A5067974158- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Semantic Web and Ontologies
- Genomics and Phylogenetic Studies
- Data Quality and Management
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Gut microbiota and health
- Distributed and Parallel Computing Systems
- Metabolomics and Mass Spectrometry Studies
- Plant Molecular Biology Research
- Big Data and Business Intelligence
- Cancer Genomics and Diagnostics
- Topic Modeling
- Service-Oriented Architecture and Web Services
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Advanced Text Analysis Techniques
- Electronic Health Records Systems
- Natural Language Processing Techniques
- Inflammatory Bowel Disease
- Health Literacy and Information Accessibility
- Web Data Mining and Analysis
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
1997-2025
Universidad Politécnica de Madrid
2016-2025
Centre for Plant Biotechnology and Genomics
2016-2025
Midland Regional Hospital Mullingar
2021-2024
Digital Research Alliance of Canada
2023
Rothamsted Research
2023
German Cancer Research Center
2023
St. Vincent's University Hospital
2016-2021
University of British Columbia
2005-2018
German Oceanographic Museum
2018
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...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into most comprehensive library Perl modules available for managing manipulating life-science information. provides easy-to-use, stable, consistent programming interface bioinformatics application programmers. have been successfully repeatedly used to reduce otherwise complex tasks only a few lines code. object model proven be...
The FAIR Data Principles propose that all scholarly output should be Findable, Accessible, Interoperable, and Reusable.As a set of guiding principles, expressing only the kinds behaviours researchers expect from contemporary data resources, how principles manifest in reality was largely open to interpretation.As support for has spread, so breadth these interpretations.In observing this creeping spread interpretation, several original authors felt it now appropriate revisit Principles,...
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 Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description arbitrary (real, hypothesized, virtual, fictional) objects, processes their attributes. specifies design patterns describe associate qualities, capabilities, functions, quantities, informational entities including textual, geometrical, mathematical entities, provides specific extensions...
The FAIR Principles 1 (https:/
BioMOBY is an Open Source research project which aims to generate architecture for the discovery and distribution of biological data through web services; services are decentralised, but availability these resources, instructions interacting with them, registered in a central location called MOBY Central. adds paradigm, as exemplified by Universal Data Discovery Integration (UDDI), having object-driven registry query system object service ontologies. This allows users traverse expansive...
In this paper, we describe an application, PubCloud that uses tagclouds for the summarization of results from queries over thePubMed database biomedical literature. responds toqueries with tag clouds generated wordsextracted abstracts returned by query. The ofa user study comparing tag-cloud ofquery standard result list provided PubMedindicated cloud interface is advantageous in presenting descriptive information and reducing frustrationbut it less effective at task enabling users to...
We have analyzed double mutants that combine late-flowering mutations at four flowering-time loci (FVE, FPA, FWA, and FT) with the LEAFY (LFY), APETALA1 (AP1), TERMINAL FLOWER1 (TFL1) involved in floral initiation process (FLIP). Double between ft-1 or fwa-1 lfy-6 completely lack flowerlike structures, indicating both FWA FT act redundantly LFY to control AP1. Moreover, phenotypes of ap1-1 are reminiscent phenotype cal-1 mutants, suggesting could also be other FLIP genes. Such extreme were...
The unusual floral organs (ufo) mutant of Arabidopsis has flowers with variable homeotic organ transformations and inflorescence-like characteristics. To determine the relationship between UFO previously characterized meristem identity genes, we cloned determined its expression pattern. gene shows extensive homology FIMBRIATA (FIM), a mediating genes in Antirrhinum. All three alleles that sequenced are predicted to produce truncated proteins. transcripts were first detected early meristems,...
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 complexity and inter-related nature of biological data poses a difficult challenge for tool integration. There has been proliferation interoperability standards projects over the past decade, none which widely adopted by bioinformatics community. Recent attempts have focused on use semantics to assist integration, Semantic Web technologies are being welcomed this community.SADI - Automated Discovery Integration is lightweight set fully standards-compliant service design patterns that...
Abstract Background The EURO-NMD Registry collects data from all neuromuscular patients seen at EURO-NMD's expert centres. In-kind contributions three patient organisations have ensured that the registry is patient-centred, meaningful, and impactful. consenting process covers other uses, such as research, cohort finding trial readiness. Results has three-layered datasets, with European Commission-mandated elements (EU-CDEs), a set of cross-neuromuscular (NMD-CDEs) dataset disease-specific...
The human sense of smell is the faculty upon which many industries rely to monitor items such as beverages, food and perfumes. Previous work has been carried out construct an instrument that mimics remarkable capabilities olfactory system. or electronic nose consists a computer-controlled multi-sensor array exhibits differential response range vapours odours. authors report on novel application artificial neural networks (ANNS) processing data gathered from integrated sensor nose. This...
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....
Using a simple example and simulations, we explore the impact of input tree shape upon broad range supertree methods. We find that can affect how conflict is resolved by several methods effects may be substantial. Standard irreversible matrix representation with parsimony (MRP), MinFlip, duplication-only Gene Tree Parsimony (GTP), an implementation average consensus method have tendency to resolve in favor relationships unbalanced trees. Purvis MRP dendrogram appear opposite tendency. Biases...
Abstract The burden of noninteroperability between on-line genomic resources is increasingly the rate-limiting step in large-scale analysis. BioMOBY a biological Web Service interoperability initiative that began as retreat representatives from model organism database community September, 2001. Its long-term goal to provide simple, extensible platform through which myriad databases and analytical tools can offer their information services fully automated interoperable way. Of two branches...