A5060194743- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Computational Drug Discovery Methods
- Semantic Web and Ontologies
- Research Data Management Practices
- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Various Chemistry Research Topics
- Wikis in Education and Collaboration
- Distributed and Parallel Computing Systems
- History and advancements in chemistry
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Analytical Chemistry and Chromatography
- Chemistry and Chemical Engineering
- Machine Learning in Materials Science
- scientometrics and bibliometrics research
- Web Data Mining and Analysis
- Microbial Metabolic Engineering and Bioproduction
- Library Science and Information Systems
- Data Quality and Management
- Cell Image Analysis Techniques
- Computational Physics and Python Applications
- Microbial infections and disease research
Maastricht University
2016-2025
University of Applied Sciences Utrecht
2024
Google (United Kingdom)
2021
Vrije Universiteit Amsterdam
2018
Diabetes Australia
2017-2018
Karolinska Institutet
2011-2017
NutriLeads (Netherlands)
2017
Netherlands Bioinformatics Centre
2017
Uppsala University
2009-2013
Radboud University Nijmegen
2000-2012
The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture capabilities as well the development an project by team of international collaborators from academic industrial institutions described. CDK provides methods many common tasks in molecular informatics, including 2D 3D rendering chemical structures, I/O routines, SMILES parsing generation, ring searches, isomorphism checking, structure diagram etc....
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database curated, machine readable way, omics data analysis and visualization is enabled. other pathway databases are used to analyze experimental by research groups many fields. Due open collaborative nature of platform, our content keeps growing getting more accurate, making reliable rich database. Previously, however, focus was primarily on genes proteins, leaving...
Abstract WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of scientific community developing curating knowledge in models, lowers all barriers accessing using content. Increasingly more content creators, initiatives, projects tools have started WikiPathways. Central this growth increased use are various communities that focus on particular subsets molecular pathways such as rare...
The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods manipulate such and perform computations on them. library implements wide variety of algorithms ranging from structure canonicalization molecular descriptor calculations pharmacophore perception. It in drug discovery, metabolomics, toxicology. Over the last 10 years, code base has grown significantly, however, resulting many...
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways data visualization analysis. Since our last NAR update, 4 years ago, has experienced massive growth in content, which continues to be contributed by hundreds individuals each year. New aspects the diversity depth collected are described from perspective researchers interested using pathway information their studies. We provide updates on extensions...
The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, data, standards. We outline recent examples of cooperation in group: shared dictionary algorithms implementations drawing from our various projects; repository data including elemental properties, atomic radii, isotopes, atom typing rules, so forth; Web services for...
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...
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis interpretation of data in natural products research. Currently, reliance on a disparate set non-standardized, insular, specialized databases presents series challenges for access, both within the discipline integration interoperability between related fields. The fundamental elements exchange are referenced structure-organism pairs that establish relationships distinct molecular...
Researchers around the world join forces to reconstruct molecular processes of virus-host interactions aiming combat cause ongoing pandemic.
WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight continuing efforts supporting WikiPathways, content growth collaboration among researchers. As evolving database, there a growing need for address overcome technical challenges. In this direction, has undergone major restructuring, enabling renewed approach sharing curating knowledge, thus providing stability future...
Abstract Background The NORMAN Association ( https://www.norman-network.com/ ) initiated the Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/ in 2015, following collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange information chemicals that are expected to occur environment, along with accompanying expert knowledge and references, has become a valuable base for “suspect screening” lists....
Abstract The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good stewardship prerequisite reproducibility. Nowadays, guides policy actions professional practices in public private sectors. Despite such endorsements, however, Principles are aspirational, remaining elusive at best, intimidating worst. To address lack of practical guidance, help with capability gaps, we developed Cookbook, an open,...
The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work resulted separation core OSCAR functionality its release as OSCAR4 library. This library features modular API (based on reduction surface coupling) that permits client programmers to easily incorporate it into external applications. offers domain-independent architecture upon which specific text-mining...
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over impact gene expression, to outcomes in clinical trials. These data are typically not connected together, which reduces ease with insights can be gained. Linking Open Drug (LODD) a task force within World Wide Web Consortium's (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly drugs, created Linked representations sets,...
Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across between studies. The best way to annotate metabolites is by chemical structures, encoded the International Chemical Identifier code (InChI) InChIKey. We have implemented a web-based Translation Service that performs batch conversions of most common compound identifiers, including CAS, CHEBI, formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG,...
PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as increasingly important approach to distribute integrate scientific data. Exposing data services may help enable automated integration management, well facilitate interoperable web applications.This work, one of a series covering the PubChemRDF project, describes translate Substance Compound information into Resource Description Framework (RDF)...
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, adheres to FAIR principles findability, accessibility, interoperability reusability. Here we describe breadth depth biomedical contained within Wikidata, discuss open-source tools have built add information synchronize it with source databases. We also demonstrate several use cases for including...
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others back Uniform Identifiers (URIs). makes the machine-readable uses extensible vocabularies for additional information, making it easier scale up inference analysis.This paper describes recent developments in an ongoing project converting from ChEMBL database into triples. Relative earlier versions, this...
Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas biology where cheminformatics plays an important role computational research, including metabolism, proteomics, and systems biology. One critical aspect these fields accurate exchange data, which increasingly accomplished through use ontologies. Ontologies formal representations objects their properties using a logic-based ontology language. Many such ontologies currently...
Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified need for computational infrastructure toxicological data management engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower harmonized approach research in nanotechnology. This setting provides number opportunities challenges representation integration ENM information originating from diverse systems. Within this cluster, eNanoMapper...