Journal article
A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics
Methods in ecology and evolution, v 15(6), pp 1129-1145
22 Apr 2024
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Image-based machine learning tools are an ascendant 'big data' research avenue. Citizen science platforms, like iNaturalist, and museum-led initiatives provide researchers with an abundance of data and knowledge to extract. These include extraction of metadata, species identification, and phenomic data. Ecological and evolutionary biologists are increasingly using complex, multi-step processes on data. These processes often include machine learning techniques, often built by others, that are difficult to reuse by other members in a collaboration. We present a conceptual workflow model for machine learning applications using image data to extract biological knowledge in the emerging field of imageomics. We derive an implementation of this conceptual workflow for a specific imageomics application that adheres to FAIR principles as a formal workflow definition that allows fully automated and reproducible execution, and consists of reusable workflow components. We outline technologies and best practices for creating an automated, reusable and modular workflow, and we show how they promote the reuse of machine learning models and their adaptation for new research questions. This conceptual workflow can be adapted: it can be semi-automated, contain different components than those presented here, or have parallel components for comparative studies. We encourage researchers-both computer scientists and biologists-to build upon this conceptual workflow that combines machine learning tools on image data to answer novel scientific questions in their respective fields.
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Details
- Title
- A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics
- Creators
- Meghan A. Balk - BattelleJohn Bradley - Duke UniversityM. Maruf - Virginia TechBahadir Altintas - Bolu Abant Izzet Baysal Univ, Dept Math & Sci Educ, Bolu, TurkiyeYasin Bakis - Tulane UniversityHenry L. Bart Jr - Tulane UniversityDavid Breen - Drexel UniversityChristopher R. Florian - National Ecological Observatory NetworkJane Greenberg - Drexel UniversityAnuj Karpatne - Virginia TechKevin Karnani - Drexel UniversityPaula Mabee - BattelleJoel Pepper - Drexel UniversityDom Jebbia - Carnegie Mellon UniversityThibault Tabarin - National Ecological Observatory NetworkXiaojun Wang - Tulane UniversityHilmar Lapp - Duke University
- Publication Details
- Methods in ecology and evolution, v 15(6), pp 1129-1145
- Publisher
- Wiley
- Number of pages
- 17
- Grant note
- National Science Foundation; National Science Foundation (NSF)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Information Science (Informatics); Computer Science (Computing)
- Web of Science ID
- WOS:001206982800001
- Scopus ID
- 2-s2.0-85191171727
- Other Identifier
- 991021874414104721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Ecology