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The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices.
Robert Guralnick1, Tom Conlin2, John Deck3
1Department of Ecology and Evolutionary Biology and the CU Museum of Natural History, University of Colorado, Boulder, Colorado, United States of America.
Plos One
|December 4, 2014
Summary
Globally unique identifiers (GUIDs) for biocollections, like the Darwin Core Triplet, are intended to link data but often contain errors. These errors prevent effective data linking, hindering biodiversity informatics research.
Area of Science:
- Biodiversity Informatics
- Data Curation
- Genomic Data Management
Background:
- The biodiversity informatics community has sought globally unique identifiers (GUIDs) for biocollections for a decade.
- The Darwin Core Triplet (institution code, collection code, catalog number) has emerged as a de facto standard for biocollections data.
- Existing identifier schemes are evaluated for their current utility in linking digital biodiversity data.
Purpose of the Study:
- To assess the practical deployment and effectiveness of Darwin Core Triplets in linking biocollections and genetic sequence data.
- To identify semantic and syntactic errors in the implementation of Darwin Core Triplets in real-world datasets.
- To determine if current identifier schemes facilitate unambiguous data discovery and linkage across online platforms.
Main Methods:
- Collected Darwin Core Triplets from VertNet, GenBank, and the Barcode of Life Data System.
- Analyzed triplet structure for adherence to recommended specifications.
- Evaluated the unambiguousness of triplets in tracking specimen to genetic sequence records.
Main Results:
- Darwin Core Triplets frequently exhibit semantic and syntactic errors in practice.
- These errors compromise the ability to reliably link specimen and genetic sequence data.
- The current implementation of Darwin Core Triplets often fails to provide unambiguous data linkage.
Conclusions:
- Carefully curated Darwin Core Triplets are essential for effective data linking.
- Uncurated Darwin Core Triplets do not currently serve a useful role in relinking biodiversity data.
- Improvements in data curation and identifier scheme implementation are necessary to overcome current limitations.
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