Philippe Rocca‐Serra
A5018395535- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Semantic Web and Ontologies
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Data Quality and Management
- Genomics and Phylogenetic Studies
- Cell Image Analysis Techniques
- Microbial Community Ecology and Physiology
- Environmental DNA in Biodiversity Studies
- Species Distribution and Climate Change
- Advanced Proteomics Techniques and Applications
- Computational Drug Discovery Methods
- Nutrition, Genetics, and Disease
- Atmospheric and Environmental Gas Dynamics
- Data Visualization and Analytics
- Single-cell and spatial transcriptomics
- Big Data and Business Intelligence
- Molecular Biology Techniques and Applications
- Isotope Analysis in Ecology
- Biomedical and Engineering Education
- Medical Imaging Techniques and Applications
University of Oxford
2015-2024
AstraZeneca (United Kingdom)
2022-2023
Science Oxford
2017-2020
Université de Bordeaux
2019
Universidad Politécnica de Madrid
2018
University of Pennsylvania
2015
Philadelphia University
2015
European Bioinformatics Institute
2003-2013
Wellcome Trust
2006-2013
University of Cambridge
2008-2013
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...
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of major providers in molecular biology. Metabolomic profiling an important tool research into biological functioning systemic perturbations caused diseases, diet environment. The effectiveness such methods depends on availability public open across a broad range conditions. repository, powered...
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the Repository—a public archive functional genomics experiments and supporting data, Warehouse—a database gene expression profiles other bio-measurements Atlas—a new summary meta-analytical tool ranked across multiple different biological conditions. The Repository contains data from over 6000 comprising approximately 200 000 assays, doubles in size every 15 months. majority are array based, but types included, most...
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability promote growth an open 'data commoning' culture. Here we describe prerequisites for data commoning present established growing ecosystem solutions using shared 'Investigation-Study-Assay' framework vision.
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological sets integration with third-party tools. consists query-optimized database interactive, user-friendly interfaces. has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval customized sets. A wide variety complex queries, on various types annotations, numerous species are supported. These can be many...
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
Abstract Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation local management of experimental metadata from high-throughput studies employing one or a combination omics other technologies; (ii) empowers users to uptake community-defined checklists ontologies; (iii) facilitates submission international public repositories. Availability Implementation: Software, documentation, case implementations at http://www.isa-tools.org...
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...
Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange information retrieval.
Abstract MetaboLights is the first general purpose, open‐access database repository for cross‐platform and cross‐species metabolomics research at European Bioinformatics Institute (EMBL‐EBI). Based upon open‐source ISA framework, provides Metabolomics Standard Initiative (MSI) compliant metadata raw experimental data associated with experiments. Users can upload their study datasets into Repository. These studies are then automatically assigned a stable unique identifier (e.g., MTBLS1) that...
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,...
Abstract Motivation: The generation of large amounts microarray data and the need to share these bring challenges for both management annotation highlights standards. MIAME specifies minimum information needed describe a experiment Microarray Gene Expression Object Model (MAGE-OM) resulting MAGE-ML provide mechanism standardize representation exchange, however common terminology is support Results: Here we MGED Ontology (MO) developed by Working Group Data (MGED) Society. MO provides terms...
Metabolomics has become a crucial phenotyping technique in range of research fields including medicine, the life sciences, biotechnology and environmental sciences. This necessitates transfer experimental information between groups, as well potentially to publishers funders. After initial efforts metabolomics standards initiative, minimum reporting were proposed which included concepts for databases. Built by community, infrastructure are still needed allow storage, exchange, comparison...
Data sharing, and the good annotation practices it depends on, must become part of fabric daily research for researchers funders.
Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). brings with it number of challenges, including management, analysis, storage sharing data. In response these we have developed new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) allows users easily...
Metabolomics is the comprehensive study of a multitude small molecules to gain insight into an organism's metabolism. The research field dynamic and expanding with applications across biomedical, biotechnological, many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, repositories, analysis tools. However, rapid progress resulted in mosaic independent, sometimes incompatible, methods that are difficult connect useful...
BioSharing (http://www.biosharing.org) is a manually curated, searchable portal of three linked registries. These resources cover standards (terminologies, formats and models, reporting guidelines), databases, data policies in the life sciences, broadly encompassing biological, environmental biomedical sciences. Launched 2011 built by same core team as successful MIBBI portal, harnesses community curation to collate cross-reference across sciences from around world. makes these findable...