A5062892160- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Semantic Web and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Computational Techniques and Applications
- Statistical and Computational Modeling
- Distributed and Parallel Computing Systems
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Data Quality and Management
- Simulation Techniques and Applications
- Genomics and Rare Diseases
- Advanced Database Systems and Queries
- Artificial Intelligence in Healthcare
- Geophysical Methods and Applications
- Diabetes Management and Research
- Computational Drug Discovery Methods
- Alzheimer's disease research and treatments
- Gene expression and cancer classification
- Diabetes and associated disorders
- Natural Language Processing Techniques
Wellcome Trust
2007-2022
European Bioinformatics Institute
2010-2022
SIB Swiss Institute of Bioinformatics
2014-2015
Research Organization of Information and Systems
2015
Babraham Institute
2013
Google (United States)
2009
Abstract Background Quantitative models of biochemical and cellular systems are used to answer a variety questions in the biological sciences. The number published quantitative is growing steadily thanks increasing interest use as well development improved software availability better, cheaper computer hardware. To maximise benefits this body models, field needs centralised model repositories that will encourage, facilitate promote dissemination reuse. Ideally, stored these should be...
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models biological processes. A large set curated to verify both correspondence the process that model seeks represent, and reproducibility simulation results as described in corresponding peer-reviewed publication. Many submitted database are annotated, cross-referencing its components external resources such records, terms from controlled vocabularies ontologies. comprises two main branches: one composed derived...
Abstract Motivation: Resource description framework (RDF) is an emerging technology for describing, publishing and linking life science data. As a major provider of bioinformatics data services, the European Bioinformatics Institute (EBI) committed to making readily accessible community in ways that meet existing demand. The EBI RDF platform has been developed increasing demand coordinate activities across institute provides new entry point querying exploring integrated resources available...
The Minimum Information Required in the Annotation of Models Registry (http://www.ebi.ac.uk/miriam) provides unique, perennial and location-independent identifiers for data used biomedical domain. At its core is a shared catalogue collections, each which an individual namespace created, extensive metadata recorded. This allows generation Uniform Resource Identifiers (URIs) to uniquely identify any record collection. Moreover, various services are provided facilitate creation resolution...
Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved helpful means enabling reuse existing work in modern biology. The Required the Annotation Models (MIRIAM) promote exchange and biochemical computational models. However, information about model alone not sufficient to enable its efficient setting. Advanced numerical algorithms complex modeling workflows used biology make reproduction simulations difficult. It therefore essential...
Abstract Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models reconstructions. However, the majority these are still created de novo , based on literature mining manual processing data. Results To increase efficiency model creation, Path2Models project has automatically generated mathematical from representations using suite freely available software. Data sources include KEGG, BioCarta, MetaCyc SABIO-RK. Depending source data,...
Background: With the ever increasing use of computational models in biosciences, need to share and reproduce results published studies efficiently easily is becoming more important. To this end, various standards have been proposed that can be used describe models, simulations, data or other essential information a consistent fashion. These constitute separate components required given scientific result. Results: We Open Modeling EXchange format (OMEX). Together with standard formats from...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...
Diabetes is a chronic and complex multifactorial disease caused by persistent hyperglycemia for which underlying pathogenesis still not completely understood. The mathematical modeling of glucose homeostasis, diabetic condition, its associated complications rapidly growing provides new insights into the mechanisms involved. Here, we discuss contributions to diabetes field over past five decades, highlighting areas where more focused research required.CPT: Pharmacometrics & Systems...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
BioModels serves as a central repository of mathematical models representing biological processes. It offers platform to make easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting broader range formats derived from diverse approaches and tools, new infrastructure for has been developed that is available at http://www.ebi.ac.uk/biomodels. This system allows submitting sharing wide with improved support other than SBML. also...
The Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) is a set guidelines for annotation and curation processes computational models, in order to facilitate their exchange reuse. An important part standard consists controlled model components, based on Uniform Resource Identifiers. enable interoperability this annotation, community has agree URIs, corresponding recognised data types. MIRIAM Resources are being developed support use those URIs. on-line services...
BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 described in literature and 140,000 automatically generated from pathway resources. Most model are cross‐linked with external resources facilitate interoperability. A large proportion manually curated ensure reproducibility simulation results. This tutorial presents BioModels' content, features,...
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards model curation. A fundamental one, MIRIAM (Minimum Information Requested Annotation Models), standardises annotation curation process quantitative models biology. To support this standard, Resources maintains a set standard data types annotating models, provides services manipulating these annotations. Furthermore, creates controlled...
The lack of a common exchange format for mathematical models in pharmacometrics has been long-standing problem. Such the potential to increase productivity and analysis quality, simplify handling complex workflows, ensure reproducibility research, facilitate reuse existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by Drug Disease Model Resources (DDMoRe) consortium, is intended become an standard providing means encode models, trial designs,...
Access to consistent, high-quality metadata is critical finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all necessary metadata. This prevents uniform indexing querying dataset repositories. Towards providing practical guide producing high quality description biomedical datasets, W3C Semantic Web Health Care Life Sciences Interest Group (HCLSIG) identified Resource Description...
Abstract Motivation: On the semantic web, in life sciences particular, data is often distributed via multiple resources. Each of these sources likely to use their own International Resource Identifier for conceptually same resource or database record. The lack correspondence between identifiers introduces a barrier when executing federated SPARQL queries across science data. Results: We introduce novel SPARQL-based service enable on-the-fly integration This uses identifier patterns defined...