A5004092158- Research Data Management Practices
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Data Quality and Management
- Genomics and Rare Diseases
- Muscle Physiology and Disorders
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Identification and Quantification in Food
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Natural Language Processing Techniques
- Bioinformatics and Genomic Networks
- Renal cell carcinoma treatment
- Genetic Neurodegenerative Diseases
- Genetics and Neurodevelopmental Disorders
- Topic Modeling
- Service-Oriented Architecture and Web Services
- Forensic and Genetic Research
- Network Security and Intrusion Detection
- Rough Sets and Fuzzy Logic
- Digital Media Forensic Detection
- Distributed and Parallel Computing Systems
- Pediatric Urology and Nephrology Studies
Leiden University Medical Center
2015-2024
Leiden University
2014-2021
Fair Isaac Corporation (United States)
2021
Linköping University
2011-2016
Swedish e-Science Research Centre
2012
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...
Abstract Duchenne muscular dystrophy (DMD) is a with high incidence of learning and behavioural problems associated neurodevelopmental disorders. To gain more insights into the role dystrophin in this cognitive phenotype, we performed comprehensive analysis expression patterns isoforms across human brain development, using unique transcriptomic data from Allen Human Brain BrainSpan atlases. Dystrophin show large changes through life pronounced differences between foetal adult brain. The...
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....
The COVID-19 pandemic has challenged healthcare systems and research worldwide. Data is collected all over the world needs to be integrated made available other researchers quickly. However, various heterogeneous information that are used in hospitals can result fragmentation of health data multiple 'silos' not interoperable for analysis. Consequently, clinical observations hospitalised patients prepared reused efficiently timely. There a need adapt management make observational patient...
Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because methods used missed cause in known gene, novel causative gene could not be identified and/or confirmed. To address these challenges, RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates collation, discovery, sharing, and analysis standardized genome-phenome...
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...
ABSTRACT Metadata, data about other digital objects, play an important role in FAIR with a direct relation to all principles. In this paper we present and discuss the Data Point (FDP), software architecture aiming define common approach publish semantically-rich machine-actionable metadata according We core components features of FDP, its provision, criteria evaluate whether application adheres FDP specifications service register, index allow users search for content available FDPs.
The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of rare disease (RD) patient data, scattered among hundreds independent and non-coordinating registries, by establishing standards for integration interoperability. first practical output this effort was a set 16 Common Data Elements (CDEs) that should be implemented all registries. Interoperability, however, requires decisions beyond data elements - including models, formats, semantics....
The genomes of thousands individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data consent captured in different ways stored across many systems organizations. This makes it difficult to discover rare disease patients, reuse for personalized medicine establish cohorts based on specific parameters. FAIR Genomes aims enable NGS by developing metadata standards the descriptions needed FAIRify while also addressing ELSI...
Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step improve patient treatments and create the most adequate tools for personalized medicine. However, growing number of disease-specific brings also new technical challenges. Usually, systems developed as closed silos, with independent formats models, lacking comprehensive mechanisms enable sharing. To tackle challenges, we Semantic Web based solution that...
Abstract Ensuring safe and healthy food is a big challenge due to the complexity of supply chains their vulnerability many internal external factors, including fraud. Recent research has shown that Artificial Intelligence (AI) based algorithms, in particularly data driven Bayesian Network (BN) models, are very suitable as tool predict future fraud hence allowing producers take proper actions avoid such problems occur. Such models become even more powerful when can be used from all actors...
Reproducing the results from a scientific paper can be challenging due to absence of data and computational tools required for their analysis. In addition, details relating procedures used obtain published difficult discern use natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), Research Objects (RO) models are conceptual modelling frameworks that structure such information papers. Computational workflow platforms...
Since their publication in 2016 we have seen a rapid adoption of the FAIR principles many scientific disciplines where inherent value research data and, therefore, importance good management and stewardship, is recognized. This has led to communities asking “What FAIR?” “How are currently?”, questions which were addressed respectively by revisiting emergence metrics. However, early adopters already run into next question: can become (more) question more difficult answer, as do not prescribe...
Abstract Rett syndrome (RTT) is a rare neurological disorder mostly caused by genetic variation in MECP2 . Making new variants and the related phenotypes available provides data for better understanding of disease mechanisms faster identification diagnosis. This is, however, currently hampered lack interoperability between genotype-phenotype databases. Here, we demonstrate on example RTT that making more Findable, Accessible, Interoperable, Reusable (FAIR), can facilitate prioritization...
Existing methods to make data Findable, Accessible, Interoperable, and Reusable (FAIR) are usually carried out in a post hoc manner: after the research project is conducted collected. De-novo FAIRification, on other hand, incorporates FAIRification steps process of project. In medical research, often collected stored via electronic Case Report Forms (eCRFs) Electronic Data Capture (EDC) systems. By implementing de novo such system, reusability and, thus, scalability across projects can be...
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants diseases. Both biological complexity (millions gene-disease associations) the accelerating rate data production necessitate computational approaches to prioritize rationalize relations. Here, we use concept profile technology expose from biomedical literature both explicitly stated (the explicitome) a...
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, 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 another,...
Abstract Background Patient data registries that are FAIR—Findable, Accessible, Interoperable, and Reusable for humans computers—facilitate research across multiple resources. This is particularly relevant to rare diseases, where often scarce scattered. Specific questions can be asked FAIR disease other resources without physically combining the data. Further, implies well-defined, transparent access conditions, which supports making sensitive as open possible closed necessary. Results We...
Data from high throughput experiments often produce far more results than can ever appear in the main text or tables of a single research article. In these cases, majority new associations are archived either as supplemental information an arbitrary format publisher-independent databases that be difficult to find. These data not only lost scientific discourse, but also elusive automated search, retrieval and processing. Here, we use nanopublication model make assertions were concluded...
One of the current challenges in ontology alignment is user involvement process. To obtain high-quality alignments needed for validation matching results as well mapping generation Further, there a need supporting tas ks such matcher selection, combination and tuning. In this paper we introduce conceptual framework that enables natural way. This achieved by introducing different kinds interruptible sessions. The allows partial computations generating suggestions, validations recommendations...
Abstract Despite great strides in the development and wide acceptance of standards for exchanging structured information about genomic variants, there is no corresponding standard phenotypic data, this has impeded sharing computational analysis. Here, we introduce Global Alliance Genomics Health (GA4GH) Phenopacket schema, which supports exchange computable longitudinal case-level diagnosis research all types disease including Mendelian complex genetic diseases, cancer, infectious diseases....
ABSTRACT While the FAIR Principles do not specify a technical solution for ‘FAIRness’, it was clear from outset of initiative that would be useful to have commodity software and tooling simplify creation FAIR-compliant resources. The Data Point is metadata repository follows DCAT(2) schema, utilizes Linked Platform manage hierarchical layers as LDP Containers. There has been recent flurry development activity around significantly improved its power ease-of-use. Here we describe five specific...