PANDA Projects

CluSTr
The CluSTr database offers an automatic classification of UniProtKB/Swiss-Prot + UniProtKB/TrEMBL proteins into groups of related proteins.


GOA
GO Annotation (GOA) is a project that aims to provide assignments of gene products to the Gene Ontology (GO) resource, a dynamic controlled vocabulary. This vocabulary will be applied to a non-redundant set of proteins described in the UniProtKB/Swiss-Prot, UniProtKB/TrEMBL and Ensembl databases that collectively provide complete proteomes for Homo sapiens and other organisms.


InterPro
The InterPro database is an integrated documentation resource for protein families, domains and functional sites.


Proteomics
The Proteomics Services Team provides databases and tools for the deposition, distribution and analysis of proteomics and proteomics-related data. IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions. The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data.


UniProt
UniProt is the world's most comprehensive catalog of information on proteins. UniProt has four components, each specialized for different uses. The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.

ChEBI Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.


IntEnz
IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.


Reactome
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI, Ensembl and UniProt, the UCSC Genome Browser, HapMap, KEGG (Gene and Compound),ChEBI, PubMed and GO.


Rhea
Rhea is a reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. We have populated the database with the reactions found in the EC list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included.

Alternative Splicing and Transcript Diversity (ASTD)
The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale.


EMBL Nucleotide Sequence Database
The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.


The European Genotype Archive (EGA)
The European Genotype Archive (EGA) is designed to be a repository for all types of genotype experiments, including case control, population, and family studies. We will include SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. This data may be either both publicly available or limited access depending on the design of the study.

European Nucleotide Archive (ENA)
Provides data repositories and services in the nucleotide sequencing domain, from raw reads, through assembled sequences to submitted functional annotation. Serving both as a public-facing resource and as a key infrastructure to other EBI services, the team's work includes the provision of submission services and data access tools and represents the European arm of the International Nucleotide Sequence Database Collaboration.


Ensembl
Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute to develop a system which produces and maintains automatic annotation on selected eukaryotic genomes. Access to all the software and data is free and without constraints of any kind. The project is primarily funded by the Wellcome Trust.


Genome Reviews
The Genome Reviews database provides an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota.


Integr8
Integr8 facilitates the integrated browsing and analysis of Bioinformatics information about organisms with completely deciphered genomes.


VectorBase
VectorBase is an NIAID bioinformatics resource centre for invertebrate vectors of human pathogens. We are responsible for the ongoing curation of genomic information for a number of important disease vectors including Anopheles gambiae (malaria) and Aedes aegypti (Yellow fever and Dengue).


HUGO Gene Nomenclature Committee (HGNC)
The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique approved gene symbol and name to every gene in the human genome. Standardised gene nomenclature is now widely recognised as an invaluable resource for all researchers and is prominently listed in numerous databases such as Ensembl, Entrez Gene, GeneCards, the UCSC Genome Browser and UniProt.

Through our outreach group we instruct and interact with users. This information is brought back to the group in the hope to enhance the user experience.