ORCID Profile
0000-0003-4524-0916
Current Organisations
Stanford University
,
The University of Texas at Austin
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Publisher: Cold Spring Harbor Laboratory
Date: 15-09-2022
DOI: 10.1101/2022.09.12.507034
Abstract: Genetic ersity within species represents a fundamental yet underappreciated level of bio ersity. Because genetic ersity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic ersity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained s les from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 in iduals or BioS les from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the s les were taken was the most easily found information about s ling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.
Publisher: Wiley
Date: 10-03-2023
DOI: 10.1111/COBI.14061
Abstract: Genetic ersity within species represents a fundamental yet underappreciated level of bio ersity. Because genetic ersity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic ersity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly s les from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets ( n = 440 data sets with data on 45,105 in iduals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data‐sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.
Publisher: Proceedings of the National Academy of Sciences
Date: 17-08-2021
Abstract: Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic ersity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world’s largest genomic data repository, we found that most archived genomic datasets (87%) lacked the spatiotemporal metadata necessary for genetic bio ersity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 39% (51% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today’s genetic bio ersity and to plug the growing metadata gap.
No related grants have been discovered for Sofia Guajardo Beskid.