A5043231938- Research Data Management Practices
- Scientific Computing and Data Management
- Data Quality and Management
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Big Data and Business Intelligence
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Topic Modeling
- Natural Language Processing Techniques
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Advanced biosensing and bioanalysis techniques
- COVID-19 diagnosis using AI
- Genomics and Rare Diseases
- Geochemistry and Geologic Mapping
- Big Data Technologies and Applications
- Bacterial Genetics and Biotechnology
- demographic modeling and climate adaptation
- Evolutionary Game Theory and Cooperation
- Artificial Intelligence in Healthcare and Education
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
Centre for Human Drug Research
2023-2025
GO FAIR Foundation
2021-2025
Leiden University
2014-2024
Leiden University Medical Center
2013-2023
University of Twente
2023
Royal Netherlands Meteorological Institute
2023
Weatherford College
2023
Vrije Universiteit Amsterdam
2022
Czech Technical University in Prague
2022
General Oceanics (United States)
2022
There is an urgent need to improve the infrastructure supporting reuse of scholarly data. A diverse set stakeholders-representing academia, industry, funding agencies, and publishers-have come together design jointly endorse a concise measureable principles that we refer as FAIR Data Principles. The intent these may act guideline for those wishing enhance reusability their data holdings. Distinct from peer initiatives focus on human scholar, Principles put specific emphasis enhancing ability...
Abstract The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines tissues using CAGE. Based on manual curation of sample information development an ontology for classification, we assemble the resulting data into a centralized resource ( http://fantom.gsc.riken.jp/5/ ). This contains web-based tools data-access points research community to search extract related samples, genes, promoter activities, factors enhancers...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
The FAIR Principles 1 (https:/
We describe a single RNA sequence that can assume either of two ribozyme folds and catalyze the respective reactions. The share no evolutionary history are completely different, with base pairs (and probably hydrogen bonds) in common. Minor variants this highly active for one or other reaction, be accessed from prototype ribozymes through series neutral mutations. Thus, course evolution, new could arise preexisting folds, without need to carry inactive intermediate sequences. This raises...
Phage display screenings are frequently employed to identify high-affinity peptides or antibodies. Although successful, phage is a laborious technology and notorious for identification of false positive hits. To accelerate improve the selection process, we have Illumina next generation sequencing deeply characterize Ph.D.-7 M13 peptide library before after several rounds biopanning on KS483 osteoblast cells. Sequencing naive one round amplification in bacteria identifies propagation...
Abstract Transparent evaluations of FAIRness are increasingly required by a wide range stakeholders, from scientists to publishers, funding agencies and policy makers. We propose scalable, automatable framework evaluate digital resources that encompasses measurable indicators, open source tools, participation guidelines, which come together accommodate domain relevant community-defined FAIR assessments. The components the are: (1) Maturity Indicators – community-authored specifications...
The FAIR guiding principles aim to enhance the Findability, Accessibility, Interoperability and Reusability of digital resources such as data, for both humans machines. process making data (“FAIRification”) can be described in multiple steps. In this paper, we describe a generic step-by-step FAIRification workflow performed multidisciplinary team guided by stewards. should applicable any type has been developed used “Bring Your Own Data” (BYOD) workshops, well e.g., rare diseases resources....
Data in the life sciences are extremely diverse and stored a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG pathway or UniProt protein data) to that general-purpose FigShare, Zenodo, Dataverse EUDAT). These have widely different levels sensitivity security considerations. For example, clinical observations about genetic mutations patients highly sensitive, while species diversity generally not. The lack uniformity models one repository...
The advances in bioinformatics required to annotate human genomic variants and place them public data repositories have not kept pace with their discovery. Moreover, a law of diminishing returns has begun operate both terms publication submission. Although the continued deposition such domain is essential maximize scientific clinical utility, rewards for sharing are few, representing serious practical impediment To date, two main strategies been adopted as means encourage submission variant...
Safe and sustainable chemicals/materials are critical for achieving European green goals. The novel SSbD framework aims to harmonize assessments during innovation. Here, we discuss the essential role of FAIR data tools in operationalizing SSbD.
The FAIR principles provide guidance on improving the Findability, Accessibility, Interoperability, and Reusability of digital resources. Since publication principles, several workflows have been proposed to support process making data (FAIRification). However, respect uniqueness different communities, both available deliberately designed remain agnostic in terms standards, tools, implementation choices. Consequently, FAIRification needs be properly planned, details must discussed with...
There is a growing need for sensitive and reliable nucleic acid detection methods that are convenient inexpensive. Responsive programmable DNA nanostructures have shown great promise as chemical systems. Here, we describe system employing the triggered self-assembly of novel dendritic nanostructure. The protocol executed autonomously without external intervention. Detection begins when specific, single-stranded target strand (T) triggers hybridization chain reaction (HCR) between two,...
Abstract The limited volume of COVID‐19 data from Africa raises concerns for global genome research, which requires a diversity genotypes accurate disease prediction, including on the provenance new SARS‐CoV‐2 mutations. Virus Outbreak Data Network (VODAN)‐Africa studied possibility increasing production clinical data, finding about ownership, and use health quality treatment at point care. To address this, VODAN developed an architecture to record research collected incidence COVID‐19,...
Global climate change requires urgent and actionable adaptation planning.Current Climate Change Adaptation (CCA) strategies often lack the necessary data other relevant information to be scientifically competent. These limitations can complicate effective action evaluation locally, in combination with regions. The recently awarded FAIR2Adapt Project aims establish a comprehensive FAIR open framework for CCA demonstrate impact of on strategies. By making FAIR, will accelerate actions that are...
dPIDs are an emerging PID technology based on decentralized architectures and self-sovereign identity [1]. containers, forming persistent storage systems where each object is identified by a unique PID. immune to content drift resolves deterministically their mapped content, providing reproducible binding between the (meta)data identifier. As take net-work protocol approach PIDs, implementation of FDOF recommendations may require further explanation [2]. This presentation primer technologies...
Numerous implementations of FAIR Digital Objects (FDOs) are actively emerging and being evaluated against FDO specifications. Here, we focus on the Nanopublication Framework as a possible implementation FDOs. Nanopublications unitary, standardised, self-contained RDF-based knowledge graphs consisting three subgraphs: an assertion graph that includes main content, provenance metadata graph, publication information graph. In thorough analysis specifications (represented by efforts Forum) based...
Abstract “FAIRness” - the degree to which a digital resource is Findable, Accessible, Interoperable, and Reusable aspirational, yet means of reaching it may be defined by increased adherence measurable indicators. We report on production core set semi-quantitative metrics having universal applicability for evaluation FAIRness, rubric within additional can generated community. This effort output from stakeholder-representative group, founded FAIR principles’ co-authors drivers. now seek input...
Abstract It is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer highly idiosyncratic criteria regarding metadata used annotate datasets. Specifically, principles require be “rich” adhere “domain-relevant” community standards. Scientific communities should able define their own machine-actionable templates for that encode these “rich,” discipline-specific elements. We have explored this...