R3ZW6Q last accessed: 2022-11-04

Other names: The SEEK datafiles

The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

Webpage:

https://fairdomhub.org/

Licence:

Name: other
URL: https://seek.sysmo-db.org/presentations/205?version=2

Publications: (6)

Publications
More detailed information about this field from each metasource.

The FAIR Guiding Principles for scientific data management and stewardship
PMID: 26978244
metasource: Fairsharing.org
version: FAIRsharing.org: FAIRDOMHub; FAIRDOMHub; DOI: https://doi.org/10.25504/FAIRsharing.nnvcr9; Last edited: Aug. 1, 2020, 7:24 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research
PMID: 27899646
metasource: Fairsharing.org
version: FAIRsharing.org: FAIRDOMHub; FAIRDOMHub; DOI: https://doi.org/10.25504/FAIRsharing.nnvcr9; Last edited: Aug. 1, 2020, 7:24 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

SEEK: a systems biology data and model management platform
PMID: 26160520
metasource: Fairsharing.org
version: FAIRsharing.org: FAIRDOMHub; FAIRDOMHub; DOI: https://doi.org/10.25504/FAIRsharing.nnvcr9; Last edited: Aug. 1, 2020, 7:24 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The SEEK: a platform for sharing data and models in systems biology
PMID: 21943917
metasource: Fairsharing.org
version: FAIRsharing.org: FAIRDOMHub; FAIRDOMHub; DOI: https://doi.org/10.25504/FAIRsharing.nnvcr9; Last edited: Aug. 1, 2020, 7:24 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

openBIS ELN-LIMS: an open-source database for academic laboratories
PMID: 26508761
metasource: Fairsharing.org
version: FAIRsharing.org: FAIRDOMHub; FAIRDOMHub; DOI: https://doi.org/10.25504/FAIRsharing.nnvcr9; Last edited: Aug. 1, 2020, 7:24 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

http://dx.doi.org/10.1093/nar/1941
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The FAIR Guiding Principles for scientific data management and stewardship PubMed citations: 1822.

1822 articles citing: The FAIR Guiding Principles for scientific data management and stewardship

African researchers do not think differently about Open Data. PMID:35910706
The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, & radiomics. PMID:35906241
The role of plant functional groups mediating climate impacts on carbon and biodiversity of alpine grasslands. PMID:35902592
Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study. PMID:35899108
Standard metadata for 3D microscopy. PMID:35896564
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. PMID:35889831
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. PMID:35888710
A Reproducible Deep-Learning-Based Computer-Aided Diagnosis Tool for Frontotemporal Dementia Using MONAI and Clinica Frameworks. PMID:35888037
Building International Capacity for Citizen Scientist Engagement in Mosquito Surveillance and Mitigation: The GLOBE Program's GLOBE Observer Mosquito Habitat Mapper. PMID:35886800
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Systematic Functional Annotation Workflow for Insects. PMID:35886762
DCSO: towards an ontology for machine-actionable data management plans. PMID:35883181
Community established best practice recommendations for tephra studies-from collection through analysis. PMID:35882866
An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. PMID:35882841
Integrating Multiscale Geospatial Environmental Data into Large Population Health Studies: Challenges and Opportunities. PMID:35878308
Getting Started with LINCS Datasets and Tools. PMID:35876555
Finding Gene Regulatory Networks in Psoriasis: Application of a Tree-Based Machine Learning Approach. PMID:35874668
Materials Discovery With Machine Learning and Knowledge Discovery. PMID:35873055
Expert tumor annotations and radiomics for locally advanced breast cancer in DCE-MRI for ACRIN 6657/I-SPY1. PMID:35871247
SARS-ANI: a global open access dataset of reported SARS-CoV-2 events in animals. PMID:35871228
In silico toxicology: From structure-activity relationships towards deep learning and adverse outcome pathways. PMID:35866138
Human populations in the world's mountains: Spatio-temporal patterns and potential controls. PMID:35857800
Data rescue: saving environmental data from extinction. PMID:35855607
A Technical Performance Study and Proposed Systematic and Comprehensive Evaluation of an ML-based CDS Solution for Pediatric Asthma. PMID:35854754
DaT3M: A Data Tracker for Multi-faceted Management of Multi-site Clinical Research Data Submission, Curation, Master Inventorying, and Sharing. PMID:35854726
Standardised data on initiatives-STARDIT: Beta version. PMID:35854364
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. PMID:35847383
Assessing author willingness to enter study information into structured data templates as part of the manuscript submission process: A pilot study. PMID:35846467
MoveApps: a serverless no-code analysis platform for animal tracking data. PMID:35843990
A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19. PMID:35841663
Performance assessment of ontology matching systems for FAIR data. PMID:35841031
Making marine image data FAIR. PMID:35840583
Leveraging Open Electronic Health Record Data and Environmental Exposures Data to Derive Insights Into Rare Pulmonary Disease. PMID:35837616
Reopening During the Unprecedented: The Association of Biomolecular Resource Facilities Community Coronavirus Disease 2019 Pandemic Response. Part 2: Efforts to Effectively Ramp Up Core Facility Activities. PMID:35837270
NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata. PMID:35836998
Using informatics to advance translational science: Environmental scan of adaptive capacity and preparedness of Clinical and Translational Science Award Program hubs. PMID:35836790
Toward a standard formal semantic representation of the model card report. PMID:35836130
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
A Decade of GigaScience: Milestones in Open Science. PMID:35818690
Digital technologies in primary care: Implications for patient care and future research. PMID:35815445
Development of the InTelligence And Machine LEarning (TAME) Toolkit for Introductory Data Science, Chemical-Biological Analyses, Predictive Modeling, and Database Mining for Environmental Health Research. PMID:35812168
Establishing a Common Nutritional Vocabulary - From Food Production to Diet. PMID:35811979
Country Compendium of the Global Register of Introduced and Invasive Species. PMID:35810161
A 26-year time series of mortality and growth of the Pacific oyster C. gigas recorded along French coasts. PMID:35810155
Multiplex Tissue Imaging: Spatial Revelations in the Tumor Microenvironment. PMID:35804939
Semantics of Dairy Fermented Foods: A Microbiologist's Perspective. PMID:35804753
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories. PMID:35804320
HistoML, a markup language for representation and exchange of histopathological features in pathology images. PMID:35803960
COVIDPUBGRAPH: A FAIR Knowledge Graph of COVID-19 Publications. PMID:35803947
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain. PMID:35784190
How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments? PMID:35783966
CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. PMID:35783295
BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications. PMID:35782729
Upcoming and urgent challenges in critical care research based on COVID-19 pandemic experience. PMID:35781076
Biomarkers of nanomaterials hazard from multi-layer data. PMID:35778420
Identification of risk factors for delirium, cognitive decline, and dementia after cardiac surgery (FINDERI-find delirium risk factors): a study protocol of a prospective observational study. PMID:35773648
ukbpheno v1.0: An R package for phenotyping health-related outcomes in the UK Biobank. PMID:35769930
Mission, Organization, and Future Direction of the Serological Sciences Network for COVID-19 (SeroNet) Epidemiologic Cohort Studies. PMID:35765315
Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research. PMID:35761389
Gene Expression Data for Investigating Glaucoma Treatment Options and Pharmacology in the Anterior Segment, State-of-the-Art and Future Directions. PMID:35757536
Open and reproducible science practices in psychoneuroendocrinology: Opportunities to foster scientific progress. PMID:35757179
Driving innovation for rare skin cancers: utilizing common tumours and machine learning to predict immune checkpoint inhibitor response. PMID:35755000
ORMEF: a Mediterranean database of exotic fish records. PMID:35752639
Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis. PMID:35751093
A multi-city urban atmospheric greenhouse gas measurement data synthesis. PMID:35750672
The Challenges of Implementing Comprehensive Clinical Data Warehouses in Hospitals. PMID:35742627
The Physical Activity and Nutritional INfluences in Ageing (PANINI) Toolkit: A Standardized Approach towards Physical Activity and Nutritional Assessment of Older Adults. PMID:35742068
Ten simple rules for good research practice. PMID:35737655
Breeding history for shattering trait in sesame: classic to genomic approach. PMID:35733066
Automated Rational Design of Metal-Organic Polyhedra. PMID:35731954
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. PMID:35729113
Capturing crop adaptation to abiotic stress using image-based technologies. PMID:35728624
Information extraction from free text for aiding transdiagnostic psychiatry: constructing NLP pipelines tailored to clinicians' needs. PMID:35715745
A focus groups study on data sharing and research data management. PMID:35715445
Better force fields start with better data: A data set of cation dipeptide interactions. PMID:35715420
Quality Criteria for Real-world Data in Pharmaceutical Research and Health Care Decision-making: Austrian Expert Consensus. PMID:35713954
Exposure Science in the 21st Century: Advancing the Science and Technology of Environmental Sensors through Cooperation and Collaboration across U.S. Federal Agencies. PMID:35711718
CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. PMID:35710652
Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications. PMID:35710456
Adamant: a JSON schema-based metadata editor for research data management workflows. PMID:35707001
Ethical Issues in Social Science Research Employing Big Data. PMID:35705883
A Decade of GigaScience: GigaDB and the Open Data Movement. PMID:35701374
A decade of GigaScience: the importance of community organizations for open and FAIR efforts in neuroinformatics. PMID:35701370
PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management. PMID:35699774
Reproducibility of prediction models in health services research. PMID:35690767
Microphysiological Systems Evaluation: Experience of TEX-VAL Tissue Chip Testing Consortium. PMID:35689632
Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study. PMID:35687541
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. PMID:35687095
Analysis of the landscape of human enhancer sequences in biological databases. PMID:35685360
Nanosafety: An Evolving Concept to Bring the Safest Possible Nanomaterials to Society and Environment. PMID:35683670
A Community-Led Approach as a Guide to Overcome Challenges for Therapy Research in Congenital Disorders of Glycosylation. PMID:35682409
National influenza surveillance systems in five European countries: a qualitative comparative framework based on WHO guidance. PMID:35681199
Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data. PMID:35677393
Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data. PMID:35677074
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. PMID:35671510
Innovations in Therapy Development for Rare Diseases Through the Rare Disease Cures Accelerator-Data and Analytics Platform. PMID:35668316
Alleviating Environmental Health Disparities Through Community Science and Data Integration. PMID:35664667
Plant Genotype to Phenotype Prediction Using Machine Learning. PMID:35664329
The evidence synthesis and meta-analysis in R conference (ESMARConf): levelling the playing field of conference accessibility and equitability. PMID:35659294
Differences Between the 2016 and 2022 Editions of the Enhanced Recovery After Bariatric Surgery (ERABS) Guidelines: Call to Action of FAIR Data and the Creation of a Global Consortium of Bariatric Care and Research. PMID:35654929
Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PMID:35653398
Predicting 30-Day Readmission Risk for Patients With Chronic Obstructive Pulmonary Disease Through a Federated Machine Learning Architecture on Findable, Accessible, Interoperable, and Reusable (FAIR) Data: Development and Validation Study. PMID:35653170
CoV2K model, a comprehensive representation of SARS-CoV-2 knowledge and data interplay. PMID:35650205
FAIR Digital Twins for Data-Intensive Research. PMID:35647536
Data standardization of plant-pollinator interactions. PMID:35639882
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar. PMID:35639788
Open science practices in general and internal medicine journals, an observational study. PMID:35639752
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. PMID:35639735
MDsrv: visual sharing and analysis of molecular dynamics simulations. PMID:35639717
Perceptions and behavior of clinical researchers and research support staff regarding data FAIRification. PMID:35624282
FAIR and Interactive Data Graphics from a Scientific Knowledge Graph. PMID:35624233
Chemical Mixtures in Household Environments: In Silico Predictions and In Vitro Testing of Potential Joint Action on PPARγ in Human Liver Cells. PMID:35622613
Running a dense air temperature measurement field campaign at the urban neighbourhood level: Protocol and lessons learned. PMID:35620757
The LOTUS initiative for open knowledge management in natural products research. PMID:35616633
A Simple Standard for Sharing Ontological Mappings (SSSOM). PMID:35616100
GEOexplorer: a webserver for gene expression analysis and visualisation. PMID:35609980
Lessons From the COVID-19 Pandemic to Improve the Health, Social Care, and Well-being of Minoritized Ethnic Groups With Chronic Conditions or Impairments: Protocol for a Mixed Methods Study. PMID:35609311
eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain. PMID:35602243
NLM's sponsorship of research in biomedical informatics (1985-2016). PMID:35600120
ADataViewer: exploring semantically harmonized Alzheimer's disease cohort datasets. PMID:35598021
Selection of data sets for FAIRification in drug discovery and development: Which, why, and how? PMID:35595012
Domain-Specific Common Data Elements for Rare Disease Registration: Conceptual Approach of a European Joint Initiative Toward Semantic Interoperability in Rare Disease Research. PMID:35594066
Engaged genomic science produces better and fairer outcomes: an engagement framework for engaging and involving participants, patients and publics in genomics research and healthcare implementation. PMID:35592835
Operationalizing "One Health" as "One Digital Health" Through a Global Framework That Emphasizes Fair and Equitable Sharing of Benefits From the Use of Artificial Intelligence and Related Digital Technologies. PMID:35592084
Slow improvement to the archiving quality of open datasets shared by researchers in ecology and evolution. PMID:35582791
Open Accessibility in Education Research: Enhancing the Credibility, Equity, Impact, and Efficiency of Research. PMID:35582472
Opportunities and challenges for the use of common controls in sequencing studies. PMID:35581355
The state of Medusozoa genomics: current evidence and future challenges. PMID:35579552
Recommendations for repositories and scientific gateways from a neuroscience perspective. PMID:35577825
Stakeholders' Requirements for Artificial Intelligence for Healthcare in Korea. PMID:35576982
Assessing and assuring interoperability of a genomics file format. PMID:35575355
Social Determinants of Health Factors for Gene-Environment COVID-19 Research: Challenges and Opportunities. PMID:35574521
BioTAGME: A Comprehensive Platform for Biological Knowledge Network Analysis. PMID:35571058
Cell-Free Circulating (Tumor) DNA before Surgery as a Prognostic Factor in Non-Metastatic Colorectal Cancer: A Systematic Review. PMID:35565347
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
The Quest for Orthologs orthology benchmark service in 2022. PMID:35552456
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY. PMID:35547570
Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review. PMID:35544100
Maximizing citizen scientists' contribution to automated species recognition. PMID:35538130
A Scalable Service to Improve Health Care Quality Through Precision Audit and Feedback: Proposal for a Randomized Controlled Trial. PMID:35536637
BioUML-towards a universal research platform. PMID:35536253
Caching and Reproducibility: Making Data Science Experiments Faster and FAIRer. PMID:35531060
Ten Points to Improve Reproducibility and Translation of Animal Research. PMID:35530730
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. PMID:35524571
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data. PMID:35516811
Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development. PMID:35516798
A call to embrace a culture of openness in cardiovascular research. PMID:35511501
Inclusion of social determinants of health improves sepsis readmission prediction models. PMID:35511233
Privacy-preserving local analysis of digital trace data: A proof-of-concept. PMID:35510190
A catalogue with semantic annotations makes multilabel datasets FAIR. PMID:35508507
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Expert range maps of global mammal distributions harmonised to three taxonomic authorities. PMID:35506011
Road to FAIR genomes: a gap analysis of NGS data generation and sharing in the Netherlands. PMID:35505836
Now Is the Time to Build a National Data Ecosystem for Materials Science and Chemistry Research Data. PMID:35505822
Replacement of animal testing by integrated approaches to testing and assessment (IATA): a call for in vivitrosi. PMID:35503372
Bringing IoT to the Lab: SiLA2 and Open-Source-Powered Gateway Module for Integrating Legacy Devices into the Digital Laboratory. PMID:35498267
Improving the design and implementation of sediment fingerprinting studies: summary and outcomes of the TRACING 2021 Scientific School. PMID:35495078
A collaborative semantic-based provenance management platform for reproducibility. PMID:35494870
Research artifacts and citations in computer systems papers. PMID:35494825
Quantitative MRI Harmonization to Maximize Clinical Impact: The RIN-Neuroimaging Network. PMID:35493836
Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. PMID:35487919
Design and methodological characteristics of studies using observational routinely collected health data for investigating the link between cancer and neurodegenerative diseases: protocol for a meta-research study. PMID:35487732
Harnessing Big Data to Advance Treatment and Understanding of Pulmonary Hypertension. PMID:35482840
Developing image analysis methods for digital pathology. PMID:35481680
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic. PMID:35468846
Availability of open data for spatial public health research. PMID:35465641
Transparency of COVID-19-Related Research in Dental Journals. PMID:35464778
Wanted: Standards for FAIR taxonomic concept representations and relationships. PMID:35462676
Artificial intelligence-enabled decision support in nephrology. PMID:35459850
New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork. PMID:35456420
A Pragmatic Ensemble Strategy for Missing Values Imputation in Health Records. PMID:35455196
AJILE12: Long-term naturalistic human intracranial neural recordings and pose. PMID:35449141
Sharing datasets of the COVID-19 epidemic in the Czech Republic. PMID:35446896
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. PMID:35446428
The Human Pangenome Project: a global resource to map genomic diversity. PMID:35444317
Electrophysiological dataset from macaque visual cortical area MST in response to a novel motion stimulus. PMID:35440786
PEGR: a flexible management platform for reproducible epigenomic and genomic research. PMID:35440038
Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework. PMID:35439943
Geohistorical dataset of ten plant species introduced into Occitania (France). PMID:35437401
The involvement of rare disease patient organisations in therapeutic innovation across rare paediatric neurological conditions: a narrative review. PMID:35436886
To err is machine: Considerations on the clinical impact of machine learning models in patients with unhealthy alcohol use. PMID:35429003
PolyMyalgia Rheumatica treatment with Methotrexate in Optimal Dose in an Early disease phase (PMR MODE): study protocol for a multicenter double-blind placebo controlled trial. PMID:35428320
A network of change: united action on research integrity. PMID:35421988
Biosecurity in an age of open science. PMID:35421093
FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. PMID:35418585
Transparency in quality of radiotherapy for breast cancer in the Netherlands: a national registration of radiotherapy-parameters. PMID:35413924
Do German university medical centres promote robust and transparent research? A cross-sectional study of institutional policies. PMID:35413846
Mapping the Proteoform Landscape of Five Human Tissues. PMID:35413190
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database. PMID:35411390
SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. PMID:35411389
What ethical approaches are used by scientists when sharing health data? An interview study. PMID:35410285
CEBA: A Data Lake for Data Sharing and Environmental Monitoring. PMID:35408347
A Search Engine Concept to Improve Food Traceability and Transparency: Preliminary Results. PMID:35407076
Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures. PMID:35404045
3D imaging for driving cancer discovery. PMID:35403737
Empowering Data Sharing and Analytics through the Open Data Commons for Traumatic Brain Injury Research. PMID:35403104
A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. PMID:35402883
Ontology-Based Classification and Analysis of Adverse Events Associated With the Usage of Chloroquine and Hydroxychloroquine. PMID:35401219
PHDD: Corpus of Physical Health Data Disclosure on Twitter During COVID-19 Pandemic. PMID:35400014
Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC). PMID:35397018
Critical Assessment of Metagenome Interpretation: the second round of challenges. PMID:35396482
Multi-decadal ocean temperature time-series and climatologies from Australia's long-term National Reference Stations. PMID:35393475
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor. PMID:35392801
Methods for Evaluating Environmental Health Impacts at Different Stages of the Policy Process in Cities. PMID:35389203
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Using Indigenous Standards to Implement the CARE Principles: Setting Expectations through Tribal Research Codes. PMID:35386282
Nextcast: A software suite to analyse and model toxicogenomics data. PMID:35386103
Testing the reproducibility and robustness of the cancer biology literature by robot. PMID:35382578
Making biological knowledge useful for humans and machines. PMID:35380659
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
JaponicusDB: rapid deployment of a model organism database for an emerging model species. PMID:35380656
ELIXIR biovalidator for semantic validation of life science metadata. PMID:35380605
In pursuit of data immortality. PMID:35379989
Making the collective knowledge of chemistry open and machine actionable. PMID:35379967
SLEAP: A deep learning system for multi-animal pose tracking. PMID:35379947
Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose. PMID:35377872
Bio-Ethics and One Health: A Case Study Approach to Building Reflexive Governance. PMID:35372246
Gene and drug landing page aggregator. PMID:35368424
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation. PMID:35363306
SINBAD, structural, experimental and clinical characterization of STAT inhibitors and their potential applications. PMID:35361787
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
Knowledge Graphs for Indication Expansion: An Explainable Target-Disease Prediction Method. PMID:35360842
Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): steps for incorporating this powerful surveillance tool. PMID:35355512
Accumulation-depuration data collection in support of toxicokinetic modelling. PMID:35354827
The TP53 Database: transition from the International Agency for Research on Cancer to the US National Cancer Institute. PMID:35352025
SynBio2Easy-a biologist-friendly tool for batch operations on SBOL designs with Excel inputs. PMID:35350192
Current State and Future Perspectives of Artificial Intelligence for Automated Coronary Angiography Imaging Analysis in Patients with Ischemic Heart Disease. PMID:35347566
Improving reusability along the data life cycle: a regulatory circuits case study. PMID:35346379
Using near-term forecasts and uncertainty partitioning to inform prediction of oligotrophic lake cyanobacterial density. PMID:35343013
Data availability in Chemical Science. PMID:35342546
Current state and call for action to accomplish findability, accessibility, interoperability, and reusability of low carbon energy data. PMID:35338179
Data Fusion in Agriculture: Resolving Ambiguities and Closing Data Gaps. PMID:35336456
The Role of Artificial Intelligence in Early Cancer Diagnosis. PMID:35326674
Ten simple rules for making a software tool workflow-ready. PMID:35324885
Good Practices in Sponge Natural Product Studies: Revising Vouchers with Isomalabaricane Triterpenes. PMID:35323489
Rare Disease Registries Are Key to Evidence-Based Personalized Medicine: Highlighting the European Experience. PMID:35317224
Community Consensus Guidelines to Support FAIR Data Standards in Clinical Research Studies in Primary Mitochondrial Disease. PMID:35317023
Bridge to the future: Important lessons from 20 years of ecosystem observations made by the OzFlux network. PMID:35315565
Sensor-based phenotyping of above-ground plant-pathogen interactions. PMID:35313920
Investigating Health Context Using a Spatial Data Analytical Tool: Development of a Geospatial Big Data Ecosystem. PMID:35311683
The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. PMID:35311178
Centralized project-specific metadata platforms: toolkit provides new perspectives on open data management within multi-institution and multidisciplinary research projects. PMID:35303952
Prescreening-Based Subset Selection for Improving Predictions of Earth System Models With Application to Regional Prediction of Red Tide. PMID:35300381
ADME prediction with KNIME: A retrospective contribution to the second "Solubility Challenge". PMID:35300359
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. PMID:35292119
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. PMID:35290070
The Biomedical Research Hub: a federated platform for patient research data. PMID:35289369
Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. PMID:35285497
Process epistemology in the COVID-19 era: rethinking the research process to avoid dangerous forms of reification. PMID:35284029
A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape. PMID:35283898
Safeguarding marine life: conservation of biodiversity and ecosystems. PMID:35280238
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. PMID:35277961
MITI minimum information guidelines for highly multiplexed tissue images. PMID:35277708
1024-channel electrophysiological recordings in macaque V1 and V4 during resting state. PMID:35277528
FAIRly big: A framework for computationally reproducible processing of large-scale data. PMID:35277501
Sim2Ls: FAIR simulation workflows and data. PMID:35271613
Improving the Quantification of Colorimetric Signals in Paper-Based Immunosensors with an Open-Source Reader. PMID:35271026
ImmuneData: an integrated data discovery system for immunology data repositories. PMID:35262674
From Platform to Knowledge Graph: Evolution of Laboratory Automation. PMID:35252980
Population health science as a unifying foundation for translational clinical and public health research. PMID:35252530
Trauma and Mental Health during the Global Pandemic: Abstract Book of the ESTSS 2021 Virtual ConferenceEditors: Annett Lotzin, A.A.A. Manik J. Djelantik, Marloes B. Eidhof, Anke de Haan, & Jana Kiralj. PMID:35251526
A framework for operationalising Aboriginal and Torres Strait Islander data sovereignty in Australia: Results of a systematic literature review of published studies. PMID:35243269
Making the Most of your Electrons: Challenges and Opportunities in Characterizing Hybrid Interfaces with STEM. PMID:35241968
PET-BIDS, an extension to the brain imaging data structure for positron emission tomography. PMID:35236846
Advancing discovery in hearing research via biologist-friendly access to multi-omic data. PMID:35235019
Medical-Blocks-A Platform for Exploration, Management, Analysis, and Sharing of Data in Biomedical Research: System Development and Integration Results. PMID:35232718
Analytic approaches to clinical validation of results from preclinical models of glioblastoma: A systematic review. PMID:35231064
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank. PMID:35230423
Disclosure of Pharmaceutical Industry Funding of Patient Organisations in Nordic Countries: Can Industry Self-Regulation Deliver on its Transparency Promise? PMID:35230175
A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae. PMID:35224233
Popular extreme sea level metrics can better communicate impacts. PMID:35221398
Linking Brain Structure, Activity, and Cognitive Function through Computation. PMID:35217544
Target 2035 - update on the quest for a probe for every protein. PMID:35211674
Towards a qAOP framework for predictive toxicology - Linking data to decisions. PMID:35211660
Identification of natural and anthropogenic signals in controlled source seismic experiments. PMID:35210484
Applying the FAIR4Health Solution to Identify Multimorbidity Patterns and Their Association with Mortality through a Frequent Pattern Growth Association Algorithm. PMID:35206230
Ten simple rules for initial data analysis. PMID:35202399
Integrating the OHIF Viewer into XNAT: Achievements, Challenges and Prospects for Quantitative Imaging Studies. PMID:35202205
Measuring Clinical, Biological, and Behavioral Variables to Elucidate Trajectories of Patient-Reported Outcomes: The PROFILES Registry. PMID:35201353
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. PMID:35199087
AI for science and global citizens. PMID:35199069
Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation. PMID:35197464
Findability of UK health datasets available for research: a mixed methods study. PMID:35193857
A large-scale study on research code quality and execution. PMID:35190569
Editorial: Transplant International Goes for GOLD! PMID:35185382
Developing, implementing and governing artificial intelligence in medicine: a step-by-step approach to prevent an artificial intelligence winter. PMID:35185012
"Escalibur"-A practical pipeline for the de novo analysis of nucleotide variation in nonmodel eukaryotes. PMID:35182034
The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases. PMID:35178824
The Scholarly Knowledge Ecosystem: Challenges and Opportunities for the Field of Information. PMID:35178498
Transparent, Open, and Reproducible Prevention Science. PMID:35175501
LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases. PMID:35169663
Design and Development of a Medical Image Databank for Assisting Studies in Radiomics. PMID:35166968
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. PMID:35166338
A FAIR and AI-ready Higgs boson decay dataset. PMID:35165298
Automation and Standardization-A Coupled Approach towards Reproducible Sample Preparation Protocols for Nanomaterial Analysis. PMID:35164246
Factors Affecting Citizen Trust and Public Engagement Relating to the Generation and Use of Real-World Evidence in Healthcare. PMID:35162696
Health Technology Assessment for In Silico Medicine: Social, Ethical and Legal Aspects. PMID:35162529
Streamlining statistical reproducibility: NHLBI ORCHID clinical trial results reproduction. PMID:35156003
Collections Education: The Extended Specimen and Data Acumen. PMID:35145351
Climate Stability Index maps, a global high resolution cartography of climate stability from Pliocene to 2100. PMID:35145118
Versioning biological cells for trustworthy cell engineering. PMID:35140226
STENCIL: A web templating engine for visualizing and sharing life science datasets. PMID:35139076
COVID restrictions impact wildlife monitoring in Australia. PMID:35136243
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. PMID:35134858
A data management infrastructure for the integration of imaging and omics data in life sciences. PMID:35130839
International federation of genomic medicine databases using GA4GH standards. PMID:35128509
An artificial intelligence framework integrating longitudinal electronic health records with real-world data enables continuous pan-cancer prognostication. PMID:35121948
Improving diagnosis and risk stratification across the ejection fraction spectrum: the Maastricht Cardiomyopathy registry. PMID:35118823
Dynamics of cumulative advantage and threats to equity in open science: a scoping review. PMID:35116143
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Authors' attitude toward adopting a new workflow to improve the computability of phenotype publications. PMID:35106535
MUON: multimodal omics analysis framework. PMID:35105358
A knowledge graph to interpret clinical proteomics data. PMID:35102292
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation. PMID:35101121
Fission stories: using PomBase to understand Schizosaccharomyces pombe biology. PMID:35100366
Trust in Scholarly Communications and Infrastructure: Indigenous Data Sovereignty. PMID:35098013
Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain. PMID:35095432
p3k14c, a synthetic global database of archaeological radiocarbon dates. PMID:35087092
Project-based learning course on metabolic network modelling in computational systems biology. PMID:35085230
Use of Clinical Data Interchange Standards Consortium (CDISC) Standards for Real-world Data: Expert Perspectives From a Qualitative Delphi Survey. PMID:35084343
Exploring the efficacy of psychological treatments for depression: a multiverse meta-analysis protocol. PMID:35078836
ExTaxsI: an exploration tool of biodiversity molecular data. PMID:35077538
The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2. PMID:35076068
Behind every great research project is great data management. PMID:35063017
Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data. PMID:35061216
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
Identifying the Steps Required to Effectively Implement Next-Generation Sequencing in Oncology at a National Level in Europe. PMID:35055387
Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection. PMID:35053148
ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath. PMID:35043937
Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life. PMID:35042810
Darwinian genomics and diversity in the tree of life. PMID:35042807
Standards recommendations for the Earth BioGenome Project. PMID:35042802
Minimal Information about MHC Multimers (MIAMM). PMID:35042788
Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning. PMID:35040699
[Precision medicine in pediatric neurology exemplified by the new treatment forms]. PMID:35037966
A first remotely-delivered guided brief intervention to reduce intrusive memories of psychological trauma for healthcare staff working during the ongoing COVID-19 pandemic: Study protocol for a randomised controlled trial. PMID:35036626
Categorizing metadata to help mobilize computable biomedical knowledge. PMID:35036552
Digital cultural heritage standards: from silo to semantic web. PMID:35035111
Regional synapse gain and loss accompany memory formation in larval zebrafish. PMID:35031564
Sleep and circadian informatics data harmonization: a workshop report from the Sleep Research Society and Sleep Research Network. PMID:35030631
A 3D total-body photography research network: the Australian experiment. PMID:35029695
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Sharing data, sharing methods, sharing science. PMID:35024349
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. PMID:35020801
SorghumBase: a web-based portal for sorghum genetic information and community advancement. PMID:35015132
Understanding the Nature of Metadata: Systematic Review. PMID:35014967
Labelling Assessment of Greek "Quality Label" Prepacked Cheeses as the Basis for a Branded Food Composition Database. PMID:35011104
Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes. PMID:35010832
Implementation of large-scale laboratory-based detection of COVID-19 in the Veterans Health Administration, March 2020 - February 2021. PMID:35007825
Advanced high-throughput plant phenotyping techniques for genome-wide association studies: A review. PMID:35003802
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach. PMID:34991705
Ten simple rules for researchers who want to develop web apps. PMID:34990469
MCX Cloud-a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing. PMID:34989198
Health data collection methods and procedures across EU member states: findings from the InfAct Joint Action on health information. PMID:34986889
HMDB 5.0: the Human Metabolome Database for 2022. PMID:34986597
Digital research data: from analysis of existing standards to a scientific foundation for a modular metadata schema in nanosafety. PMID:34983569
The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities. PMID:34980221
Orphan Medicine Incentives: How to Address the Unmet Needs of Rare Disease Patients by Optimizing the European Orphan Medicinal Product Landscape Guiding Principles and Policy Proposals by the European Expert Group for Orphan Drug Incentives (OD Expert Group). PMID:34975469
Facilitating cancer systems epidemiology research. PMID:34972102
Building FAIR Functionality: Annotating Events in Time Series Data Using Hierarchical Event Descriptors (HED). PMID:34970709
Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature. PMID:34966925
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. PMID:34956127
Common-sense approaches to sharing tabular data alongside publication. PMID:34950899
A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. PMID:34949993
Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families. PMID:34944388
[Linkage of claims data with data from epidemiological cancer registries: possibilities and limitations in the German federal states]. PMID:34940893
Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. PMID:34938269
The values of web archives. PMID:34934903
Advancing tools for human early lifecourse exposome research and translation (ATHLETE): Project overview. PMID:34934888
Ancient Metagenomic Studies: Considerations for the Wider Scientific Community. PMID:34931883
Improving research quality: the view from the UK Reproducibility Network institutional leads for research improvement. PMID:34930427
Data protection, data management, and data sharing: Stakeholder perspectives on the protection of personal health information in South Africa. PMID:34928950
Foster thy young: enhanced prediction of orphan genes in assembled genomes. PMID:34928390
Good Reporting Practice for Thermophysical and Thermochemical Property Measurements (IUPAC Technical Report). PMID:34924633
Development of RIKEN Plant Metabolome MetaDatabase. PMID:34918130
International data governance for neuroscience. PMID:34914921
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
A botanical demonstration of the potential of linking data using unique identifiers for people. PMID:34905557
Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials. PMID:34901127
Leveraging National Claims and Hospital Big Data: Cohort Study on a Statin-Drug Interaction Use Case. PMID:34898457
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. PMID:34890448
Surgical data science - from concepts toward clinical translation. PMID:34879287
Laboratory Information Management Systems for Electron Microscopy: Evaluation of the 4CeeD Data Curation Platform. PMID:34877182
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
IMGT® databases, related tools and web resources through three main axes of research and development. PMID:34875068
Challenges for assessing replicability in preclinical cancer biology. PMID:34874008
The COPE-Trial-Communicating prognosis to parents in the neonatal ICU: Optimistic vs. PEssimistic: study protocol for a randomized controlled crossover trial using two different scripted video vignettes to explore communication preferences of parents of preterm infants. PMID:34872601
Sequencing-based genome-wide association studies reporting standards. PMID:34870259
The ReIMAGINE Multimodal Warehouse: Using Artificial Intelligence for Accurate Risk Stratification of Prostate Cancer. PMID:34870187
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
New system for archiving integrative structures. PMID:34866606
Submission of structural biology data for review purposes. PMID:34866604
Submission of structural biology data for review purposes. PMID:34866597
Safe- and sustainable-by-design: The case of Smart Nanomaterials. A perspective based on a European workshop. PMID:34864125
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. PMID:34862503
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. PMID:34862501
ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. PMID:34862403
Health sciences librarians' engagement in open science: a scoping review. PMID:34858084
Trellis for efficient data and task management in the VA Million Veteran Program. PMID:34853358
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
The European Bioinformatics Institute (EMBL-EBI) in 2021. PMID:34850134
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
The Sequence Read Archive: a decade more of explosive growth. PMID:34850094
The iTHRIV Commons: a cross-institution information and health research data sharing architecture and web application. PMID:34850002
The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics. PMID:34849976
The Collaborative Metadata Repository (CoMetaR) Web App: Quantitative and Qualitative Usability Evaluation. PMID:34847059
ENIGMA + COINSTAC: Improving Findability, Accessibility, Interoperability, and Re-usability. PMID:34846691
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies. PMID:34845388
Transformational machine learning: Learning how to learn from many related scientific problems. PMID:34845013
Encoding Collective Knowledge, Instructing Data Reusers: The Collaborative Fixation of a Digital Scientific Data Set. PMID:34840429
Commentary on: Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON. PMID:34840333
Modified WCRF/AICR Score and All-Cause, Digestive System, Cardiovascular, Cancer and Other-Cause-Related Mortality: A Competing Risk Analysis of Two Cohort Studies Conducted in Southern Italy. PMID:34836259
Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use. PMID:34834625
The Quality Evaluation of Rare Disease Registries-An Assessment of the Essential Features of a Disease Registry. PMID:34831724
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. PMID:34824477
Digital twins for predictive oncology will be a paradigm shift for precision cancer care. PMID:34824458
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example. PMID:34823588
Grapevine and Wine Metabolomics-Based Guidelines for FAIR Data and Metadata Management. PMID:34822415
Comparison of (Cost-)Effectiveness of Magnetic Resonance Image-Guided High-Intensity-Focused Ultrasound With Standard (Minimally) Invasive Fibroid Treatments: Protocol for a Multicenter Randomized Controlled Trial (MYCHOICE). PMID:34821569
The Data Use Ontology to streamline responsible access to human biomedical datasets. PMID:34820659
An automated solution for measuring the progress toward FAIR research data. PMID:34820651
FAIRification of nanosafety data to improve applicability of (Q)SAR approaches: A case study on in vitro Comet assay genotoxicity data. PMID:34820591
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. PMID:34811556
Now is the time to assess the effects of open science practiceswith randomized control trials. PMID:34807632
Federated Analysis of Neuroimaging Data: A Review of the Field. PMID:34807353
Perspectives on automated composition of workflows in the life sciences. PMID:34804501
FAIR Data Reuse in Traumatic Brain Injury: Exploring Inflammation and Age as Moderators of Recovery in the TRACK-TBI Pilot. PMID:34803899
Enhancing reproducibility in developmental EEG research: BIDS, cluster-based permutation tests, and effect sizes. PMID:34801856
Increased adoption of best practices in ecological forecasting enables comparisons of forecastability. PMID:34800082
NP-MRD: the Natural Products Magnetic Resonance Database. PMID:34791429
ProteomicsDB: toward a FAIR open-source resource for life-science research. PMID:34791421
The European Genome-phenome Archive in 2021. PMID:34791407
Approaching Trust: Case Studies for Developing Global Research Infrastructures. PMID:34790884
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data. PMID:34785977
Open health data: Mapping the ecosystem. PMID:34777853
Validation of GWAS-Identified Variants for Anti-TNF Drug Response in Rheumatoid Arthritis: A Meta-Analysis of Two Large Cohorts. PMID:34777329
Functional Outcomes After Surgery for Total Colonic, Long-Segment, Versus Rectosigmoid Segment Hirschsprung Disease. PMID:34775429
From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. PMID:34769461
The data-index: An author-level metric that values impactful data and incentivizes data sharing. PMID:34765110
Indigenous Data Governance: Strategies from United States Native Nations. PMID:34764990
Seven steps toward more transparency in statistical practice. PMID:34764461
Increasing best practice data sharing at PLOS Pathogens. PMID:34762715
The experience of teaching introductory programming skills to bioscientists in Brazil. PMID:34762646
Open science, data sharing and solidarity: who benefits? PMID:34762203
Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research. PMID:34761219
Browser-based Data Annotation, Active Learning, and Real-Time Distribution of Artificial Intelligence Models: From Tumor Tissue Microarrays to COVID-19 Radiology. PMID:34760334
The Human Disease Ontology 2022 update. PMID:34755882
Data-sharing practices in publications funded by the Canadian Institutes of Health Research: a descriptive analysis. PMID:34753787
CEBS update: curated toxicology database with enhanced tools for data integration. PMID:34751388
Bridging the Gap Between Remote Sensing and Plant Phenotyping-Challenges and Opportunities for the Next Generation of Sustainable Agriculture. PMID:34751225
Consensus-based guidance for conducting and reporting multi-analyst studies. PMID:34751133
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. PMID:34750536
The Swiss data cube, analysis ready data archive using earth observations of Switzerland. PMID:34750391
mapMECFS: a portal to enhance data discovery across biological disciplines and collaborative sites. PMID:34749736
RESCRIPt: Reproducible sequence taxonomy reference database management. PMID:34748542
EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments. PMID:34746357
Chemometric analysis in Raman spectroscopy from experimental design to machine learning-based modeling. PMID:34741152
RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. PMID:34739839
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. PMID:34739369
Unraveling biogeochemical complexity through better integration of experiments and modeling. PMID:34739021
Design considerations for workflow management systems use in production genomics research and the clinic. PMID:34737383
Low statistical power and overestimated anthropogenic impacts, exacerbated by publication bias, dominate field studies in global change biology. PMID:34736291
Open Data Practices among Users of Primary Biodiversity Data. PMID:34733117
Patients' priorities and expectations on an EU registry for rare bone and mineral conditions. PMID:34732217
The importance of adherence to international standards for depositing open data in public repositories. PMID:34727971
Chemputation and the Standardization of Chemical Informatics. PMID:34723260
The European Variation Archive: a FAIR resource of genomic variation for all species. PMID:34718739
The Natural Products Atlas 2.0: a database of microbially-derived natural products. PMID:34718710
Tutorial: methods for three-dimensional visualization of archival tissue material. PMID:34716449
On the Annotation of Health Care Pathways to Allow the Application of Care-Plans That Generate Data for Multiple Purposes. PMID:34713160
Personalized Health Care and Public Health in the Digital Age. PMID:34713084
The normalised Sentinel-1 Global Backscatter Model, mapping Earth's land surface with C-band microwaves. PMID:34711850
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
Digital Endpoints: Definition, Benefits, and Current Barriers in Accelerating Development and Adoption. PMID:34703976
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. PMID:34697637
Progress toward a comprehensive teaching approach to the FAIR data principles. PMID:34693369
The Deep-Time Digital Earth program: data-driven discovery in geosciences. PMID:34691735
MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. PMID:34681649
Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. PMID:34681121
Sperm Repository for a Breeding Program of the Eastern Oyster Crassostrea virginica: Sample Collection, Processing, Cryopreservation, and Data Management Plan. PMID:34679857
MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools. PMID:34677393
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
Opportunities and Challenges for Machine Learning in Rare Diseases. PMID:34676229
Identifying Actionability as a Key Factor for the Adoption of 'Intelligent' Systems for Drug Safety: Lessons Learned from a User-Centred Design Approach. PMID:34674190
Ethics of DNA research on human remains: five globally applicable guidelines. PMID:34671160
A knowledge graph representation of baseline characteristics for the Dutch proton therapy research registry. PMID:34667884
Open and strong-scaling tools for atom-probe crystallography: high-throughput methods for indexing crystal structure and orientation. PMID:34667452
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
Federated Networks for Distributed Analysis of Health Data. PMID:34660512
Machine Learning Techniques for Personalised Medicine Approaches in Immune-Mediated Chronic Inflammatory Diseases: Applications and Challenges. PMID:34658859
The OpenNeuro resource for sharing of neuroscience data. PMID:34658334
Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences. PMID:34655133
The changing face of floodplains in the Mississippi River Basin detected by a 60-year land use change dataset. PMID:34654838
The World Spider Trait database: a centralized global open repository for curated data on spider traits. PMID:34651181
Open Data Resources on COVID-19 in Six European Countries: Issues and Opportunities. PMID:34639796
Indigenous and Tribal Peoples Data Governance in Health Research: A Systematic Review. PMID:34639617
Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. PMID:34637742
A field guide to cultivating computational biology. PMID:34618807
COVID-19 knowledge graph from semantic integration of biomedical literature and databases. PMID:34613368
Towards the Representation of Network Assets in Health Care Environments Using Ontologies. PMID:34610645
Orchestrating and sharing large multimodal data for transparent and reproducible research. PMID:34608132
Artificial intelligence for microbial biotechnology: beyond the hype. PMID:34606686
Data Ecosystems for Scientific Experiments: Managing Combustion Experiments and Simulation Analyses in Chemical Engineering. PMID:34604739
A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling. PMID:34601704
A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. PMID:34600518
Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank. PMID:34594153
AusTraits, a curated plant trait database for the Australian flora. PMID:34593819
MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. PMID:34592929
CellExplorer: A framework for visualizing and characterizing single neurons. PMID:34592168
A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma. PMID:34592158
Short review: The impact of sex on neuroimmune and cognitive outcomes after traumatic brain injury. PMID:34589813
The "Narratives" fMRI dataset for evaluating models of naturalistic language comprehension. PMID:34584100
Standardizing data reporting in the research community to enhance the utility of open data for SARS-CoV-2 wastewater surveillance. PMID:34567579
The role of metadata in reproducible computational research. PMID:34553169
Gene-by-environment modulation of lifespan and weight gain in the murine BXD family. PMID:34552269
A scalable workflow to characterize the human exposome. PMID:34552080
Individual notions of fair data sharing from the perspectives of Swiss stakeholders. PMID:34551742
Subcellular proteomics. PMID:34549195
A Guideline for Reporting Mediation Analyses of Randomized Trials and Observational Studies: The AGReMA Statement. PMID:34546296
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. PMID:34544477
Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes. PMID:34543288
Development of Privacy Features on Anecdata.org, a Free Citizen Science Platform for Collecting Datasets for Climate Change and Related Projects. PMID:34541525
Opportunities for the use of health information technology to support research. PMID:34541462
Estimating the reproducibility of social learning research published between 1955 and 2018. PMID:34540248
Data Management and Modeling in Plant Biology. PMID:34539712
Individual Patient-Level Data Sharing for Continuous Learning: A Strategy for Trial Data Sharing. PMID:34532668
(Hyper)active Data Curation: A Video Case Study from Behavioral Science. PMID:34532153
Artificial Intelligence Applied to Battery Research: Hype or Reality? PMID:34529918
Assessing direct healthcare costs when restricted to self-reported data: a scoping review. PMID:34529165
ISA API: An open platform for interoperable life science experimental metadata. PMID:34528664
Towards Machine-Readable (Meta) Data and the FAIR Value for Artificial Intelligence Exploration of COVID-19 and Cancer Research Data. PMID:34527943
Creation of a universal experimental protocol for the investigation of transfer and persistence of trace evidence: Part 1 - From design to implementation for particulate evidence. PMID:34527896
Creation of a universal experimental protocol for the investigation of transfer and persistence of trace evidence: Part 2 - Implementation and preliminary data. PMID:34527895
Four key challenges in the open-data revolution. PMID:34525215
A comparative study between state-of-the-art MRI deidentification and AnonyMI, a new method combining re-identification risk reduction and geometrical preservation. PMID:34520074
Design of a FAIR digital data health infrastructure in Africa for COVID-19 reporting and research. PMID:34514430
Assessment of the adequacy of mobile applications for disaster reduction. PMID:34512121
Desiderata for the development of next-generation electronic health record phenotype libraries. PMID:34508578
Data Management Plans in the genomics research revolution of Africa: Challenges and recommendations. PMID:34506960
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Community-Driven Harmonized Language. PMID:34501574
Nanoparticle Additivation Effects on Laser Powder Bed Fusion of Metals and Polymers-A Theoretical Concept for an Inter-Laboratory Study Design All Along the Process Chain, Including Research Data Management. PMID:34500981
A roadmap for the Human Developmental Cell Atlas. PMID:34497388
ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves. PMID:34492004
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
EANM recommendations based on systematic analysis of small animal radionuclide imaging in inflammatory musculoskeletal diseases. PMID:34487263
3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories. PMID:34485386
Farmers' Rights and Digital Sequence Information: Crisis or Opportunity to Reclaim Stewardship Over Agrobiodiversity? PMID:34484258
The de novo FAIRification process of a registry for vascular anomalies. PMID:34481493
Closing the knowledge-action gap in conservation with open science. PMID:34476839
Advances in flux balance analysis by integrating machine learning and mechanism-based models. PMID:34471504
Investigator initiated trials versus industry sponsored trials - translation of randomized controlled trials into clinical practice (IMPACT). PMID:34465296
RNA Sequencing Analyses for Deciphering Potato Molecular Responses. PMID:34448155
Genetic Resources and Vulnerabilities of Major Cucurbit Crops. PMID:34440396
Challenges in the Use of Artificial Intelligence for Prostate Cancer Diagnosis from Multiparametric Imaging Data. PMID:34439099
Atmospheric Carbon and Transport - America (ACT-America) Data Sets: Description, Management, and Delivery. PMID:34435081
The Dutch National TissueArchive Portal enables efficient, consistent, and transparent procurement of diagnostic tissue samples for scientific use. PMID:34432159
Fair enough: A sideways look. PMID:34430934
Inter-laboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysis. PMID:34429429
A unified platform to manage, share, and archive morphological and functional data in insect neuroscience. PMID:34427185
Sysrev: A FAIR Platform for Data Curation and Systematic Evidence Review. PMID:34423285
Solutions in microbiome engineering: prioritizing barriers to organism establishment. PMID:34420034
A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer. PMID:34412551
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Opportunities and challenges of macrogenetic studies. PMID:34408318
Status, use and impact of sharing individual participant data from clinical trials: a scoping review. PMID:34408052
Poor data stewardship will hinder global genetic diversity surveillance. PMID:34404731
Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers. PMID:34400655
Colonization Ability and Impact on Human Gut Microbiota of Foodborne Microbes From Traditional or Probiotic-Added Fermented Foods: A Systematic Review. PMID:34395494
Kakila database: Towards a FAIR community approved database of cetacean presence in the waters of the Guadeloupe Archipelago, based on citizen science. PMID:34393586
Saving collections: taxonomic revision of the herpetological collection of the Instituto de Investigação Científica Tropical, Lisbon (Portugal) with a protocol to rescue abandoned collections. PMID:34393554
A strategy for building and using a human reference pangenome. PMID:34386196
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets. PMID:34384353
An end-to-end automated platform process for high-throughput engineering of next-generation multi-specific antibody therapeutics. PMID:34382900
Systematic review of the status of veterinary epidemiological research in two species regarding the FAIR guiding principles. PMID:34380468
EBiSC best practice: How to ensure optimal generation, qualification, and distribution of iPSC lines. PMID:34380020
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. PMID:34367618
Data Shepherding in Nanotechnology. The Exposure Field Campaign Template. PMID:34361203
Linking norms, ratings, and relations of words and concepts across multiple language varieties. PMID:34357536
Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database. PMID:34354820
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Machine learning for modeling the progression of Alzheimer disease dementia using clinical data: a systematic literature review. PMID:34350389
Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons for Spinal Cord Injury (odc-sci.org). PMID:34347243
Privacy considerations for sharing genomics data. PMID:34345236
Remove obstacles to sharing health data with researchers outside of the European Union. PMID:34345050
ppx: Programmatic Access to Proteomics Data Repositories. PMID:34342226
How Patient Organizations Can Drive FAIR Data Efforts to Facilitate Research and Health Care: A Report of the Virtual Second International Meeting on Duchenne Data Sharing, March 3, 2021. PMID:34334415
Developing a tool to monitor knowledge translation in the health system: results from an international Delphi study. PMID:34333628
INFRAFRONTIER quality principles in systemic phenotyping. PMID:34328547
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. PMID:34327299
AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. PMID:34326396
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
DOME: recommendations for supervised machine learning validation in biology. PMID:34316068
Introduction to the National Cancer Imaging Translational Accelerator (NCITA): a UK-wide infrastructure for multicentre clinical translation of cancer imaging biomarkers. PMID:34316019
Metadata Made Easy: Develop and Use Domain-Specific Metadata Schemes by following the dmdScheme approach. PMID:34306613
Opportunities and limits of controlled-environment plant phenotyping for climate response traits. PMID:34302493
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
[Making COVID-19 research data more accessible-building a nationwide information infrastructure]. PMID:34297162
Fostering reproducibility, reusability, and technology transfer in health informatics. PMID:34296072
Ensuring Prevention Science Research is Synthesis-Ready for Immediate and Lasting Scientific Impact. PMID:34291384
A Conceptual Framework of Data Readiness: The Contextual Intersection of Quality, Availability, Interoperability, and Provenance. PMID:34289504
Exploring polypharmacy with artificial intelligence: data analysis protocol. PMID:34284765
Forming Consensus To Advance Urobiome Research. PMID:34282932
Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda. PMID:34282528
Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node. PMID:34280231
The PERSonalized Glucose Optimization Through Nutritional Intervention (PERSON) Study: Rationale, Design and Preliminary Screening Results. PMID:34277687
Editorial: Curriculum Applications in Microbiology: Bioinformatics in the Classroom. PMID:34276638
Mining Public Metagenomes for Environmental Surveillance of Parasites: A Proof of Principle. PMID:34276576
Knowledge and Attitudes Among Life Scientists Toward Reproducibility Within Journal Articles: A Research Survey. PMID:34268467
Microplastics accumulate fungal pathogens in terrestrial ecosystems. PMID:34267241
FAIRSCAPE: a Framework for FAIR and Reproducible Biomedical Analytics. PMID:34264488
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. PMID:34251419
Recommendations for the FAIRification of genomic track metadata. PMID:34249331
The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. PMID:34248680
A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles. PMID:34242248
Curated Data In - Trustworthy In Silico Models Out: The Impact of Data Quality on the Reliability of Artificial Intelligence Models as Alternatives to Animal Testing. PMID:34233495
Ethical Artificial Intelligence in Chemical Research and Development: A Dual Advantage for Sustainability. PMID:34231042
Rising antimicrobial resistance: an evolving epidemic in a pandemic. PMID:34230918
Data Sharing in Southeast Asia During the First Wave of the COVID-19 Pandemic. PMID:34222173
The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes. PMID:34220930
The Sedimentary Geochemistry and Paleoenvironments Project. PMID:34219351
A critical overview of computational approaches employed for COVID-19 drug discovery. PMID:34212944
Sharing Biomedical Data: Strengthening AI Development in Healthcare. PMID:34208830
Predictive Markers of Immunogenicity and Efficacy for Human Vaccines. PMID:34205932
The European Union Is Still Unable to Find Nemo and Dory-Time for a Reliable Traceability System for the Marine Aquarium Trade. PMID:34205203
The Research Centers in Minority Institutions (RCMI) Consortium: A Blueprint for Inclusive Excellence. PMID:34202383
Data Shepherding in Nanotechnology. The Initiation. PMID:34201308
UAS-Based Plant Phenotyping for Research and Breeding Applications. PMID:34195621
Open science datasets from PREVENT-AD, a longitudinal cohort of pre-symptomatic Alzheimer's disease. PMID:34192666
Artificial intelligence and hybrid imaging: the best match for personalized medicine in oncology. PMID:34191197
NCI Imaging Data Commons. PMID:34185678
Universal Spectrum Identifier for mass spectra. PMID:34183830
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations. PMID:34181736
ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale. PMID:34175941
A meta-review of transparency and reproducibility-related reporting practices in published meta-analyses on clinical psychological interventions (2000-2020). PMID:34173943
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. PMID:34172972
Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms. PMID:34168517
Tribochemistry, Mechanical Alloying, Mechanochemistry: What is in a Name? PMID:34164379
A data-driven perspective on the colours of metal-organic frameworks. PMID:34163632
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
MRI biomarkers in neuro-oncology. PMID:34149051
Protecting Privacy and Transforming COVID-19 Case Surveillance Datasets for Public Use. PMID:34139910
Are Artificial Intelligence Challenges Becoming Radiology's New "Bee's Knees"? PMID:34138989
Bioimage analysis workflows: community resources to navigate through a complex ecosystem. PMID:34136134
The DisGeNET cytoscape app: Exploring and visualizing disease genomics data. PMID:34136095
Ten simple rules for making a vocabulary FAIR. PMID:34133421
libOmexMeta: Enabling semantic annotation of models to support FAIR principles. PMID:34132740
Context aware benchmarking and tuning of a TByte-scale air quality database and web service. PMID:34122663
Cric searchable image database as a public platform for conventional pap smear cytology data. PMID:34112812
Data challenges for future plant gene editing: expert opinion. PMID:34106390
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. PMID:34096994
The Centre for Data and Knowledge Integration for Health (CIDACS): Linking Health and Social Data in Brazil. PMID:34095542
The ARRIVE guidelines 2.0: updated guidelines for reporting animal research. PMID:34095516
RiboDoc: A Docker-based package for ribosome profiling analysis. PMID:34093996
Social media attention and citations of published outputs from re-use of clinical trial data: a matched comparison with articles published in the same journals. PMID:34092224
Translational precision medicine: an industry perspective. PMID:34090480
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing. PMID:34088715
Methodology over metrics: current scientific standards are a disservice to patients and society. PMID:34077797
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments. PMID:34076589
Developing a topic-based repository of clinical trial individual patient data: experiences and lessons learned from a pilot project. PMID:34059123
Up-to-the-Minute Privacy Policies via Gossips in Participatory Epidemiological Studies. PMID:34056584
Open Science in Kenya: Where Are We? PMID:34056516
Systematic reviews and meta-analyses for the WHO/ILO Joint Estimates of the Work-related Burden of Disease and Injury. PMID:34051644
Clinical Quality Considerations when Using Next-Generation Sequencing (NGS) in Clinical Drug Development. PMID:34046876
A large-scale comparative study on peptide encodings for biomedical classification. PMID:34046590
Recommendations for a Dutch Sustainable Biobanking Environment. PMID:34042498
A one health glossary to support communication and information exchange between the human health, animal health and food safety sectors. PMID:34041347
The Finnish Biodiversity Information Facility as a best-practice model for biodiversity data infrastructures. PMID:34035315
Systemic Fairness for Sharing Health Data: Perspectives From Swiss Stakeholders. PMID:34026719
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. PMID:34021280
Data management and sharing: Practices and perceptions of psychology researchers. PMID:34019600
Data Sharing in Education Science. PMID:34012996
The data-driven future of high-energy-density physics. PMID:34012079
A Topical Collection on ICT for Health Science Research - EFMI Special Topic Conference. PMID:34002277
Shortcomings of SARS-CoV-2 genomic metadata. PMID:34001211
Preliminary Minimum Reporting Requirements for In-Vivo Neural Interface Research: I. Implantable Neural Interfaces. PMID:33997788
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
A descriptive analysis of the data availability statements accompanying medRxiv preprints and a comparison with their published counterparts. PMID:33983972
Ten simple rules to cultivate transdisciplinary collaboration in data science. PMID:33983959
Strengthening data collection for neglected tropical diseases: What data are needed for models to better inform tailored intervention programmes? PMID:33983937
Serial EXTEM, FIBTEM, and tPA Rotational Thromboelastometry Observations in the Maastricht Intensive Care COVID Cohort-Persistence of Hypercoagulability and Hypofibrinolysis Despite Anticoagulation. PMID:33981736
Artificial intelligence and machine learning for medical imaging: A technology review. PMID:33979715
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols. PMID:33978761
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
Funders' responsibility to ensure value in research: a self-audit by the Health Research Board Ireland. PMID:33977226
Understanding experiments and research practices for reproducibility: an exploratory study. PMID:33976964
Evidence-Based Health Informatics as the Foundation for the COVID-19 Response: A Joint Call for Action. PMID:33975375
Scan Once, Analyse Many: Using Large Open-Access Neuroimaging Datasets to Understand the Brain. PMID:33974213
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension. PMID:33960637
Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples. PMID:33960385
Knowledge-Based Biomedical Data Science. PMID:33954284
Validation of the Crystallography Open Database using the Crystallographic Information Framework. PMID:33953659
The Protein Data Bank Archive. PMID:33950382
The digital biomarker discovery pipeline: An open-source software platform for the development of digital biomarkers using mHealth and wearables data. PMID:33948242
Eight practices for data management to enable team data science. PMID:33948240
A resource to explore the discovery of rare diseases and their causative genes. PMID:33947870
How to capture developmental brain dynamics: gaps and solutions. PMID:33941785
Identifying the challenges in implementing open science [version 1; peer review: 2 approved]. PMID:33937623
VANTAGE6: an open source priVAcy preserviNg federaTed leArninG infrastructurE for Secure Insight eXchange. PMID:33936462
A semantic database for integrated management of image and dosimetric data in low radiation dose research in medical imaging. PMID:33936422
Opportunities and Challenges in Democratizing Immunology Datasets. PMID:33936065
Management and Quality Control of Large Neuroimaging Datasets: Developments From the Barcelonaβeta Brain Research Center. PMID:33935631
The sharing of research data facing the COVID-19 pandemic. PMID:33935332
The Treatabolome, an emerging concept. PMID:33935101
How to publish a new fungal species, or name, version 3.0. PMID:33934723
Artificial intelligence for clinical oncology. PMID:33930310
The Need for a Human Pangenome Reference Sequence. PMID:33929893
How Might AI and Chest Imaging Help Unravel COVID-19's Mysteries? PMID:33928254
Deep Learning in Virtual Screening: Recent Applications and Developments. PMID:33922714
Antibiotic Resistance in Wastewater Treatment Plants and Transmission Risks for Employees and Residents: The Concept of the AWARE Study. PMID:33919179
Pulmonary Hypertension in Association with Lung Disease: Quantitative CT and Artificial Intelligence to the Rescue? State-of-the-Art Review. PMID:33918838
Comparison and Fusion of Machine Learning Algorithms for Prospective Validation of PET/CT Radiomic Features Prognostic Value in Stage II-III Non-Small Cell Lung Cancer. PMID:33918681
A Statistical Analysis of Death Rates in Italy for the Years 2015-2020 and a Comparison with the Casualties Reported from the COVID-19 Pandemic. PMID:33915702
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
Open Science in regulatory environmental risk assessment. PMID:33913617
NexusLIMS: A Laboratory Information Management System for Shared-Use Electron Microscopy Facilities. PMID:33908340
Fungal taxonomy and sequence-based nomenclature. PMID:33903746
Gene and transgenics nomenclature for the laboratory axolotl-Ambystoma mexicanum. PMID:33896069
Integration of evidence across human and model organism studies: A meeting report. PMID:33893716
NHLBI-CMREF Workshop Report on Pulmonary Vascular Disease Classification: JACC State-of-the-Art Review. PMID:33888254
The EU Child Cohort Network's core data: establishing a set of findable, accessible, interoperable and re-usable (FAIR) variables. PMID:33884544
Primary Care Informatics Response to Covid-19 Pandemic: Adaptation, Progress, and Lessons from Four Countries with High ICT Development. PMID:33882603
Investigating the Scientific 'Infodemic' Phenomenon Related to the COVID-19 Pandemic. PMID:33882597
Digital Health during COVID-19: Informatics Dialogue with the World Health Organization. PMID:33882596
Flame: an open source framework for model development, hosting, and usage in production environments. PMID:33875019
Where Do Early Career Researchers Stand on Open Science Practices? A Survey Within the Max Planck Society. PMID:33870051
High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery. PMID:33868223
Operationalizing the CARE and FAIR Principles for Indigenous data futures. PMID:33863927
Improving the completeness of public metadata accompanying omics studies. PMID:33858487
Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. PMID:33852055
Quantum computing's reproducibility crisis: Majorana fermions. PMID:33846620
Treatable inherited metabolic disorders causing intellectual disability: 2021 review and digital app. PMID:33845862
Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. PMID:33841364
Building a biofoundry. PMID:33817343
Towards FAIR protocols and workflows: the OpenPREDICT use case. PMID:33816932
Towards computational reproducibility: researcher perspectives on the use and sharing of software. PMID:33816816
Strengthening the global network for sharing of marine biological collections: recommendations for a new agreement for biodiversity beyond national jurisdiction. PMID:33814897
Facilitating harmonized data quality assessments. A data quality framework for observational health research data collections with software implementations in R. PMID:33810787
Polymorphisms within Autophagy-Related Genes Influence the Risk of Developing Colorectal Cancer: A Meta-Analysis of Four Large Cohorts. PMID:33809172
The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. PMID:33808985
Reliable Surface Analysis Data of Nanomaterials in Support of Risk Assessment Based on Minimum Information Requirements. PMID:33807515
gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites. PMID:33807334
Untargeted In Silico Compound Classification-A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes. PMID:33806786
Metabolomics and Lipidomics: Expanding the Molecular Landscape of Exercise Biology. PMID:33799958
Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. PMID:33794662
The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: analysis of high-throughput epigenetic and gene expression studies. PMID:33791744
One Health Surveillance Codex: promoting the adoption of One Health solutions within and across European countries. PMID:33786360
Bioinformatics tools developed to support BioCompute Objects. PMID:33784373
PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. PMID:33781993
Evaluation of a shared decision-making strategy with online decision aids in surgical and orthopaedic practice: study protocol for the E-valuAID, a multicentre study with a stepped-wedge design. PMID:33781253
Data Sharing Goals for Nonprofit Funders of Clinical Trials. PMID:33779573
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. PMID:33779550
Centralizing environmental datasets to support (inter)national chronic disease research: Values, challenges, and recommendations. PMID:33778361
Data-Driven Surveillance: Effective Collection, Integration, and Interpretation of Data to Support Decision Making. PMID:33778039
Adoption of artificial intelligence in breast imaging: evaluation, ethical constraints and limitations. PMID:33772149
From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences. PMID:33770077
Genomic prediction models trained with historical records enable populating the German ex situ genebank bio-digital resource center of barley (Hordeum sp.) with information on resistances to soilborne barley mosaic viruses. PMID:33768281
CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. PMID:33768211
Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS). PMID:33763204
[Real-time data from medical care settings to guide public health action]. PMID:33760934
Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs? PMID:33760822
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses. PMID:33758032
Why and how to engage expert stakeholders in ontology development: insights from social and behavioural sciences. PMID:33757593
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. PMID:33757278
Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge. PMID:33755673
Fault2SHA Central Apennines database and structuring active fault data for seismic hazard assessment. PMID:33753737
Risk Factors for Severe Outcomes in Patients With Systemic Vasculitis and COVID-19: A Binational, Registry-Based Cohort Study. PMID:33750043
Taking a fresh look at FAIR for research software. PMID:33748799
The National Children's Study Archive Model: A 3-Tier Framework for Dissemination of Data and Specimens for General Use and Secondary Analysis. PMID:33748052
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Using Word Embeddings to Learn a Better Food Ontology. PMID:33733222
isa4j: a scalable Java library for creating ISA-Tab metadata. PMID:33728038
Targeted Therapies for Metabolic Myopathies Related to Glycogen Storage and Lipid Metabolism: a Systematic Review and Steps Towards a 'Treatabolome'. PMID:33720849
Disease diagnostic coding to facilitate evidence-based medicine: current and future perspectives. PMID:33719780
A Second Look at FAIR in Proteomic Investigations. PMID:33719446
Openness in Big Data and Data Repositories: The Application of an Ethics Framework for Big Data in Health and Research. PMID:33717315
Challenges and Solutions for Collecting and Analyzing Real World Data: The Eric CLL Database as an Illustrative Example. PMID:33709059
Clinical genetics in transition-a comparison of genetic services in Estonia, Finland, and the Netherlands. PMID:33704686
Decentralized but Globally Coordinated Biodiversity Data. PMID:33693407
Perspective: Acknowledging Data Work in the Social Media Research Lifecycle. PMID:33693406
The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. PMID:33693395
Open Science, Open Data, and Open Scholarship: European Policies to Make Science Fit for the Twenty-First Century. PMID:33693366
Improving reporting standards for polygenic scores in risk prediction studies. PMID:33692554
Laminopathies' Treatments Systematic Review: A Contribution Towards a 'Treatabolome'. PMID:33682723
Intestinal microbiota alterations by dietary exposure to chemicals from food cooking and processing. Application of data science for risk prediction. PMID:33680352
Editorial: Advances in Applied Bioinformatics in Crops. PMID:33679855
Research perspectives on animal health in the era of artificial intelligence. PMID:33676570
DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. PMID:33673098
Future Medical Artificial Intelligence Application Requirements and Expectations of Physicians in German University Hospitals: Web-Based Survey. PMID:33666563
An Early Stage Researcher's Primer on Systems Medicine Terminology. PMID:33659919
Rethinking data and metadata in the age of machine intelligence. PMID:33659917
Data hygiene factors. PMID:33659916
Barely sufficient practices in scientific computing. PMID:33659915
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
What is the role of cheminformatics in a pandemic? PMID:33653411
Motivating data contributions via a distinct career currency. PMID:33653143
Excavating FAIR Data: the Case of the Multicenter Animal Spinal Cord Injury Study (MASCIS), Blood Pressure, and Neuro-Recovery. PMID:33651310
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. PMID:33649565
Toward assessing clinical trial publications for reporting transparency. PMID:33647518
Essential requirements for establishing and operating data trusts: practical guidance co-developed by representatives from fifteen canadian organizations and initiatives. PMID:33644412
The Ethics of Artificial Intelligence in Pathology and Laboratory Medicine: Principles and Practice. PMID:33644301
Advances in cancer research dissemination through the pandemic and beyond. PMID:33636283
Using Machine Learning to Collect and Facilitate Remote Access to Biomedical Databases: Development of the Biomedical Database Inventory. PMID:33629960
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers. PMID:33625229
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. PMID:33622857
Science as collaborative knowledge generation. PMID:33616965
Influenza and Respiratory Virus Surveillance, Vaccine Uptake, and Effectiveness at a Time of Cocirculating COVID-19: Protocol for the English Primary Care Sentinel System for 2020-2021. PMID:33605892
Public data sources to support systems toxicology applications. PMID:33604492
Operationalisation of the Randomized Embedded Multifactorial Adaptive Platform for COVID-19 trials in a low and lower-middle income critical care learning health system. PMID:33604455
The need for standardisation in life science research - an approach to excellence and trust. PMID:33604028
Evidence-based interventions to reduce mortality among preterm and low-birthweight neonates in low-income and middle-income countries: a systematic review and meta-analysis. PMID:33602687
Ten simple rules for navigating the computational aspect of an interdisciplinary PhD. PMID:33600411
Is Sharing Datasets the Answer to the New Challenges of Reproductive Biology Research? PMID:33594650
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. PMID:33589928
A community resource for paired genomic and metabolomic data mining. PMID:33589842
Towards implementing artificial intelligence post-processing in weather and climate: proposed actions from the Oxford 2019 workshop. PMID:33583264
Data Sharing Under the General Data Protection Regulation: Time to Harmonize Law and Research Ethics? PMID:33583200
ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future. PMID:33565128
How FAIR are plant sciences in the twenty-first century? The pressing need for reproducibility in plant ecology and evolution. PMID:33563121
Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials. PMID:33558569
Complicated legacies: The human genome at 20. PMID:33542123
Can Big Data guide prognosis and clinical decisions in epilepsy? PMID:33529363
Initiatives, Concepts, and Implementation Practices of FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles in Health Data Stewardship Practice: Protocol for a Scoping Review. PMID:33528373
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
Data integration enables global biodiversity synthesis. PMID:33526679
Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium. PMID:33522965
How Do Data Bolster Pandemic Preparedness and Response? How Do We Improve Data and Systems to Be Better Prepared? PMID:33511371
Connected Research: The Potential of the PID Graph. PMID:33511369
Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs. PMID:33507738
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. PMID:33506383
biotoolsSchema: a formalized schema for bioinformatics software description. PMID:33506265
Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group. PMID:33501381
Deep aspirations: towards a sustainable offshore Blue Economy. PMID:33500602
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. PMID:33500403
Quality assessment of real-world data repositories across the data life cycle: A literature review. PMID:33496785
Cohort Profile: The Norwegian Life Course, Ageing and Generation Study (NorLAG). PMID:33496326
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
Addressing priorities for surgical research in Africa: implementation of a multicentre cloud-based peri-operative registry in Ethiopia. PMID:33492690
Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications. PMID:33490973
Summary of third annual MCBK public meeting: Mobilizing computable biomedical knowledge-Accelerating the second knowledge revolution. PMID:33490385
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Highlights from the Era of Open Source Web-Based Tools. PMID:33472826
A platform for experimental precision medicine: The extended BXD mouse family. PMID:33472028
Initial experience with introducing national guidelines for CT- and MRI-based delineation of organs at risk in radiotherapy. PMID:33458285
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
Thyrotrophin and thyroxine support immune homeostasis in humans. PMID:33454989
Ethical Principles, Constraints and Opportunities in Clinical Proteomics. PMID:33453411
Standardization and digitization of clinical data in multiple sclerosis. PMID:33452493
A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration. PMID:33452270
Challenges for Computational Stem Cell Biology: A Discussion for the Field. PMID:33440181
People are essential to linking biodiversity data. PMID:33439246
Streamlining data-intensive biology with workflow systems. PMID:33438730
African genetic diversity and adaptation inform a precision medicine agenda. PMID:33432191
Review on natural products databases: where to find data in 2020. PMID:33431011
HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard. PMID:33430999
Towards reproducible computational drug discovery. PMID:33430992
Researcher Perspectives on Data Sharing in Deep Brain Stimulation. PMID:33424563
Using Community Science to Reveal the Global Chemogeography of River Metabolomes. PMID:33419380
PM4NGS, a project management framework for next-generation sequencing data analysis. PMID:33410471
An ontology-based approach for developing a harmonised data-validation tool for European cancer registration. PMID:33407816
Opportunities for increased reproducibility and replicability of developmental neuroimaging. PMID:33383554
Ten quick tips for making things findable. PMID:33382681
Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations. PMID:33381478
Polymorphisms within the TNFSF4 and MAPKAPK2 Loci Influence the Risk of Developing Invasive Aspergillosis: A Two-Stage Case Control Study in the Context of the aspBIOmics Consortium. PMID:33374839
Community Approaches for Integrating Environmental Exposures into Human Models of Disease. PMID:33369481
Open Science to Address COVID-19: Sharing Data to Make Our Research Investment Go Further. PMID:33368019
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. PMID:33363701
Historical natural kinds and mineralogy: Systematizing contingency in the context of necessity. PMID:33361151
Knowledge Organization Systems for Systematic Chemical Assessments. PMID:33356525
IOCBIO Kinetics: An open-source software solution for analysis of data traces. PMID:33351800
Towards the Development of Digital Twins for the Bio-manufacturing Industry. PMID:33349908
Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. PMID:33349503
A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368
Editorial: Phenotyping; From Plant, to Data, to Impact and Highlights of the International Plant Phenotyping Symposium - IPPS 2018. PMID:33343612
Obstacles to the reuse of study metadata in ClinicalTrials.gov. PMID:33339830
Common Problems, Common Data Model Solutions: Evidence Generation for Health Technology Assessment. PMID:33336320
A New Era for Space Life Science: International Standards for Space Omics Processing. PMID:33336201
At the Epicenter of COVID-19-the Tragic Failure of the Global Supply Chain for Medical Supplies. PMID:33335876
Plasma-MDS, a metadata schema for plasma science with examples from plasma technology. PMID:33335096
Menoci: lightweight extensible web portal enhancing data management for biomedical research projects. PMID:33334310
Mini Review: Clinical Routine Microbiology in the Era of Automation and Digital Health. PMID:33330127
Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II-practical challenges. PMID:33323463
NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. PMID:33322070
Making experimental data tables in the life sciences more FAIR: a pragmatic approach. PMID:33319910
Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites. PMID:33319904
Development of minimal basic data set to report COVID-19. PMID:33315989
"Macrobot": An Automated Segmentation-Based System for Powdery Mildew Disease Quantification. PMID:33313559
Plant Phenotyping: Past, Present, and Future. PMID:33313536
Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. PMID:33313522
MP3: Medical Software for Processing Multi-Parametric Images Pipelines. PMID:33304261
ideal: an R/Bioconductor package for interactive differential expression analysis. PMID:33297942
Systematizing Effective Practice, Embedding It in Standard Practice. PMID:33294880
Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease. PMID:33294866
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
Meta-analysis of viscosity of aqueous deep eutectic solvents and their components. PMID:33288787
A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds. PMID:33281840
Text mining approaches for dealing with the rapidly expanding literature on COVID-19. PMID:33279995
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. PMID:33279989
Too Many Materials and Too Many Applications: An Experimental Problem Waiting for a Computational Solution. PMID:33274268
GPCRdb in 2021: integrating GPCR sequence, structure and function. PMID:33270898
Using Personal Genomic Data within Primary Care: A Bioinformatics Approach to Pharmacogenomics. PMID:33266138
Towards a unified open access dataset of molecular interactions. PMID:33262342
Isabl Platform, a digital biobank for processing multimodal patient data. PMID:33256603
Challenges and Prospects for the Conservation of Crop Genetic Resources in Field Genebanks, in In Vitro Collections and/or in Liquid Nitrogen. PMID:33255385
Machine Learning Electronic Health Record Identification of Patients with Rheumatoid Arthritis: Algorithm Pipeline Development and Validation Study. PMID:33252349
Promoting resilience of large international collaborative research programs in times of global crisis. PMID:33250993
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. PMID:33247931
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775
MarkerDB: an online database of molecular biomarkers. PMID:33245771
A survey of research quality in core facilities. PMID:33241998
Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology. PMID:33231642
A collaborative resource platform for non-human primate neuroimaging. PMID:33227425
Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. PMID:33226702
Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes. PMID:33216896
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
WikiPathways: connecting communities. PMID:33211851
Machine learning in cardiovascular radiology: ESCR position statement on design requirements, quality assessment, current applications, opportunities, and challenges. PMID:33211147
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Reproducibility Starts from You Today. PMID:33205134
The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database. PMID:33205130
dtoolAI: Reproducibility for Deep Learning. PMID:33205122
Recommendations for Services in a FAIR Data Ecosystem. PMID:33205119
Metadata and Reuse: Antidotes to Information Entropy. PMID:33205081
Language experience in LSF development: Behavioral evidence from a sentence repetition task. PMID:33201887
Improving target assessment in biomedical research: the GOT-IT recommendations. PMID:33199880
A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. PMID:33197228
Towards a unified data infrastructure to support European and global microbiome research: a call to action. PMID:33196130
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. PMID:33193131
Biodiversidata: A novel dataset for the vascular plant species diversity in Uruguay. PMID:33192152
Governance of research consortia: challenges of implementing Responsible Research and Innovation within Europe. PMID:33190636
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
Bringing Big Data to Bear in Environmental Public Health: Challenges and Recommendations. PMID:33184612
Multiscale dynamic human mobility flow dataset in the U.S. during the COVID-19 epidemic. PMID:33184280
A checklist recipe: making species data open and FAIR. PMID:33181821
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. PMID:33179748
Opening Pandora's Box: Peeking inside Psychology's data sharing practices, and seven recommendations for change. PMID:33179123
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). PMID:33178355
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. PMID:33174597
The Role of Machine Learning in the Understanding and Design of Materials. PMID:33170678
A comprehensive quality assessment framework for scientific events. PMID:33169040
Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. PMID:33169034
Pathway information extracted from 25 years of pathway figures. PMID:33168034
Reducing bias and improving transparency in medical research: a critical overview of the problems, progress and suggested next steps. PMID:33167771
Maximizing the reusability of gene expression data by predicting missing metadata. PMID:33156882
DDBJ update: streamlining submission and access of human data. PMID:33156332
PK-DB: pharmacokinetics database for individualized and stratified computational modeling. PMID:33151297
Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. PMID:33150057
Biocuration - mapping resources and needs. PMID:33145007
New acquisition techniques and their prospects for the achievable resolution of fMRI. PMID:33130229
Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume I-conceptual challenges. PMID:33127656
Reproducibility analysis of multi-institutional paired expert annotations and radiomic features of the Ivy Glioblastoma Atlas Project (Ivy GAP) dataset. PMID:33118182
Strategic vision for improving human health at The Forefront of Genomics. PMID:33116284
Bridging research integrity and global health epidemiology (BRIDGE) guidelines: explanation and elaboration. PMID:33115860
Bridging research integrity and global health epidemiology (BRIDGE) statement: guidelines for good epidemiological practice. PMID:33115859
COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology. PMID:33112762
fiddle: a tool to combat publication bias by getting research out of the file drawer and into the scientific community. PMID:33111948
Design, development and deployment of a web-based interoperable registry for inherited retinal dystrophies in Portugal: the IRD-PT. PMID:33109251
Towards data-driven next-generation transmission electron microscopy. PMID:33106651
The Semantic Data Dictionary - An Approach for Describing and Annotating Data. PMID:33103120
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. PMID:33103064
A Conceptual Enterprise Framework for Managing Scientific Data Stewardship. PMID:33101400
Sex as a Biological Variable in Preclinical Modeling of Blast-Related Traumatic Brain Injury. PMID:33101170
Health Heatmap of India: An Open Data Platform. PMID:33100615
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. PMID:33092028
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. PMID:33090199
Optimizing High-Performance Computing Systems for Biomedical Workloads. PMID:33088611
Simultaneous BOLD-fMRI and constant infusion FDG-PET data of the resting human brain. PMID:33087725
A qualitative study of big data and the opioid epidemic: recommendations for data governance. PMID:33087123
The AD Knowledge Portal: A Repository for Multi-Omic Data on Alzheimer's Disease and Aging. PMID:33085189
Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. PMID:33082281
A Python-Based Pipeline for Preprocessing LC-MS Data for Untargeted Metabolomics Workflows. PMID:33081373
NASA GeneLab: interfaces for the exploration of space omics data. PMID:33080015
Metadata Stewardship in Nanosafety Research: Community-Driven Organisation of Metadata Schemas to Support FAIR Nanoscience Data. PMID:33076428
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging. PMID:33068112
A high-stringency blueprint of the human proteome. PMID:33067450
On the application, reporting, and sharing of in silico simulations for genetic studies. PMID:33063887
Coronavirus disease 2019 (COVID-19) surveillance system: Development of COVID-19 minimum data set and interoperable reporting framework. PMID:33062736
Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients. PMID:33051456
Digitally Enabled, Patient-Centric Clinical Trials: Shifting the Drug Development Paradigm. PMID:33048475
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC-MS based untargeted metabolomics practitioners. PMID:33044703
The YOUth cohort study: MRI protocol and test-retest reliability in adults. PMID:33040972
Commentary to Gusenbauer and Haddaway 2020: Evaluating retrieval qualities of Google Scholar and PubMed. PMID:33031632
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Continuous quality improvement in statistical code: avoiding errors and improving transparency. PMID:33023935
Analysis of data dictionary formats of HIV clinical trials. PMID:33017454
The MOMENTUM Study: An International Registry for the Evidence-Based Introduction of MR-Guided Adaptive Therapy. PMID:33014774
Secondary research use of personal medical data: attitudes from patient and population surveys in The Netherlands and Germany. PMID:33005018
Effect of the Albumin Corona on the Toxicity of Combined Graphene Oxide and Cadmium to Daphnia magna and Integration of the Datasets into the NanoCommons Knowledge Base. PMID:33003330
Serial measurements in COVID-19-induced acute respiratory disease to unravel heterogeneity of the disease course: design of the Maastricht Intensive Care COVID cohort (MaastrICCht). PMID:32994259
Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective. PMID:32993675
Towards a unified Latin American Natural Products Database: LANaPD. PMID:32983559
Mining data from legacy taxonomic literature and application for sampling spiders of the Teutamus group (Araneae; Liocranidae) in Southeast Asia. PMID:32978432
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. PMID:32976578
Integrating trials into a whole-population cohort of children and parents: statement of intent (trials) for the Generation Victoria (GenV) cohort. PMID:32972373
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research. PMID:32958507
Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. PMID:32954378
What drives and inhibits researchers to share and use open research data? A systematic literature review to analyze factors influencing open research data adoption. PMID:32946521
Gold Standard for macromolecular crystallography diffraction data. PMID:32939270
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
Facilitating author-driven, machine-readable descriptions with the new minISA metadata format. PMID:32934235
MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. PMID:32929271
NIDA vision for big data science to understand the biological underpinnings of substance use disorders. PMID:32917969
Poikilosis - pervasive biological variation. PMID:32913639
Brazilian Maternal and Child Nutrition Consortium: establishment, data harmonization and basic characteristics. PMID:32913200
SCALEUS-FD: A FAIR Data Tool for Biomedical Applications. PMID:32908882
Bending the curve of terrestrial biodiversity needs an integrated strategy. PMID:32908312
FAIR, safe and high-quality data: The data infrastructure and accessibility of the YOUth cohort study. PMID:32906086
Materials Cloud, a platform for open computational science. PMID:32901046
AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance. PMID:32901044
LifeTime and improving European healthcare through cell-based interceptive medicine. PMID:32894860
Position paper on COVID-19 imaging and AI: From the clinical needs and technological challenges to initial AI solutions at the lab and national level towards a new era for AI in healthcare. PMID:32890777
Meeting the Challenge of Scientific Dissemination in the Era of COVID-19: Toward a Modular Approach to Knowledge-Sharing for Radiation Oncology. PMID:32890543
Capturing the Spatial Relatedness of Long-Distance Caregiving: A Mixed-Methods Approach. PMID:32887508
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". PMID:32883210
Ten simple rules for open human health research. PMID:32881878
Ten simple rules on how to write a standard operating procedure. PMID:32881868
Sharing and organizing research products as R packages. PMID:32875401
Data synthesis for crop variety evaluation. A review. PMID:32863892
The archives are half-empty: an assessment of the availability of microbial community sequencing data. PMID:32859925
Research data sharing in the Australian national science agency: Understanding the relative importance of organisational, disciplinary and domain-specific influences. PMID:32857794
Compressive Big Data Analytics: An ensemble meta-algorithm for high-dimensional multisource datasets. PMID:32857775
Microbial natural product databases: moving forward in the multi-omics era. PMID:32856641
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Ten simple rules to power drug discovery with data science. PMID:32853229
Measuring health promotion: translating science into policy. PMID:32852581
Community standards to facilitate development and address challenges in metabolic modeling. PMID:32845080
The road ahead in genetics and genomics. PMID:32839576
Interoperability of population-based patient registries. PMID:32838295
Global academic response to COVID-19: Cross-sectional study. PMID:32836910
Towards standardization guidelines for in silico approaches in personalized medicine. PMID:32827396
Reporting of methodologies used for clonogenic assays to determine radiosensitivity. PMID:32823284
A novel curation system to facilitate data integration across regional citizen science survey programs. PMID:32821528
Identifying disease trajectories with predicate information from a knowledge graph. PMID:32819419
FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results. PMID:32815545
ReDU: a framework to find and reanalyze public mass spectrometry data. PMID:32807955
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. PMID:32805036
Toward a global and reproducible science for brain imaging in neurotrauma: the ENIGMA adult moderate/severe traumatic brain injury working group. PMID:32797398
Publishing reproducible dynamic kinetic models. PMID:32793969
A guide to writing systematic reviews of rare disease treatments to generate FAIR-compliant datasets: building a Treatabolome. PMID:32787960
The Repository Chemotion: Infrastructure for Sustainable Research in Chemistry*. PMID:32785962
APRICOT: Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools. PMID:32777825
The Effects of Gamification on Computerized Cognitive Training: Systematic Review and Meta-Analysis. PMID:32773374
DICOM re-encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules. PMID:32772385
PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO. PMID:32766455
WHONDRS-GUI: a web application for global survey of surface water metabolites. PMID:32765964
An inexpensive and easy-to-implement approach to a Quality Management System for an academic research lab. PMID:32765843
NCBI Taxonomy: a comprehensive update on curation, resources and tools. PMID:32761142
Development of an informatics system for accelerating biomedical research. PMID:32760576
Use and users of a social science research data archive. PMID:32760066
Structure of the Pandemic. PMID:32755569
The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview. PMID:32754723
Marine Terpenoids from Polar Latitudes and Their Potential Applications in Biotechnology. PMID:32751369
PleThora: Pleural effusion and thoracic cavity segmentations in diseased lungs for benchmarking chest CT processing pipelines. PMID:32749075
Tolerability and efficacy of vortioxetine versus SSRIs in elderly with major depression. Study protocol of the VESPA study: a pragmatic, multicentre, open-label, parallel-group, superiority, randomized trial. PMID:32746941
Accelerating ophthalmic artificial intelligence research: the role of an open access data repository. PMID:32740059
NxGen evidence: Redesigning the Agency for Healthcare Research and Quality Effective Health Care website to promote engagement, interactivity, and usability of systematic reviews. PMID:32737924
Veterinary informatics: forging the future between veterinary medicine, human medicine, and One Health initiatives-a joint paper by the Association for Veterinary Informatics (AVI) and the CTSA One Health Alliance (COHA). PMID:32734172
HDR UK supporting mobilising computable biomedical knowledge in the UK. PMID:32723851
Low availability of code in ecology: A call for urgent action. PMID:32722681
Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis. PMID:32722118
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
Host immune genetic variations influence the risk of developing acute myeloid leukaemia: results from the NuCLEAR consortium. PMID:32678078
The Hong Kong Principles for assessing researchers: Fostering research integrity. PMID:32673304
Translational neuroscience: the state of the nation (a PhD student perspective). PMID:32671338
Metabolite AutoPlotter - an application to process and visualise metabolite data in the web browser. PMID:32670572
The ARRIVE guidelines 2.0: updated guidelines for reporting animal research. PMID:32666574
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PMID:32666546
Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0. PMID:32663221
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PMID:32663219
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PMID:32663096
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PMID:32662519
A dataset describing data discovery and reuse practices in research. PMID:32661229
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PMID:32660541
Big data requirements for artificial intelligence. PMID:32657996
Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research. PMID:32655481
West-Life: A Virtual Research Environment for structural biology. PMID:32647812
Towards Interoperability in Clinical Research - Enabling FHIR on the Open-Source Research Platform XNAT. PMID:32642856
Enabling ad-hoc reuse of private data repositories through schema extraction. PMID:32641124
Design and Rationale for Common Data Elements for Clinical Research in Pediatric Critical Care Medicine. PMID:32639472
Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. PMID:32637961
Enabling a fast annotation process with the Table2Annotation tool. PMID:32634873
Clinical decision trees support systematic evaluation of multidisciplinary team recommendations. PMID:32627108
Storing, combining and analysing turkey experimental data in the Big Data era. PMID:32624081
Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. PMID:32621602
Recognizing, reporting and reducing the data curation debt of cohort studies. PMID:32617581
Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm. PMID:32610615
AI in Medical Imaging Informatics: Current Challenges and Future Directions. PMID:32609615
The international X-linked hypophosphataemia (XLH) registry (NCT03193476): rationale for and description of an international, observational study. PMID:32605590
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
The NEUBIAS Gateway: a hub for bioimage analysis methods and materials. PMID:32595963
BRIDGE - A Visual Analytics Web Tool for Barley Genebank Genomics. PMID:32595658
A pragmatic tool for drug discovery. PMID:32593660
Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. PMID:32589957
Long-term monitoring of the Iberian ibex population in the Sierra Nevada of the southeast Iberian Peninsula. PMID:32587252
Academic criteria for promotion and tenure in biomedical sciences faculties: cross sectional analysis of international sample of universities. PMID:32586791
"Yes, but will it work for my patients?" Driving clinically relevant research with benchmark datasets. PMID:32577534
The Zebra Mussel (Dreissena polymorpha) as a Model Organism for Ecotoxicological Studies: A Prior 1H NMR Spectrum Interpretation of a Whole Body Extract for Metabolism Monitoring. PMID:32570933
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
A call to action: strengthening the capacity for data capture and computational modelling of HIV integrated care in low- and middle-income countries. PMID:32562312
COVID-19 pandemic reveals the peril of ignoring metadata standards. PMID:32561801
FOBI: an ontology to represent food intake data and associate it with metabolomic data. PMID:32556148
Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. PMID:32554617
An integrated chemical environment with tools for chemical safety testing. PMID:32553663
National Cancer Institute Workshop on Artificial Intelligence in Radiation Oncology: Training the Next Generation. PMID:32544635
Bringing Code to Data: Do Not Forget Governance. PMID:32540846
Studying the pathophysiology of coronavirus disease 2019: a protocol for the Berlin prospective COVID-19 patient cohort (Pa-COVID-19). PMID:32535877
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
Ten recommendations for supporting open pathogen genomic analysis in public health. PMID:32528156
DDIEM: drug database for inborn errors of metabolism. PMID:32527280
FAIR-compliant clinical, radiomics and DICOM metadata of RIDER, interobserver, Lung1 and head-Neck1 TCIA collections. PMID:32521049
Big-Data Science in Porous Materials: Materials Genomics and Machine Learning. PMID:32520531
The origin and widespread occurrence of Sli-based self-compatibility in potato. PMID:32514711
Perspective: Towards Automated Tracking of Content and Evidence Appraisal of Nutrition Research. PMID:32504536
GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs. PMID:32492127
Imaging-Based Prediction of Molecular Therapy Targets in NSCLC by Radiogenomics and AI Approaches: A Systematic Review. PMID:32486314
The Oxford Royal College of General Practitioners Clinical Informatics Digital Hub: Protocol to Develop Extended COVID-19 Surveillance and Trial Platforms. PMID:32484782
Scoring functions for drug-effect similarity. PMID:32484516
Reliability and prognostic value of radiomic features are highly dependent on choice of feature extraction platform. PMID:32483644
Recommendations to enhance rigor and reproducibility in biomedical research. PMID:32479592
PRISM: A Platform for Imaging in Precision Medicine. PMID:32479186
ATP measurement as an objective method to measure environmental contamination in 9 hospitals in the Dutch/Belgian border area. PMID:32466792
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). PMID:32463383
[Digital public health-leverage for community capacity building in health promotion : Current situation, developmental issues and TEAviisari as a model implementation]. PMID:32451594
BBMRI-ERIC's contributions to research and knowledge exchange on COVID-19. PMID:32444797
High-throughput screening platform for solid electrolytes combining hierarchical ion-transport prediction algorithms. PMID:32439922
Ten simple rules for making training materials FAIR. PMID:32437350
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
Improving reproducibility in computational biology research. PMID:32427998
Machine and deep learning methods for radiomics. PMID:32418336
The TRUST Principles for digital repositories. PMID:32409645
Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions. PMID:32398275
Community standards for open cell migration data. PMID:32396199
RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. PMID:32395768
Pofatu, a curated and open-access database for geochemical sourcing of archaeological materials. PMID:32393758
Quantitative Imaging Informatics for Cancer Research. PMID:32392097
Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities. PMID:32382253
Implementation of eHealth and AI integrated diagnostics with multidisciplinary digitized data: are we ready from an international perspective? PMID:32377810
The VODAN IN: support of a FAIR-based infrastructure for COVID-19. PMID:32376989
The Quest for Orthologs benchmark service and consensus calls in 2020. PMID:32374845
The omics discovery REST interface. PMID:32374843
The Elements of Data Sharing. PMID:32360769
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Sharing Is Caring-Data Sharing Initiatives in Healthcare. PMID:32349396
Data-driven classification of the certainty of scholarly assertions. PMID:32341891
Embracing data preservation, sharing, and re-use in traumatic stress research. PMID:32341765
VarFish: comprehensive DNA variant analysis for diagnostics and research. PMID:32338743
Plant, space and time - linked together in an integrative and scalable data management system for phenomic approaches in agronomic field trials. PMID:32336978
The Dementias Platform UK (DPUK) Data Portal. PMID:32328990
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
Summary of second annual MCBK public meeting: Mobilizing Computable Biomedical Knowledge-A movement to accelerate translation of knowledge into action. PMID:32313839
Sharing research data. PMID:32312188
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
ITCBio, a Clinical and Translational Research Platform. PMID:32308862
Ethical Use of Electronic Health Record Data and Artificial Intelligence: Recommendations of the Primary Care Informatics Working Group of the International Medical Informatics Association. PMID:32303098
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. PMID:32302568
Extending the Minimum Information About BIobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events. PMID:32302498
Be FAIR to your data. PMID:32300841
Repositories for Taxonomic Data: Where We Are and What is Missing. PMID:32298457
An examination of the effects of a patient-designed-and-informed participant information sheet in comparison with a standard, researcher-designed information sheet on recruitment, retention and understanding: Protocol for a study-within-a-trial. PMID:32296752
A living systematic review protocol for COVID-19 clinical trial registrations. PMID:32292826
A fine-tuned global distribution dataset of marine forests. PMID:32286314
Development of an international data repository and research resource: the Prospective studies of Acute Child Trauma and Recovery (PACT/R) Data Archive. PMID:32284820
Leveraging legacy archaeological collections as proxies for climate and environmental research. PMID:32284414
An open-source GIS-enabled lookup service for Nagoya Protocol party information. PMID:32283554
Structured reviews for data and knowledge-driven research. PMID:32283553
Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment. PMID:32276469
Toward Reducing Health Information Inequities in the Caribbean: Our Experience Building a Participatory Health Informatics Project. PMID:32269461
Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data. PMID:32251390
GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. PMID:32249310
Global coalition to accelerate COVID-19 clinical research in resource-limited settings. PMID:32247324
Every fifth published metagenome is not available to science. PMID:32243442
Geographic assessment of cancer genome profiling studies. PMID:32239182
Automated gene data integration with Databio. PMID:32238171
Transactions from the 69th Annual Meeting of the American Crystallographic Association: Data best practices-current state and future needs. PMID:32232073
Humanizing Big Data: Recognizing the Human Aspect of Big Data. PMID:32231993
NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. PMID:32226594
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. PMID:32219223
Biobanking in Molecular Biomarker Research for the Early Detection of Cancer. PMID:32218259
Establishing Patient Registries for Rare Diseases: Rationale and Challenges. PMID:32215853
Ten simple rules for providing effective bioinformatics research support. PMID:32214318
Optimizing COVID-19 Candidate Therapeutics: Thinking Without Borders. PMID:32212378
bertha: Project skeleton for scientific software. PMID:32203531
Benchmarking the MinION: Evaluating long reads for microbial profiling. PMID:32198413
Evaluating the feasibility and preliminary efficacy of a Cognitive Occupation-Based programme for people with Multiple Sclerosis (COB-MS): protocol for a feasibility cluster-randomised controlled trial. PMID:32183874
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
OpenDose: Open-Access Resource for Nuclear Medicine Dosimetry. PMID:32169912
Guidelines for systematic reporting of sequence alignments. PMID:32161811
An open data infrastructure for the study of anthropogenic hazards linked to georesource exploitation. PMID:32161264
Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide. PMID:32160189
Regime shifts occur disproportionately faster in larger ecosystems. PMID:32157098
Progress and prospects for accelerating materials science with automated and autonomous workflows. PMID:32153744
New tools for calibrating diffraction setups. PMID:32153298
NFKB2 polymorphisms associate with the risk of developing rheumatoid arthritis and response to TNF inhibitors: Results from the REPAIR consortium. PMID:32152480
Arthroscopic meniscectomy versus non-surgical or sham treatment in patients with MRI confirmed degenerative meniscus lesions: a protocol for an individual participant data meta-analysis. PMID:32152157
Holistic Environmental Approaches and Aichi Biodiversity Targets: accomplishments and perspectives for marine ecosystems. PMID:32140297
Systematic Review of Privacy-Preserving Distributed Machine Learning From Federated Databases in Health Care. PMID:32134684
Storm impacts on phytoplankton community dynamics in lakes. PMID:32133744
CORR Insights®: No Difference in 5-year Clinical or Radiographic Outcomes Between Kinematic and Mechanical Alignment in TKA: A Randomized Controlled Trial. PMID:32118601
SCelVis: exploratory single cell data analysis on the desktop and in the cloud. PMID:32117635
NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis. PMID:32117417
Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey. PMID:32111833
Semantic concept schema of the linear mixed model of experimental observations. PMID:32109232
A combined experimental and modelling approach for the Weimberg pathway optimisation. PMID:32107375
Data libraries - the missing element for modeling biological systems. PMID:32100391
Informatics Approaches for Harmonized Intelligent Integration of Stem Cell Research. PMID:32099411
Repertoire of morphable proteins in an organism. PMID:32095378
Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes. PMID:32078367
Natural Language Processing in Dutch Free Text Radiology Reports: Challenges in a Small Language Area Staging Pulmonary Oncology. PMID:32076924
Towards a European health research and innovation cloud (HRIC). PMID:32075696
The Data Must Be Accessible to All. PMID:32071148
The data must be accessible to all. PMID:32071082
The data must be accessible to all. PMID:32071074
Preparing Medical Imaging Data for Machine Learning. PMID:32068507
Impact of the Protein Data Bank on antineoplastic approvals. PMID:32068073
"Ethics When You Least Expect It": A Modular Approach to Short Course Data Ethics Instruction. PMID:32067185
Defining the content of a minimal dataset for acquired brain injury using a Delphi procedure. PMID:32066447
A systems approach to infectious disease. PMID:32060427
Reproducible research practices, openness and transparency in health economic evaluations: study protocol for a cross-sectional comparative analysis. PMID:32060160
An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms. PMID:32055857
ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies. PMID:32047873
The Rural Household Multiple Indicator Survey, data from 13,310 farm households in 21 countries. PMID:32047158
Biomarkers for Traumatic Brain Injury: Data Standards and Statistical Considerations. PMID:32046588
An Evaluation of Nephrology Literature for Transparency and Reproducibility Indicators: Cross-Sectional Review. PMID:32043031
Real-world applications of deep convolutional neural networks in diagnostic cancer imaging. PMID:32036673
The Data Tags Suite (DATS) model for discovering data access and use requirements. PMID:32031623
Machine Learning and Multidrug-Resistant Gram-Negative Bacteria: An Interesting Combination for Current and Future Research. PMID:32023986
Organizing genome engineering for the gigabase scale. PMID:32019919
Variation benchmark datasets: update, criteria, quality and applications. PMID:32016318
Machine learning can predict survival of patients with heart failure from serum creatinine and ejection fraction alone. PMID:32013925
Development of a Precision Medicine Workflow in Hematological Cancers, Aalborg University Hospital, Denmark. PMID:32013121
Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine. PMID:32013105
BioMagResBank (BMRB) as a Resource for Structural Biology. PMID:32006287
Data linkage in medical science using the resource description framework: the AVERT model. PMID:32002509
Sharing data-taming the beast: barriers to meta-analyses of individual patient data (IPD) and solutions. PMID:32001519
Coral restoration - A systematic review of current methods, successes, failures and future directions. PMID:31999709
Refgenie: a reference genome resource manager. PMID:31995185
From the Data on Many, Precision Medicine for "One": The Case for Widespread Genomic Data Sharing. PMID:31988941
Effect of Cold-Sintering Parameters on Structure, Density, and Topology of Fe-Cu Nanocomposites. PMID:31979235
Performance of Qure.ai automatic classifiers against a large annotated database of patients with diverse forms of tuberculosis. PMID:31978149
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. PMID:31971940
A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. PMID:31969795
Virus Metagenomics in Farm Animals: A Systematic Review. PMID:31963174
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. PMID:31960040
Metabolomic and Lipidomic Signatures of Metabolic Syndrome and its Physiological Components in Adults: A Systematic Review. PMID:31959772
Comparing the effectiveness and cost-effectiveness of self-management interventions in four high-priority chronic conditions in Europe (COMPAR-EU): a research protocol. PMID:31959612
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. PMID:31956905
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Transgenic Testing Does Not Support a Role for Additional Candidate Genes in Wolbachia Male Killing or Cytoplasmic Incompatibility. PMID:31937677
Axes of a revolution: challenges and promises of big data in healthcare. PMID:31932803
The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies. PMID:31932593
Programmatic Access to FAIRified Digital Plant Genetic Resources. PMID:31913851
No Dataset Left Behind: Mechanistic Insights into Thyroid Receptor Signaling Through Transcriptomic Consensome Meta-Analysis. PMID:31910096
A multitrophic perspective on biodiversity-ecosystem functioning research. PMID:31908360
Machine and deep learning approaches for cancer drug repurposing. PMID:31904426
Efficacy and safety of D,L-3-hydroxybutyrate (D,L-3-HB) treatment in multiple acyl-CoA dehydrogenase deficiency. PMID:31904027
Data, the future of Science and Clinical Practice. PMID:31902447
Democratic librarianship: the role of the medical library in promoting democracy and social justice. PMID:31897065
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
A data management workflow of biodiversity data from the field to data users. PMID:31890356
OHMI: the ontology of host-microbiome interactions. PMID:31888755
The COMPARE Data Hubs. PMID:31868882
Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation. PMID:31862013
Explainable Deep Learning for Augmentation of Small RNA Expression Profiles. PMID:31855058
Big Data - How to Realize the Promise. PMID:31846513
MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment. PMID:31844073
Engaging a community to enable disease-centric data sharing with the NF Data Portal. PMID:31836719
Experiment design driven FAIRification of omics data matrices, an exemplar. PMID:31831744
An intrinsically disordered proteins community for ELIXIR. PMID:31824649
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
Improved standardization of transcribed digital specimen data. PMID:31819990
NeoPeptide: an immunoinformatic database of T-cell-defined neoantigens. PMID:31819989
Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. PMID:31816088
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery. PMID:31807684
Rethinking drug design in the artificial intelligence era. PMID:31801986
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. PMID:31800038
DAISY: A Data Information System for accountability under the General Data Protection Regulation. PMID:31800037
Species occurrence of ticks in South America, and interactions with biotic and abiotic traits. PMID:31796749
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Leveraging real-world data to investigate multiple sclerosis disease behavior, prognosis, and treatment. PMID:31778094
A structured open data collection on occupant behaviour in buildings. PMID:31772182
Proposed minimum information guideline for kidney disease-research and clinical data reporting: a cross-sectional study. PMID:31772086
The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years. PMID:31768399
Experimental Design and Sample Preparation in Forest Tree Metabolomics. PMID:31766588
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Assessing the feasibility and impact of specially adapted exercise interventions, aimed at improving the multi-dimensional health and functional capacity of frail geriatric hospital inpatients: protocol for a feasibility study. PMID:31753876
Towards Prepared mums (TOP-mums) for a healthy start, a lifestyle intervention for women with overweight and a child wish: study protocol for a randomised controlled trial in the Netherlands. PMID:31748290
On the difficulties of being rigorous in environmental geochemistry studies: some recommendations for designing an impactful paper. PMID:31745782
PHI-base: the pathogen-host interactions database. PMID:31733065
Data-Driven Materials Science: Status, Challenges, and Perspectives. PMID:31728276
The OncoLifeS data-biobank for oncology: a comprehensive repository of clinical data, biological samples, and the patient's perspective. PMID:31727094
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. PMID:31725862
Data Science in Environmental Health Research. PMID:31723546
A deafening silence: a lack of data and reproducibility in published bioacoustics research? PMID:31723333
The European Nucleotide Archive in 2019. PMID:31722421
Translational Health Disparities Research in a Data-Rich World. PMID:31720554
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
The Dundee Resource for Sequence Analysis and Structure Prediction. PMID:31710725
Host-associated microbiomes drive structure and function of marine ecosystems. PMID:31710600
Unlocking the Power of Artificial Intelligence and Big Data in Medicine. PMID:31702565
BioModels-15 years of sharing computational models in life science. PMID:31701150
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. PMID:31701147
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. PMID:31701143
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Effective Phenotyping Applications Require Matching Trait and Platform and More Attention to Theory. PMID:31695718
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources. PMID:31677972
Annot: a Django-based sample, reagent, and experiment metadata tracking system. PMID:31675914
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv. PMID:31675414
FACT and FAIR with Big Data allows objectivity in science: The view of crystallography. PMID:31673568
The Personal Genome Project-UK, an open access resource of human multi-omics data. PMID:31672996
The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways. PMID:31672983
Making multi-omics data accessible to researchers. PMID:31672978
Collaborative National Quality and Efficacy Registry (CONQUER) for Scleroderma: outcomes from a multicenter US-based systemic sclerosis registry. PMID:31667644
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
ProteomicsDB: a multi-omics and multi-organism resource for life science research. PMID:31665479
Analytic Correlation Filtration: A New Tool to Reduce Analytical Complexity of Metabolomic Datasets. PMID:31653057
Key challenges facing data-driven multicellular systems biology. PMID:31648301
Measuring sustainability of seed-funded earth science informatics projects. PMID:31644537
Distributed radiomics as a signature validation study using the Personal Health Train infrastructure. PMID:31641134
"Après Mois, Le Déluge": Preparing for the Coming Data Flood in the MRI-Guided Radiotherapy Era. PMID:31632914
Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. PMID:31626635
Computational approaches to therapeutic antibody design: established methods and emerging trends. PMID:31626279
Ten simple rules to aid in achieving a vision. PMID:31622329
Data - from objects to assets. PMID:31616093
Statistical learning goes beyond the d-band model providing the thermochemistry of adsorbates on transition metals. PMID:31615991
The use or generation of biomedical data and existing medicines to discover and establish new treatments for patients with rare diseases - recommendations of the IRDiRC Data Mining and Repurposing Task Force. PMID:31615551
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
EMR-integrated minimal core dataset for routine health care and multiple research settings: A case study for neuroinflammatory demyelinating diseases. PMID:31613917
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
Six Laws of Open Source Drug Discovery. PMID:31612602
odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments. PMID:31611781
FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research. PMID:31608767
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. PMID:31597973
Technical Note: Ontology-guided radiomics analysis workflow (O-RAW). PMID:31580484
Bringing Open Data to Whole Slide Imaging. PMID:31579322
Building Open Access to Research (OAR) Data Infrastructure at NIST. PMID:31579260
Opportunities for Improved Disease Surveillance and Control by Use of Integrated Data on Animal and Human Health. PMID:31572735
The metaRbolomics Toolbox in Bioconductor and beyond. PMID:31548506
Signaling the trustworthiness of science. PMID:31548409
The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PMID:31545807
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software. PMID:31544213
The Future of Digital Sequence Information for Plant Genetic Resources for Food and Agriculture. PMID:31543884
Evaluating FAIR maturity through a scalable, automated, community-governed framework. PMID:31541130
FAIR adoption, assessment and challenges at UniProt. PMID:31541106
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. PMID:31527408
Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing. PMID:31522294
scOrange-a tool for hands-on training of concepts from single-cell data analytics. PMID:31510695
Research applications of primary biodiversity databases in the digital age. PMID:31509534
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. PMID:31506435
The path of biomolecular mass spectrometry into open research. PMID:31501439
Preregistration of Analyses of Preexisting Data. PMID:31497308
Open Up - the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science. PMID:31497307
The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. PMID:31481752
Creating reproducible pharmacogenomic analysis pipelines. PMID:31481707
FABIO-The Construction of the Food and Agriculture Biomass Input-Output Model. PMID:31479245
Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials. PMID:31471301
Spatial and temporal tools for building a human cell atlas. PMID:31465255
Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data. PMID:31459544
Applicability of Tail Corrections in the Molecular Simulations of Porous Materials. PMID:31442035
The "All of Us" Research Program. PMID:31412182
PlatformTM, a standards-based data custodianship platform for translational medicine research. PMID:31409798
Opinion: To advance sustainable stewardship, we must document not only biodiversity but geodiversity. PMID:31409742
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming. PMID:31392324
Quantifying the impact of public omics data. PMID:31383865
Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection. PMID:31358775
Food Composition at Present: New Challenges. PMID:31349634
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
Assessing the feasibility and impact of an adapted resistance training intervention, aimed at improving the multi-dimensional health and functional capacity of frail older adults in residential care settings: protocol for a feasibility study. PMID:31321070
Phenotype annotation with the ontology of microbial phenotypes (OMP). PMID:31307550
Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications. PMID:31307129
Pharmacogenomics Clinical Annotation Tool (PharmCAT). PMID:31306493
A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. PMID:31302153
RD-RAP: beyond rare disease patient registries, devising a comprehensive data and analytic framework. PMID:31300021
Use cases, best practice and reporting standards for metabolomics in regulatory toxicology. PMID:31292445
iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences. PMID:31289831
Journal of Cheminformatics, ORCID, and GitHub. PMID:31281945
Biodiversidata: An Open-Access Biodiversity Database for Uruguay. PMID:31274982
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. PMID:31272374
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. PMID:31263868
The Human Brain Project-Synergy between neuroscience, computing, informatics, and brain-inspired technologies. PMID:31260438
Preparing healthcare delivery organizations for managing computable knowledge. PMID:31245601
Desiderata for sharable computable biomedical knowledge for learning health systems. PMID:31245589
The Knowledge Object Reference Ontology (KORO): A formalism to support management and sharing of computable biomedical knowledge for learning health systems. PMID:31245583
Progress update from the hippocampal subfields group. PMID:31245529
Open Humans: A platform for participant-centered research and personal data exploration. PMID:31241153
Radiomics in nuclear medicine: robustness, reproducibility, standardization, and how to avoid data analysis traps and replication crisis. PMID:31240330
EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. PMID:31239435
A Comprehensive Framework to Capture the Arcana of Neuroimaging Analysis. PMID:31236848
Barriers to accessing public cancer genomic data. PMID:31222016
Organizing phenotypic data-a semantic data model for anatomy. PMID:31221226
Crop Phenomics: Current Status and Perspectives. PMID:31214228
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. PMID:31210270
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. PMID:31195976
An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content. PMID:31181762
The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis. PMID:31178829
Facilitating validation of prediction models: a comparison of manual and semi-automated validation using registry-based data of breast cancer patients in the Netherlands. PMID:31176362
Credit data generators for data reuse. PMID:31164773
Make scientific data FAIR. PMID:31164768
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594
NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. PMID:31159440
MENDA: a comprehensive curated resource of metabolic characterization in depression. PMID:31157825
From data sharing to data publishing [version 2; peer review: 2 approved, 1 approved with reservations]. PMID:31157322
Practical Solutions for Sharing Data and Materials From Psychological Research. PMID:31157320
An overview of publicly available patient-centered prostate cancer datasets. PMID:31143673
The Integrative Human Microbiome Project. PMID:31142853
How to use relevant data for maximal benefit with minimal risk: digital health data governance to protect vulnerable populations in low-income and middle-income countries. PMID:31139457
Catalysis-Hub.org, an open electronic structure database for surface reactions. PMID:31138816
Five years of Scientific Data. PMID:31138807
The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. PMID:31123325
TB DEPOT (Data Exploration Portal): A multi-domain tuberculosis data analysis resource. PMID:31120982
European Society of Paediatric Radiology 2019 strategic research agenda: improving imaging for tomorrow's children. PMID:31115616
Responsible Data Governance of Neuroscience Big Data. PMID:31110477
Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets. PMID:31094000
A global, empirical, harmonised dataset of soil organic carbon changes under perennial crops. PMID:31086193
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
DrugComb: an integrative cancer drug combination data portal. PMID:31066443
Envisioning data sharing for the biocomputing community. PMID:31065349
Putting FAIR Evidence into Practice. PMID:31062227
MVApp-Multivariate Analysis Application for Streamlined Data Analysis and Curation. PMID:31061104
Advancing Biomarker Development Through Convergent Engagement: Summary Report of the 2nd International Danube Symposium on Biomarker Development, Molecular Imaging and Applied Diagnostics; March 14-16, 2018; Vienna, Austria. PMID:31049831
Datastorr: a workflow and package for delivering successive versions of 'evolving data' directly into R. PMID:31042286
Open access image repositories: high-quality data to enable machine learning research. PMID:31040006
A consensus guide to capturing the ability to inhibit actions and impulsive behaviors in the stop-signal task. PMID:31033438
Psychology, not technology, is our biggest challenge to open digital morphology data. PMID:31028285
Head and Neck Cancer Adaptive Radiation Therapy (ART): Conceptual Considerations for the Informed Clinician. PMID:31027643
MIReAD, a minimum information standard for reporting arthropod abundance data. PMID:31024009
More Than the Sum of the Respiratory Events: Personalized Medicine Approaches for Obstructive Sleep Apnea. PMID:31022356
To clean or not to clean phenotypic datasets for outlier plants in genetic analyses? PMID:31020325
Improving the Utility of the Tox21 Dataset by Deep Metadata Annotations and Constructing Reusable Benchmarked Chemical Reference Signatures. PMID:31018579
The lab management practices of "Research Exemplars" that foster research rigor and regulatory compliance: A qualitative study of successful principal investigators. PMID:31017929
Review: New sensors and data-driven approaches-A path to next generation phenomics. PMID:31003608
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. PMID:30999855
What is a Medical Information Commons? PMID:30994065
FAIR data needed to liberate hepatitis B virus (HBV) from the catch-22 of neglect. PMID:30992982
The 2019 mathematical oncology roadmap. PMID:30991381
A Roadmap for Foundational Research on Artificial Intelligence in Medical Imaging: From the 2018 NIH/RSNA/ACR/The Academy Workshop. PMID:30990384
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
The Natural History Museum Data Portal. PMID:30985890
International collaborative actions and transparency to understand, diagnose, and develop therapies for rare diseases. PMID:30979709
Reproducible big data science: A case study in continuous FAIRness. PMID:30973881
A review of attitudes towards the reuse of health data among people in the European Union: The primacy of purpose and the common good. PMID:30961905
FAIRsharing as a community approach to standards, repositories and policies. PMID:30940948
Targeted therapies for congenital myasthenic syndromes: systematic review and steps towards a treatabolome. PMID:30931400
Quant Data Science meets Dexterous Artistry. PMID:30923735
Ten principles for machine-actionable data management plans. PMID:30921316
An analysis and metric of reusable data licensing practices for biomedical resources. PMID:30917137
Evaluating reproducibility of AI algorithms in digital pathology with DAPPER. PMID:30917113
Anticipating innovations in structural biology. PMID:30912485
Real-World Evidence Gathering in Oncology: The Need for a Biomedical Big Data Insight-Providing Federated Network. PMID:30906740
BrAPI-an application programming interface for plant breeding applications. PMID:30903186
Connecting data and expertise: a new alliance for biodiversity knowledge. PMID:30886531
From Big Data to Precision Medicine. PMID:30881956
From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research. PMID:30881299
Patients to learn from: on the need for systematic integration of research and care in academic health care. PMID:30873488
Lightweight data management with dtool. PMID:30867992
Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive. PMID:30864322
Interoperable and scalable data analysis with microservices: applications in metabolomics. PMID:30851093
A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics. PMID:30841575
Data science for the scientific life cycle. PMID:30839275
Critical review of reporting of the data analysis step in metabolomics. PMID:30830321
Sustainability considerations for clinical and translational research informatics infrastructure. PMID:30828467
FAIRness and Usability for Open-access Omics Data Systems. PMID:30815061
Clinical trials in radiology and data sharing: results from a survey of the European Society of Radiology (ESR) research committee. PMID:30810796
Brain-wide distribution of reporter expression in five transgenic tetracycline-transactivator mouse lines. PMID:30806643
Precision health: Advancing symptom and self-management science. PMID:30795850
Data Dissemination: Shortening the Long Tail of Traumatic Brain Injury Dark Data. PMID:30794049
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. PMID:30792636
The variable quality of metadata about biological samples used in biomedical experiments. PMID:30778255
Term sets: A transparent and reproducible representation of clinical code sets. PMID:30763407
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. PMID:30763315
Reliable novelty: New should not trump true. PMID:30753184
An open source web application for distributed geospatial data exploration. PMID:30747919
RepetDB: a unified resource for transposable element references. PMID:30719103
Annotation of gene product function from high-throughput studies using the Gene Ontology. PMID:30715275
Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research. PMID:30715273
Translational Health Disparities Research in a Data-Rich World. PMID:30699034
Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. PMID:30692868
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data. PMID:30691868
mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. PMID:30688441
The principles of tomorrow's university. PMID:30687499
Data Science for Child Health. PMID:30686480
Genetic and environmental risk factors for chronic kidney disease. PMID:30675423
Serverless OpenHealth at data commons scale-traversing the 20 million patient records of New York's SPARCS dataset in real-time. PMID:30671301
P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data. PMID:30667224
From Data Silos to Standardized, Linked, and FAIR Data for Pharmacovigilance: Current Advances and Challenges with Observational Healthcare Data. PMID:30666591
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PMID:30653494
The PLOS ONE collection on machine learning in health and biomedicine: Towards open code and open data. PMID:30645625
Integration of "omics" Data and Phenotypic Data Within a Unified Extensible Multimodal Framework. PMID:30631270
EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. PMID:30629718
An ontological foundation for ocular phenotypes and rare eye diseases. PMID:30626441
National Neuroinformatics Framework for Canadian Consortium on Neurodegeneration in Aging (CCNA). PMID:30622468
The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. PMID:30621600
Prospects and challenges for clinical decision support in the era of big data. PMID:30613823
Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur. PMID:30597007
Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PMID:30596645
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
Mining data and metadata from the gene expression omnibus. PMID:30594974
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. PMID:30576493
Cloud-based relational database for multimodal animal data. PMID:30576483
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Data citation: what, when, why? PMID:30559142
DAWN: a resource for yielding insights into the diversity among wheat genomes. PMID:30558550
ProvCaRe: Characterizing scientific reproducibility of biomedical research studies using semantic provenance metadata. PMID:30545485
Eleven quick tips to build a usable REST API for life sciences. PMID:30543619
PhenoMeNal: processing and analysis of metabolomics data in the cloud. PMID:30535405
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database. PMID:30515166
An annotated test-retest collection of prostate multiparametric MRI. PMID:30512014
Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection. PMID:30512010
Are Publicly Funded Health Databases Geographically Detailed and Timely Enough to Support Patient-Centered Outcomes Research? PMID:30511288
A System for an Accountable Data Analysis Process in R. PMID:30505573
Computational aspects underlying genome to phenome analysis in plants. PMID:30500991
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Building a local community of practice in scientific programming for life scientists. PMID:30485260
Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae. PMID:30480660
A nomenclature and classification for the congenital myasthenic syndromes: preparing for FAIR data in the genomic era. PMID:30477555
It's Hard to Avoid Avoidance: Uncoupling the Evolutionary Connection between Plant Growth, Productivity and Stress "Tolerance". PMID:30463352
Harmonizing semantic annotations for computational models in biology. PMID:30462164
The CAMH Neuroinformatics Platform: A Hospital-Focused Brain-CODE Implementation. PMID:30459587
A data citation roadmap for scientific publishers. PMID:30457573
A reference set of curated biomedical data and metadata from clinical case reports. PMID:30457569
Developing a healthcare dataset information resource (DIR) based on Semantic Web. PMID:30453940
Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies. PMID:30450039
BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. PMID:30447998
Leveraging mobile health applications for biomedical research and citizen science: a scoping review. PMID:30445467
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. PMID:30445434
X-search: an open access interface for cross-cohort exploration of the National Sleep Research Resource. PMID:30424756
Ontology-based validation and identification of regulatory phenotypes. PMID:30423068
Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools. PMID:30419504
Essential Characteristics of Pharmacogenomics Study Publications. PMID:30406943
Data integration strategies for predictive analytics in precision medicine. PMID:30387695
Automated Metadata Suggestion During Repository Submission. PMID:30382537
Neurotrauma as a big-data problem. PMID:30379703
A call for public archives for biological image data. PMID:30377375
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
The Pfam protein families database in 2019. PMID:30357350
Long-term preservation of biomedical research data. PMID:30356367
A large-scale dataset of in vivo pharmacology assay results. PMID:30351302
The Dat Project, an open and decentralized research data tool. PMID:30351300
Overview of the BioCreative VI text-mining services for Kinome Curation Track. PMID:30329035
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Cross-Linguistic Data Formats, advancing data sharing and re-use in comparative linguistics. PMID:30325347
Project Tycho 2.0: a repository to improve the integration and reuse of data for global population health. PMID:30321381
ClinGen Allele Registry links information about genetic variants. PMID:30311374
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. PMID:30311252
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. PMID:30299502
A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts. PMID:30295669
The Italian neuromuscular registry: a coordinated platform where patient organizations and clinicians collaborate for data collection and multiple usage. PMID:30286784
Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics. PMID:30280721
Seasonal variation of secondary metabolites in nine different bryophytes. PMID:30271570
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis. PMID:30256983
Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART. PMID:30256906
An open database of productivity in Vietnam's social sciences and humanities for public use. PMID:30251992
Role of supplementary material in biomedical journal articles: surveys of authors, reviewers and readers. PMID:30249629
Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. PMID:30248891
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Treatment data and technical process challenges for practical big data efforts in radiation oncology. PMID:30226286
Model organism data evolving in support of translational medicine. PMID:30224793
Enhancing diversity to reduce health information disparities and build an evidence base for genomic medicine. PMID:30209973
A bioinformatics approach to identifying Wolbachia infections in arthropods. PMID:30202647
DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R. PMID:30186360
Eight years after an international workshop on myotonic dystrophy patient registries: case study of a global collaboration for a rare disease. PMID:30185236
The governance structure for data access in the DIRECT consortium: an innovative medicines initiative (IMI) project. PMID:30182269
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. PMID:30166985
MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians. PMID:30165396
Controlled feature selection and compressive big data analytics: Applications to biomedical and health studies. PMID:30161148
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes. PMID:30152810
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data. PMID:30130366
Conclusion: harmonisation in genomic and health data sharing for research: an impossible dream? PMID:30120573
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. PMID:30115101
Mind the Gap: From Tool to Knowledge Base. PMID:30102551
Genetic Simulation Resources and the GSR Certification Program. PMID:30101297
Glycomics@ExPASy: Bridging the Gap. PMID:30097532
A systems genetics resource and analysis of sleep regulation in the mouse. PMID:30091978
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
Recommendations for Improving the Quality of Rare Disease Registries. PMID:30081484
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array. PMID:30054510
Digital open science-Teaching digital tools for reproducible and transparent research. PMID:30048447
Fostering population-based cohort data discovery: The Maelstrom Research cataloguing toolkit. PMID:30040866
Smart Medical Information Technology for Healthcare (SMITH). PMID:30016815
MIRACUM: Medical Informatics in Research and Care in University Medicine. PMID:30016814
HiGHmed - An Open Platform Approach to Enhance Care and Research across Institutional Boundaries. PMID:30016813
Data Integration for Future Medicine (DIFUTURE). PMID:30016812
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers. PMID:30011302
The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. PMID:30003207
OpenPVSignal: Advancing Information Search, Sharing and Reuse on Pharmacovigilance Signals via FAIR Principles and Semantic Web Technologies. PMID:29997499
Data on Determinants Are Needed to Curb the Sedentary Epidemic in Europe. Lessons Learnt from the DEDIPAC European Knowledge Hub. PMID:29973511
Associations of self-reported physical activity and depression in 10,000 Irish adults across harmonised datasets: a DEDIPAC-study. PMID:29960595
Community-Driven Data Analysis Training for Biology. PMID:29953864
iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. PMID:29944754
A design framework and exemplar metrics for FAIRness. PMID:29944145
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Cloud computing applications for biomedical science: A perspective. PMID:29902176
Review and gap analysis: molecular pathways leading to fetal alcohol spectrum disorders. PMID:29892052
Brain-CODE: A Secure Neuroinformatics Platform for Management, Federation, Sharing and Analysis of Multi-Dimensional Neuroscience Data. PMID:29875648
Changing Trends in Computational Drug Repositioning. PMID:29874824
A guideline for reporting experimental protocols in life sciences. PMID:29868256
VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. PMID:29867956
A Science Products Inventory for Citizen-Science Planning and Evaluation. PMID:29867254
A Science Products Inventory for Citizen-Science Planning and Evaluation. PMID:29867253
Big data sharing and analysis to advance research in post-traumatic epilepsy. PMID:29864492
The National Sleep Research Resource: towards a sleep data commons. PMID:29860441
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. PMID:29854196
Big data in healthcare - the promises, challenges and opportunities from a research perspective: A case study with a model database. PMID:29854102
Sharing and reusing cell image data. PMID:29851565
Integrating Multimodal Radiation Therapy Data into i2b2. PMID:29847842
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
QTLTableMiner++: semantic mining of QTL tables in scientific articles. PMID:29801439
Development of an International Canine Spinal Cord Injury observational registry: a collaborative data-sharing network to optimize translational studies of SCI. PMID:29795173
Progress Toward Cancer Data Ecosystems. PMID:29794537
The FAIR guiding principles for data stewardship: fair enough? PMID:29777206
Caring for individuals with a difference of sex development (DSD): a Consensus Statement. PMID:29769693
The electronic Rothamsted Archive (e-RA), an online resource for data from the Rothamsted long-term experiments. PMID:29762552
Pre-Clinical Testing of Therapies for Traumatic Brain Injury. PMID:29756522
ERMrest: A Collaborative Data Catalog with Fine Grain Access Control. PMID:29756002
Experiences with Deriva: An Asset Management Platform for Accelerating eScience. PMID:29756001
ONS: an ontology for a standardized description of interventions and observational studies in nutrition. PMID:29736190
Current Challenges in Plant Eco-Metabolomics. PMID:29734799
Herbarium data: Global biodiversity and societal botanical needs for novel research. PMID:29732255
Data sharing in PLOS ONE: An analysis of Data Availability Statements. PMID:29719004
A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository. PMID:29706851
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. PMID:29704307
Integrated Chemometrics and Statistics to Drive Successful Proteomics Biomarker Discovery. PMID:29701723
Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. PMID:29700073
Biology Needs Evolutionary Software Tools: Let's Build Them Right. PMID:29688462
Signalling maps in cancer research: construction and data analysis. PMID:29688383
YummyData: providing high-quality open life science data. PMID:29688370
Micropublication: incentivizing community curation and placing unpublished data into the public domain. PMID:29688367
Prevention of data duplication for high throughput sequencing repositories. PMID:29688363
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing. PMID:29688348
Machine learning for nuclear cardiology: The way forward. PMID:29679221
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Eleven quick tips for finding research data. PMID:29649206
High-throughput mouse phenomics for characterizing mammalian gene function. PMID:29626206
An open experimental database for exploring inorganic materials. PMID:29611842
Cell type discovery using single-cell transcriptomics: implications for ontological representation. PMID:29590361
Minimizing publication bias in Epilepsia Open: Negative or confirmatory studies and preliminary reports. PMID:29588931
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. PMID:29579036
Ten steps to get started in Genome Assembly and Annotation. PMID:29568489
DASH, the data and specimen hub of the National Institute of Child Health and Human Development. PMID:29557977
A FAIR guide for data providers to maximise sharing of human genomic data. PMID:29543799
Hidden concerns of sharing research data by low/middle-income country scientists. PMID:29503603
Pharmacognosy in the digital era: shifting to contextualized metabolomics. PMID:29499476
When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors. PMID:29495643
RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases. PMID:29487416
Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. PMID:29485625
High-quality science requires high-quality open data infrastructure. PMID:29485623
Interoperable and accessible census and survey data from IPUMS. PMID:29485621
Responsible practices for data sharing. PMID:29481108
Data sharing in psychology. PMID:29481105
Refining the aggregate exposure pathway. PMID:29465734
[Big data from clinical routine]. PMID:29453548
American Heart Association Precision Medicine Platform. PMID:29440193
Toward a Tiered Model to Share Clinical Trial Data and Samples in Precision Oncology. PMID:29435448
A roadmap towards personalized immunology. PMID:29423275
Microkinetics of alcohol reforming for H2 production from a FAIR density functional theory database. PMID:29410476
The RD-Connect Registry & Biobank Finder: a tool for sharing aggregated data and metadata among rare disease researchers. PMID:29396563
Dark data see the light. PMID:29384509
Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health. PMID:29359962
qPortal: A platform for data-driven biomedical research. PMID:29352322
Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology. PMID:29351341
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge. PMID:29322916
Usage of cell nomenclature in biomedical literature. PMID:29322912
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells. PMID:29320760
Balancing the local and the universal in maintaining ethical access to a genomics biobank. PMID:29282045
Data Sharing: Convert Challenges into Opportunities. PMID:29270401
Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. PMID:29267850
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
Fair data for next-generation management of multiple sclerosis. PMID:29254434
Data discovery with DATS: exemplar adoptions and lessons learned. PMID:29228196
Indispensable benefit of independent investigator-driven research in a changing clinical trial landscape. PMID:29226919
Improving average ranking precision in user searches for biomedical research datasets. PMID:29220475
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. PMID:29220453
CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. PMID:29220450
New extension software modules to enhance searching and display of transcriptome data in Tripal databases. PMID:29220446
The international MAQC Society launches to enhance reproducibility of high-throughput technologies. PMID:29220036
Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's disease. PMID:29218889
The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. PMID:29199020
The international nucleotide sequence database collaboration. PMID:29190397
SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles. PMID:29186322
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. PMID:29186302
SATORI: a system for ontology-guided visual exploration of biomedical data repositories. PMID:29186292
Responsible Radiomics Research for Faster Clinical Translation. PMID:29175982
The International Rare Diseases Research Consortium: Policies and Guidelines to maximize impact. PMID:29158551
Ensembl 2018. PMID:29155950
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. PMID:29149325
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. PMID:29144493
Early career researchers want Open Science. PMID:29141654
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD. PMID:29138947
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. PMID:29136241
Using semantics for representing experimental protocols. PMID:29132408
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. PMID:29123641
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. PMID:29106479
Determinants of diet and physical activity (DEDIPAC): a summary of findings. PMID:29100542
dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM. PMID:29092948
Helping to improve the practice of cheminformatics. PMID:29086066
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
ACCESS climate data management. PMID:29067641
Health Data for Public Health: Towards New Ways of Combining Data Sources to Support Research Efforts in Europe. PMID:29063571
Clinical Research Informatics: Contributions from 2016. PMID:29063566
Grappling with the Future Use of Big Data for Translational Medicine and Clinical Care. PMID:29063545
Secondary Use of Patient Data: Review of the Literature Published in 2016. PMID:29063536
Identifying and sharing data for secondary data analysis of physical activity, sedentary behaviour and their determinants across the life course in Europe: general principles and an example from DEDIPAC. PMID:29061620
Plant phenomics: an overview of image acquisition technologies and image data analysis algorithms. PMID:29048559
Parallel sequencing lives, or what makes large sequencing projects successful. PMID:29048533
Neural Network for Nanoscience Scanning Electron Microscope Image Recognition. PMID:29038550
ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. PMID:29036529
A Case for Data Commons: Toward Data Science as a Service. PMID:29033693
Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination. PMID:29025122
Formalizing drug indications on the road to therapeutic intent. PMID:29016968
Chronic disease research in Europe and the need for integrated population cohorts. PMID:28986739
Bioinformatics in the Netherlands: the value of a nationwide community. PMID:28968694
Big data management challenges in health research-a literature review. PMID:28968677
Comprehending the Health Informatics Spectrum: Grappling with System Entropy and Advancing Quality Clinical Research. PMID:28959687
Compliance with minimum information guidelines in public metabolomics repositories. PMID:28949328
Looking back: forward looking. PMID:28938718
Tapping the Vast Potential of the Data Deluge in Small-scale Food-Animal Production Businesses: Challenges to Near Real-time Data Analysis and Interpretation. PMID:28932740
The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training. PMID:28928938
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
Perspective: An Extension of the STROBE Statement for Observational Studies in Nutritional Epidemiology (STROBE-nut): Explanation and Elaboration. PMID:28916567
Perspective: Essential Study Quality Descriptors for Data from Nutritional Epidemiologic Research. PMID:28916566
Reporting to Improve Reproducibility and Facilitate Validity Assessment for Healthcare Database Studies V1.0. PMID:28913963
The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis. PMID:28904183
Data Management Rubric for Video Data in Organismal Biology. PMID:28881939
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. PMID:28870259
MRC Centre Neuromuscular Biobank (Newcastle and London): Supporting and facilitating rare and neuromuscular disease research worldwide. PMID:28864117
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action. PMID:28781745
Scientific user requirements for a herbarium data portal. PMID:28781551
Challenges for visualizing three-dimensional data in genomic browsers. PMID:28771695
Four simple recommendations to encourage best practices in research software. PMID:28751965
Translational Stroke Research: Vision and Opportunities. PMID:28751554
Open data: support from Swiss funder. PMID:28748938
Building the biomedical data science workforce. PMID:28715407
A community proposal to integrate proteomics activities in ELIXIR. PMID:28713550
The metagenomic data life-cycle: standards and best practices. PMID:28637310
Biomedical text mining for research rigor and integrity: tasks, challenges, directions. PMID:28633401
Identification of miRNAs involved in DRG neurite outgrowth and their putative targets. PMID:28626869
Open for business. PMID:28608857
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
Developing a data sharing community for spinal cord injury research. PMID:28576567
Finding useful data across multiple biomedical data repositories using DataMed. PMID:28546571
quantGenius: implementation of a decision support system for qPCR-based gene quantification. PMID:28545393
Towards a systems approach for chronic diseases, based on health state modeling. PMID:28529704
Medical Image Data and Datasets in the Era of Machine Learning-Whitepaper from the 2016 C-MIMI Meeting Dataset Session. PMID:28516233
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. PMID:28501646
Discovering and linking public omics data sets using the Omics Discovery Index. PMID:28486464
Progress in promoting data sharing in public health emergencies. PMID:28479616
Reproducible and reusable research: are journal data sharing policies meeting the mark? PMID:28462024
Bridging the translational innovation gap through good biomarker practice. PMID:28450744
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Guideline recommendations for diagnosis and clinical management of Ring14 syndrome-first report of an ad hoc task force. PMID:28399932
Should biomedical research be like Airbnb? PMID:28388615
Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion. PMID:28377873
Envisioning the future of 'big data' biomedicine. PMID:28366789
The 'Molecule of the Month' Website-An Extraordinary Chemistry Educational Resource Online for over 20 Years. PMID:28353654
Reproducibility of histopathological findings in experimental pathology of the mouse: a sorry tail. PMID:28328876
An assessment of the quality of the I-DSD and the I-CAH registries - international registries for rare conditions affecting sex development. PMID:28320446
A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. PMID:28302053
Analysis of the time and workers needed to conduct systematic reviews of medical interventions using data from the PROSPERO registry. PMID:28242767
Integration of EGA secure data access into Galaxy. PMID:28232859
SCALEUS: Semantic Web Services Integration for Biomedical Applications. PMID:28214993
A metadata-driven approach to data repository design. PMID:28184255
Perspectives and expectations in structural bioinformatics of metalloproteins. PMID:28168746
Propelling the paradigm shift from reductionism to systems nutrition. PMID:28138347
Big and disparate data: considerations for pediatric consortia. PMID:28134706
Irreproducibility of published bioscience research: Diagnosis, pathogenesis and therapy. PMID:28123930
Cyberinfrastructure for Open Science at the Montreal Neurological Institute. PMID:28111547
Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders. PMID:28018353
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. PMID:27924018
Towards an open grapevine information system. PMID:27917288
PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. PMID:27915230
Blowing a breath of fresh share on data. PMID:27909938
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. PMID:27899646
Measures for interoperability of phenotypic data: minimum information requirements and formatting. PMID:27843484
Empowering pharmacoinformatics by linked life science data. PMID:27830428
Host and Environmental Factors Influencing Individual Human Cytokine Responses. PMID:27814508
Big Data in radiation therapy: challenges and opportunities. PMID:27781485
Redefining 'stress resistance genes', and why it matters. PMID:27702993
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
The health care and life sciences community profile for dataset descriptions. PMID:27602295
Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution. PMID:27570508
European Open Science Cloud. PMID:27463394
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. PMID:27433158
Making sense of big data in health research: Towards an EU action plan. PMID:27338147
Reproducibility will only come with data liberation. PMID:27194726
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. PMID:27189610
Let referees see the data. PMID:27164552
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research PubMed citations: 36.

36 articles citing: FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata. PMID:35836998
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. PMID:35759037
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. PMID:35671510
FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. PMID:35418585
Exploring the evolution of biochemical models at the network level. PMID:35312734
Scalp Acupuncture and Treadmill Training Inhibits Neuronal Apoptosis through Activating cIAP1 in Cerebral Ischemia Rats. PMID:34804173
Electroacupuncture Preconditioning Reduces Oxidative Stress in the Acute Phase of Cerebral Ischemia-Reperfusion in Rats by Regulating Iron Metabolism Pathways. PMID:34790244
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
[Making COVID-19 research data more accessible-building a nationwide information infrastructure]. PMID:34297162
Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node. PMID:34280231
An Overview of Systematic Reviews of Using Chinese Medicine to Treat Polycystic Ovary Syndrome. PMID:34135988
Diet and Life Stage-Associated Lipidome Remodeling in Atlantic Salmon. PMID:33754702
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. PMID:33589928
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species. PMID:33324679
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. PMID:33090199
A workflow to build PBTK models for novel species. PMID:33033842
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato. PMID:32709858
Systems biology of acidophile biofilms for efficient metal extraction. PMID:32636389
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. PMID:32371892
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. PMID:32341162
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
A combined experimental and modelling approach for the Weimberg pathway optimisation. PMID:32107375
Organizing genome engineering for the gigabase scale. PMID:32019919
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Harmonizing semantic annotations for computational models in biology. PMID:30462164
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
Community-driven roadmap for integrated disease maps. PMID:29688273
A roadmap towards personalized immunology. PMID:29423275
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT. PMID:29150517
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
SEEK: a systems biology data and model management platform PubMed citations: 30.

30 articles citing: SEEK: a systems biology data and model management platform

NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata. PMID:35836998
ELIXIR biovalidator for semantic validation of life science metadata. PMID:35380605
ISA API: An open platform for interoperable life science experimental metadata. PMID:34528664
[Making COVID-19 research data more accessible-building a nationwide information infrastructure]. PMID:34297162
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. PMID:34083542
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. PMID:33589928
IOCBIO Kinetics: An open-source software solution for analysis of data traces. PMID:33351800
Making experimental data tables in the life sciences more FAIR: a pragmatic approach. PMID:33319910
A workflow to build PBTK models for novel species. PMID:33033842
Ten simple rules on how to write a standard operating procedure. PMID:32881868
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results. PMID:32815545
Publishing reproducible dynamic kinetic models. PMID:32793969
APRICOT: Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools. PMID:32777825
Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs. PMID:31423466
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. PMID:30271948
Norwegian e-Infrastructure for Life Sciences (NeLS). PMID:30271575
Emerging whole-cell modeling principles and methods. PMID:29275251
Protein abundance of AKT and ERK pathway components governs cell type-specific regulation of proliferation. PMID:28123004
Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. PMID:28031032
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. PMID:27899646
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. PMID:27765035
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Are Randomized Controlled Trials the (G)old Standard? From Clinical Intelligence to Prescriptive Analytics. PMID:27383622
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
The FAIR Guiding Principles for scientific data management and stewardship. PMID:26978244
The evolution of standards and data management practices in systems biology. PMID:26700851
An algorithm to detect and communicate the differences in computational models describing biological systems. PMID:26490504
Systems Medicine: The Application of Systems Biology Approaches for Modern Medical Research and Drug Development. PMID:26357572
The SEEK: a platform for sharing data and models in systems biology PubMed citations: 15.

15 articles citing: The SEEK: a platform for sharing data and models in systems biology

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects. PMID:33334310
Publishing reproducible dynamic kinetic models. PMID:32793969
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus. PMID:28692669
GESDB: a platform of simulation resources for genetic epidemiology studies. PMID:27242038
Taking Bioinformatics to Systems Medicine. PMID:26677177
SEEK: a systems biology data and model management platform. PMID:26160520
A review on computational systems biology of pathogen-host interactions. PMID:25914674
Improving collaboration by standardization efforts in systems biology. PMID:25538939
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
A digital repository with an extensible data model for biobanking and genomic analysis management. PMID:25077808
The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences. PMID:24682735
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
openBIS: a flexible framework for managing and analyzing complex data in biology research. PMID:22151573
openBIS ELN-LIMS: an open-source database for academic laboratories PubMed citations: 9.

9 articles citing: openBIS ELN-LIMS: an open-source database for academic laboratories

Making the collective knowledge of chemistry open and machine actionable. PMID:35379967
SwissPKcdw - A clinical data warehouse for the optimization of pediatric dosing regimens. PMID:34729953
IOCBIO Kinetics: An open-source software solution for analysis of data traces. PMID:33351800
Menoci: lightweight extensible web portal enhancing data management for biomedical research projects. PMID:33334310
Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. PMID:31260318
Plant Synthetic Biology: Quantifying the "Known Unknowns" and Discovering the "Unknown Unknowns". PMID:30630870
Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory. PMID:29201138
Chemotion ELN: an Open Source electronic lab notebook for chemists in academia. PMID:29086216
Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks. PMID:27098025

http://dx.doi.org/10.1093/nar/1941

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version: FAIRsharing.org: FAIRDOMHub; FAIRDOMHub; DOI: https://doi.org/10.25504/FAIRsharing.nnvcr9; Last edited: Aug. 1, 2020, 7:24 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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proteomics
metasource: re3data.org
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metasource: re3data.org
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metasource: re3data.org
version: re3data.org: FAIRDOMHub; editing status 2022-05-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3ZW6Q last accessed: 2022-11-04

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