris Castillo, Ray Idaszak, Stanley C. Ahalt, Jason Williams, Stephan Schurer, Daniel J. Cooper, Ricardo de Miranda Azevedo, Juergen A. Klenk, Melissa A. Haendel, Jared Nedzel, Paul Avillach, Mary E. Shimoyama, Rayna M. Harris, Meredith Gamble, Rudy Poten, Amanda L. Charbonneau, Jennie Larkin, C. Titus Brown, Vivien R. Bonazzi, Michel J. Dumontier, Susanna-Assunta Sansone, Avi Ma’ayan
bioRxiv 657676; doi: https://doi.org/10.1101/657676
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FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources
Daniel J. B. Clarke, Lily Wang, Alex Jones, Megan L. Wojciechowicz, Denis Torre, Kathleen M. Jagodnik, Sherry L. Jenkins, Peter McQuilton, Zachary Flamholz, Moshe C. Silverstein, Brian M. Schilder, Kimberly Robasky, Claris Castillo, Ray Idaszak, Stanley C. Ahalt, Jason Williams, Stephan Schurer, Daniel J. Cooper, Ricardo de Miranda Azevedo, Juergen A. Klenk, Melissa A. Haendel, Jared Nedzel, Paul Avillach, Mary E. Shimoyama, Rayna M. Harris, Meredith Gamble, Rudy Poten, Amanda L. Charbonneau, Jennie Larkin, C. Titus Brown, Vivien R. Bonazzi, Michel J. Dumontier, Susanna-Assunta Sansone, Avi Ma’ayan
bioRxiv 657676; doi: https://doi.org/10.1101/657676

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