A5044603792- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Research Data Management Practices
- Molecular Biology Techniques and Applications
- Fungal and yeast genetics research
- RNA and protein synthesis mechanisms
- Plant-Microbe Interactions and Immunity
- Ethics in Clinical Research
- vaccines and immunoinformatics approaches
- Biotin and Related Studies
- Microbial Community Ecology and Physiology
- Genomics and Rare Diseases
- Cell Image Analysis Techniques
- Ubiquitin and proteasome pathways
- Isotope Analysis in Ecology
- Advanced Biosensing Techniques and Applications
- Single-cell and spatial transcriptomics
European Bioinformatics Institute
2016-2025
Wellcome Trust
2016-2025
Open Targets
2021-2024
VIB-UGent Center for Medical Biotechnology
2023
Ramem (Spain)
2017
University of Groningen
2015
Center for Systems Biology
2014
Digital Proteomics (United States)
2014
University of Liverpool
2013
SIB Swiss Institute of Bioinformatics
2013
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and one founding members global ProteomeXchange (PX) consortium. In this manuscript, we summarize developments in PRIDE resources related tools since previous update manuscript was published Nucleic Acids Research 2016. last 3 years, public sharing through (as part PX) has definitely become norm field. parallel, re-use increased...
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE one founding members global ProteomeXchange (PX) consortium and an ELIXIR core resource. In this manuscript, we summarize developments in resources related tools since previous update manuscript was published Nucleic Acids Research 2019. number submitted datasets to Archive (the archival component PRIDE) has reached...
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories mass spectrometry (MS)-based proteomics data. Since beginning 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) new archival system, replacing original database. Here we summarize developments in resources and related tools since previous update manuscript Database Issue 2013. constitutes a complete redevelopment PRIDE, comprising storage backend, submission system web interface, among other...
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of most prominent data repositories mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in PRIDE and related tools. First, provide up-to-date statistics content, splitting figures by groups organisms species, including peptide protein identifications, post-translational modifications. We then describe tools that are part submission...
The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination mass spectrometry worldwide. We give an overview the current consortium activities describe advances past few years. Augmenting PX founding members (PRIDE PeptideAtlas, including PASSEL resource), two new have joined consortium: MassIVE jPOST. ProteomeCentral remains as common access portal, providing ability search for...
There is a need for standardized, practical annotation structures of lipid species derived from mass spectrometric approaches; i.e., high-throughput data obtained instruments operating in either high- or low-resolution modes. This proposal based on common, officially accepted terms and builds upon the LIPID MAPS terminology. It aims to add defined levels information below nomenclature, as detailed chemical structures, including stereochemistry, are usually not automatically provided by...
Abstract The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination mass spectrometry worldwide since 2012. In this paper, we describe the main developments previous update manuscript was published in Nucleic Acids Research 2017. Since then, addition to four PX existing members at time (PRIDE, PeptideAtlas including PASSEL resource, MassIVE jPOST), two new have joined PX: iProX (China) Panorama Public (USA)....
Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources compiles data on the abundance localisation of RNA proteins in various biological systems contexts provides open access to this research community. With increased availability single cell RNA-Seq datasets public archives, we have now extended with a new added-value service display expression cells. Single Cell was launched 2018 currently includes 123 studies from 12 species. The website can be...
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination public MS data. It now 10 years since initial workflow implemented. In this manuscript, we describe main developments PX previous update manuscript Nucleic Acids Research published 2020. six members Consortium are PRIDE,...
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species contexts, such as tissue, developmental stage, disease or cell type. The available public controlled access data sets from sources are curated re-analysed using standardized, open source pipelines made for queries, download visualization. As of August 2017, holds 3,126 studies across 33 species, including 731 plants. Data large-scale RNA...
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of main repositories mass spectrometry-derived proteomics data. For last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 peptides and over 50 spectra by September 2009. We here describe several new improved features in PRIDE, including revised submission process, which...
Medicine and healthcare are undergoing profound changes. Whole-genome sequencing high-resolution imaging technologies key drivers of this rapid crucial transformation. Technological innovation combined with automation miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How we going to deal exponential increase production? The potential "big data" for improving health is enormous but, at the same time, face a wide range challenges overcome...
The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein interest expressed. brings together data from >4500 expression studies >65 different species, across tissues. It makes these freely available in easy visualise form, after expert curation accurately represent intended experimental design,...
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's leading mass spectrometry (MS)-based proteomics data repository and one of founding members ProteomeXchange consortium. This manuscript summarizes developments in PRIDE resources related tools for last three years. number submitted datasets to Archive (the archival component PRIDE) has reached on average around 534 per month. been possible thanks continuous improvements infrastructure such as a new...
Abstract The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride ) is one of the main repositories MS derived proteomics data. Here, we point out functionalities PRIDE both as a submission repository and source for We describe features data retrieval visualization available through web BioMart interfaces. also highlight mechanism by which tailored queries in can join to other resources such Reactome, Ensembl or UniProt execute extremely powerful across‐domain queries. then...
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by Proteomics Standards Initiative. The format was developed Initiative in collaboration with instrument software vendors, developers major open-source projects proteomics. Software implementations have been to enable conversion from most popular proprietary formats, mzIdentML will soon be supported public repositories. These developments proteomics scientists start working...