Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Public Data Archiving in Ecology and Evolution: How Well Are We Doing?

ABSTRACT: Policies that mandate public data archiving (PDA) successfully increase accessibility to data underlying scientific publications. However, is the data quality sufficient to allow reuse and reanalysis? We surveyed 100 datasets associated with nonmolecular studies in journals that commonly publish ecological and evolutionary research and have a strong PDA policy. Out of these datasets, 56% were incomplete, and 64% were archived in a way that partially or entirely prevented reuse. We suggest that cultural shifts facilitating clearer benefits to authors are necessary to achieve high-quality PDA and highlight key guidelines to help authors increase their data's reuse potential and compliance with journal data policies.

SUBMITTER: Roche DG

PROVIDER: S-EPMC4640582 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Public Data Archiving in Ecology and Evolution: How Well Are We Doing?

Roche Dominique G DG Kruuk Loeske E B LE Lanfear Robert R Binning Sandra A SA

PLoS biology 20151110 11

Policies that mandate public data archiving (PDA) successfully increase accessibility to data underlying scientific publications. However, is the data quality sufficient to allow reuse and reanalysis? We surveyed 100 datasets associated with nonmolecular studies in journals that commonly publish ecological and evolutionary research and have a strong PDA policy. Out of these datasets, 56% were incomplete, and 64% were archived in a way that partially or entirely prevented reuse. We suggest that c ...[more]

PMID: 26556502

Similar Datasets

Troubleshooting public data archiving: suggestions to increase participation.

Project description:An increasing number of publishers and funding agencies require public data archiving (PDA) in open-access databases. PDA has obvious group benefits for the scientific community, but many researchers are reluctant to share their data publicly because of real or perceived individual costs. Improving participation in PDA will require lowering costs and/or increasing benefits for primary data collectors. Small, simple changes can enhance existing measures to ensure that more scientific data are properly archived and made publicly available: (1) facilitate more flexible embargoes on archived data, (2) encourage communication between data generators and re-users, (3) disclose data re-use ethics, and (4) encourage increased recognition of publicly archived data.

| S-EPMC3904821 | biostudies-literature

Gauging the Purported Costs of Public Data Archiving for Long-Term Population Studies.

Project description:It was recently proposed that long-term population studies be exempted from the expectation that authors publicly archive the primary data underlying published articles. Such studies are valuable to many areas of ecological and evolutionary biological research, and multiple risks to their viability were anticipated as a result of public data archiving (PDA), ultimately all stemming from independent reuse of archived data. However, empirical assessment was missing, making it difficult to determine whether such fears are realistic. I addressed this by surveying data packages from long-term population studies archived in the Dryad Digital Repository. I found no evidence that PDA results in reuse of data by independent parties, suggesting the purported costs of PDA for long-term population studies have been overstated.

| S-EPMC4825988 | biostudies-literature

Beyond ADHD: How Well Are We Doing?

Project description:There has been increasing emphasis on the role of the pediatrician with respect to behavioral, learning, and mental health (MH) issues, and developmental behavioral rotations are now required in pediatric residency programs. We sought to examine whether this newer emphasis on MH is reflected in pediatricians' reports of their current practices.Data from 2 periodic surveys conducted in 2004 and 2013 by the American Academy of Pediatrics were examined to see whether there were differences in self-reported behaviors of usually inquiring/screening, treating/managing/comanaging, or referring patients for attention-deficit/hyperactivity disorder (ADHD), anxiety, depression, behavioral problems, or learning problems. We examined patterns for all practicing members and for those who practiced general pediatrics exclusively.There were few changes over the decade in the percentage who inquired or screened among all clinicians; among those exclusively practicing general pediatrics, the percentage who inquired or screened increased about 10% for ADHD and depression. ADHD remained the only condition for which the majority of respondents treated/managed/comanaged (57%). While there was some increase in the percentages who treated other conditions, the other conditions were usually treated by <30% of respondents. A similar pattern of results was observed in analyses adjusted for physician, practice, and patient characteristics.Despite the changing nature of pediatric practice and increased efforts to emphasize the importance of behavior, learning, and MH, the pediatric community appears to be making little progress toward providing for the long-term behavioral, learning, and MH needs of children and adolescents in its care.

| S-EPMC5560870 | biostudies-other

Evidence-based practice and patient-centered care: Doing both well.

Project description:Health care organizations increasingly strive to deliver care that is both evidence based and patient centered. Although often complementary, fundamental contradictions may exist between these goals, and the organizational culture and infrastructure necessary to be successful in one domain may inherently diminish performance in the other. We assessed the relationship between evidence-based practice (EBP) and patient-centered care (PCC) by seeking to identify specific behavioral and process mechanisms, along with organizational characteristics that distinguish medical centers that are able to provide inpatient care that is both evidence based and patient centered from those where performance is either mixed or low in both domains. We analyzed interview data from 142 employees at 12 Veterans Affairs Medical Centers selected based on EBP and PCC performance (high, low, or mixed) using a priori constructs consistent with organizational literature, as well as emergent themes. We confirmed that tensions may arise when attempting to deliver both EBP and PCC and found unique characteristics of organizations that do both well. High-performing sites exhibited organizational cultures of empowerment where both EBP and PCC expectations were emphasized; provided formal and informal institutional supports and structures with regard to PCC and EBP; and fostered multidisciplinary, multidirectional approaches to care and communication that facilitated delivery of both EBP and PCC. Organizations that excel in providing both EBP and PCC exhibit unique characteristics and processes. Recognizing that some characteristics such as culture are difficult to change, these findings nonetheless highlight areas that could be enhanced by medical centers striving to deliver care that is both evidence based and patient centered.

| S-EPMC8162222 | biostudies-literature

The archiving and dissemination of biological structure data.

Project description:The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day.

| S-EPMC5161703 | biostudies-literature

Public data from three US states provide new insights into well integrity.

Project description:Oil and gas wells with compromised integrity are a concern because they can potentially leak hydrocarbons or other fluids into groundwater and/or the atmosphere. Most states in the United States require some form of integrity testing, but few jurisdictions mandate widespread testing and open reporting on a scale informative for leakage risk assessment. In this study, we searched 33 US state oil and gas regulatory agency databases and identified records useful for evaluating well integrity in Colorado, New Mexico, and Pennsylvania. In total, we compiled 474,621 testing records from 105,031 wells across these states into a uniform dataset. We found that 14.1% of wells tested prior to 2018 in Pennsylvania exhibited sustained casing pressure (SCP) or casing vent flow (CVF)-two indicators of compromised well integrity. Data from different hydrocarbon-producing regions within Colorado and New Mexico revealed a wider range (0.3 to 26.5%) of SCP and/or CVF occurrence than previously reported, highlighting the need to better understand regional trends in well integrity. Directional wells were more likely to exhibit SCP and/or CVF than vertical wells in Colorado and Pennsylvania, and their installation corresponded with statewide increases in SCP and/or CVF occurrence in Colorado (2005 to 2009) and Pennsylvania (2007 to 2011). Testing the ground around wells for indicators of gas leakage is not a widespread practice in the states considered. However, 3.0% of Colorado wells tested and 0.1% of New Mexico wells tested exhibited a degree of SCP sufficient to potentially induce leakage outside the well.

| S-EPMC8040654 | biostudies-literature

PMD: A Resource for Archiving and Analyzing Protein Microarray data.

Project description:Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

| S-EPMC4728683 | biostudies-other

Lineage and ecology define liver tumor evolution in response to treatment

Project description:Single-cell transcriptome-based strategy to determine the evolutionary trajectories of longitudinal tumor biopsies from liver cancer patients by measuring cellular lineage and ecology. Our study provides a framework for monitoring tumor evolution in response to therapeutic intervention.

2023-12-22 | GSE229772 | GEO

Is the alcohol industry doing well by 'doing good'? Findings from a content analysis of the alcohol industry's actions to reduce harmful drinking.

Project description:ObjectivesThe aims of this study were to: (1) describe alcohol industry corporate social responsibility (CSR) actions conducted across six global geographic regions; (2) identify the benefits accruing to the industry ('doing well'); and (3) estimate the public health impact of the actions ('doing good').SettingActions from six global geographic regions.ParticipantsA web-based compendium of 3551 industry actions, representing the efforts of the alcohol industry to reduce harmful alcohol use, was issued in 2012. The compendium consisted of short descriptions of each action, plus other information about the sponsorship, content and evaluation of the activities. Public health professionals (n=19) rated a sample (n=1046) of the actions using a reliable content rating procedure.Outcome measuresWHO Global strategy target area, estimated population reach, risk of harm, advertising potential, policy impact potential and other aspects of the activity.ResultsThe industry actions were conducted disproportionately in regions with high-income countries (Europe and North America), with lower proportions in Latin America, Africa and Asia. Only 27% conformed to recommended WHO target areas for global action to reduce the harmful use of alcohol. The overwhelming majority (96.8%) of industry actions lacked scientific support (p<0.01) and 11.0% had the potential for doing harm. The benefits accruing to the industry ('doing well') included brand marketing and the use of CSR to manage risk and achieve strategic goals.ConclusionAlcohol industry CSR activities are unlikely to reduce harmful alcohol use but they do provide commercial strategic advantage while at the same time appearing to have a public health purpose.

| S-EPMC6224758 | biostudies-literature

Structural biology data archiving - where we are and what lies ahead.

Project description:For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists.

| S-EPMC6019198 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data