Proteome databases | Sequence data analysis

Supplies an access to several biological data resources and bioinformatics services. EBI is a platform that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems, pathways, ontologies and literature. Databases, tools, as well as web services are provided for sharing data, performing queries and analyzing results. Users can also deposit their data through a data submission page. All the resources are freely available without restriction, with few exceptions.

Offers a seamless integration of and navigation through protein-related data. NeXtProt contains proteomics data for over 85% of human proteins. Moreover, this tool includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. All of the data are available via a user interface and FTP site. An API access and a SPARQL endpoint are also provided for more technical applications.

Permits users to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform stores biological and technical metadata from public data sets using an indexing system. It can integrate different biological entities, including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed.

Enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology. ProteomicsDB is a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data. It contains 81,721 unique phosphorylated peptides representing 11,025 human genes, demonstrating that more than half of all human proteins are substrates of kinases.

An atlas of protein expression of Medicago truncatula in association with Sinorhizobium meliloti. The Medicago Proteome Atlas provides evidence for more than 23013 protein groups (19679 from the eukaryotic host plant, M. truncatula; 3334 from S. meliloti) along with 20120 phosphorylation sites and 734 lysine acetylation sites. Further mining of this proteomic resource may enable engineering of crops and their microbial partners to increase agricultural productivity and sustainability.