A5083760052- Semantic Web and Ontologies
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Scientific Computing and Data Management
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Complement system in diseases
- Bioinformatics and Genomic Networks
- Barrier Structure and Function Studies
- Single-cell and spatial transcriptomics
- Data Quality and Management
- Gut microbiota and health
- Topic Modeling
- Microbial Metabolic Engineering and Bioproduction
- Medical Imaging and Pathology Studies
- Natural Language Processing Techniques
- Bacterial Identification and Susceptibility Testing
- Stress Responses and Cortisol
- Digestive system and related health
- Pneumonia and Respiratory Infections
- Epigenetics and DNA Methylation
- Diet and metabolism studies
- Tryptophan and brain disorders
- Cystic Fibrosis Research Advances
- Antimicrobial Resistance in Staphylococcus
Amsterdam University Medical Centers
2021-2024
University of Amsterdam
2021-2024
Public Health Service of Amsterdam
2023-2024
Digital Health Cooperative Research Centre
2023
Wageningen University & Research
2015-2023
Institut de Biologie systémique et synthétique
2017
Unit of Virus Host Cell Interactions
2017
Linköping University
2011-2012
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....
Abstract Introduction Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these Findable, Accessible, Interoperable, Reusable (FAIR) for humans machines at source enables federated discovery analysis across custodians. This facilitates accurate diagnosis, optimal clinical management, personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare domains. The...
Abstract Objectives To provide a real-world example on how and to what extent Health Level Seven Fast Healthcare Interoperability Resources (FHIR) implements the Findable, Accessible, Interoperable, Reusable (FAIR) guiding principles for scientific data. Additionally, presents list of FAIR implementation choices supporting future implementations that use FHIR. Materials methods A case study was conducted Medical Information Mart Intensive Care-IV Emergency Department (MIMIC-ED) dataset,...
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess impact of different and animal health. Thirty-six wildtype male C57BL/6J mice 35 d age (n = 6/group; mean ± SEM body weight 21.9 0.25 g) were randomly assigned groups fed four weeks with semi synthetic diets prepared one following containing (300 g/kg as basis): soybean meal (SBM), casein, partially...
Abstract Introduction The Semantic Web community provides a common Resource Description Framework (RDF) that allows representation of resources such they can be linked. To maximize the potential linked data - machine-actionable interlinked on certain level quality RDF should established, particularly in biomedical domain which concepts are complex and high-quality ontologies high demand. However, it is unclear metrics for exist automated, required given multitude resources. Therefore, we aim...
Evidence is accumulating that perturbation of early life microbial colonization the gut induces long-lasting adverse health effects in individuals. Understanding mechanisms behind these will facilitate modulation intestinal health. The objective this study was to identify biological processes involved long lasting and (molecular) factors regulate them. We used an antibiotic same combination with stress on piglets as perturbation. Then we host gene expression data from (jejunum) tissue...
Faced with heterogeneity of healthcare data, we propose a novel approach for harmonizing data elements (i.e., attributes) across health standards. This focuses on the implicit concept that is represented by element. The process includes following steps: identifying concepts, clustering similar concepts and constructing mappings between clusters using Simple Standard Sharing Ontological Mappings (SSSOM) Resource Description Framework (RDF), enabling creation reusable mappings. As...
Objective: This paper reports on the development of a dynamic data management planning questionnaire to guide stewards European Reference Network (ERN) rare disease patient registries make their findable, accessible, interoperable, and reusable (FAIR). As part this work, was validated through expert review aligned with existing resources diseases FAIR management. Materials Methods: The developed for Data Stewardship Wizard, tool planning. Knowledge sources data, ERN registries, were used...
The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli maintain homeostasis. To improve our understanding of this plasticity, we performed high-level data integration 14 whole-genome transcriptomics datasets from samples intestinal mouse mucosa. We used the tool Centrality based Pathway Analysis (CePa), along with information Reactome database.The results show an integrated mucosa challenges agents introduced orally were...
Abstract Background Necrotising soft tissue infections (NSTIs) are rapidly progressing bacterial usually caused by either several pathogens in unison (polymicrobial infections) or Streptococcus pyogenes (mono-microbial infection). These rare and associated with high mortality rates. However, the underlying pathogenic mechanisms this heterogeneous group remain elusive. Methods In study, we built interactomes at both population individual levels consisting of host-pathogen interactions...
Mycoplasma hyopneumoniae (M. hyopneumoniae) causes enzootic pneumonia in pigs but it is still largely unknown which host-pathogen interactions enable persistent infection and cause disease. In this study, we analyzed the host bacterial transcriptomes during using RNA sequencing. Comparison of transcriptome lung lesion tissue from infected with non-infected animals, identified 424 differentially expressed genes (FDR < 0.01 fold change > 1.5LOG2). These were part following major pathways...
The genotype and external phenotype of organisms are linked by so-called internal phenotypes which influenced environmental conditions. In this study, we used five existing –omics datasets representing different layers phenotypes, were simultaneously measured in dietarily perturbed mice. We performed ten pair-wise correlation analyses verified with a null model built from randomized data. Subsequently, the inferred networks merged literature mined for co-occurrences identified nodes. Densely...
Abstract Introduction: Healthcare data and the knowledge gleaned from it play a key role in improving health of current future patients. These sources are regularly represented as ‘linked’ resources based on Resource Description Framework (RDF). Making ‘linkable' to facilitate their interoperability is especially important rare-disease domain, where scattered scarce. However, benefit using RDF, need be good quality. Based existing metrics, we aim assess quality RDF related rare diseases...
Abstract Introduction Healthcare data and the knowledge gleaned from it play a key role in improving health of current future patients. These sources are regularly represented as ‘linked’ resources based on Resource Description Framework (RDF). Making ‘linkable’ to facilitate their interoperability is especially important rare-disease domain, where scattered scarce. However, benefit using RDF, need be good quality. Based existing metrics, we aim assess quality RDF related rare diseases...
<ns4:p>Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve information this scripting language R using package <ns4:italic>rBiopaxParser</ns4:italic>, converts to one readable R. It also has a function build regulatory network from pathway information. Here we describe extension of function. The new allows user graphs entire pathways, including regulated as well non-regulated elements, and therefore provides maximum...
<ns4:p>Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. We can retrieve information this scripting language R using package <ns4:italic>rBiopaxParser</ns4:italic>, converts to one readable R. It also has a function build regulatory network from pathway information, here we describe extension of function. The new will include non-regulatory interactions and thus allow extraction maximum information. This be as part the<ns4:italic>...
Abstract Introduction Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these Findable, Accessible, Interoperable, Reusable (FAIR) for humans machines at source enables federated discovery analysis across custodians. This facilitates accurate diagnosis, optimal clinical management, personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare domains. The...
Abstract Background 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,...
Abstract Background Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple sources can use different ontologies for annotating their and, thus, creating need dynamic ontology services. In this experimental study, we assessed performance systems in context a real-life application from rare disease domain. Additionally, present method analyzing top-level classes improve precision. Results We included three...
Interoperability between clinical datasets is challenging due to, in part, the number of data models and vocabularies use variety implementations. Here we describe first steps an ongoing effort to achieve interoperability two currently being constructed within independent international projects. Both are utilizing FAIR Principles but have their independently selected different ontologies. In this initial exploratory experiment, examined degree which a mapping both into schema, Biolink, can...
Ontologies listed in the OBO Foundry are often regarded as reliable choices to be reused but ontology interoperability of them remains unknown. This study evaluated resolvability URIs and consistency axioms library, BFO ontology, CIDO ontology. All had nonresolvable URIs, library additional issues regarding use incorrect prefixes, mixing up with ontologies, inconsistency property. These detected reflected real-world common problems that were not significant from human beings' point view...