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http://www.ebi.ac.uk/GenomeReviews/

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized 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. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed.

Proper citation: Genome Reviews (RRID:SCR_007685) Copy   

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http://www.ebi.ac.uk/ipd/hpa/

A centralised repository for the data which define the human platelet antigens (HPA). Alloantibodies against human platelet antigens are involved in neonatal alloimmune thrombocytopenia, post-transfusion purpura and refractoriness to random donor platelets. The Human Platelet Antigen (HPA) nomenclature system was adopted in 1990 to overcome problems with the previous nomenclature. Since then more antigens have been described and meanwhile the molecular basis of many has been resolved, and the nomenclature was revised in 2003.

Proper citation: IPD-HPA - Human Platelet Antigens (RRID:SCR_007747) Copy   

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http://www.ebi.ac.uk/integr8/

The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.

Proper citation: Integr8 : Access to complete genomes and proteomes (RRID:SCR_007740) Copy   

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http://www.ebi.ac.uk/asd/aedb/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs.

Proper citation: Alternative Exon Database (RRID:SCR_008157) Copy   

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http://www.ebi.ac.uk/asd/altextron/indexhtml

THIS RESOURCE IS NO LONGER IN SERVICE. A computer generated high quality dataset of human transcript-confirmed constitutive and alternative exons and introns. The alternative events have been delineated and annotated with various characterizations. AltExtron is the prototype database for the production version AltSplice. AltExtron is more geared towards investigating various aspects of the methodologies used, and focuses in general on the biology behind alternative splicing. The complete data used in this work is available for downloading in several flat files, containing human genes, introns, exons, isoform events, human-mouse comparisons, and additional information on GC-AG introns. Two versions of AltExtron data are available - one as prototype (for human) and another as latest build (for human, drosophila, mouse, and others) based on EMBL/GenBank (Feb 2003).

Proper citation: AltExtron Database (RRID:SCR_008404) Copy   

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http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+FSSP

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, below 30%% sequence identity), as well as all structures in the Protein Data Bank with 70-30%% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70 % sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically and by anonymous ftp (file transfer protocol).

Proper citation: FSSP - Families of Structurally Similar Proteins (RRID:SCR_003534) Copy   

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http://www.ebi.ac.uk/uniprot-das

The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. The UniProt DAS server provides access to sequence and annotation from UniProt, UniParc and IPI. Researchers can then provide annotation of their own results in the context of UniProt annotation, IPI annotation and UniParc cross references through the use of suitable DAS client such as Dasty2, the Ensembl DAS client or SPICE. The server also gives access to Gene Ontology Annotation of UniProt sequences (GOA) and theoretical tryptic digests of protein sequences in UniProt and IPI. An extremely useful resource for users of DAS is the DAS Registration Server that supports registry and discovery of DAS services. The datasources provided by the UniProt DAS server are all registered with this service.

Proper citation: UniProt DAS (RRID:SCR_004663) Copy   

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http://orchem.sourceforge.net

OrChem is an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today''s powerful database servers to provide fast response times in equally large data sets. OrChem is an Oracle chemistry plug-in using the Chemistry Development Kit (CDK). The CDK is an open source Java library for Chemoinformatics and Bioinformatics. OrChem is maintained by the chemoinformatics and metabolism team of the European Bioinformatics Institute. Oracle Data cartridges extend the capabilities of the Oracle server. For chemistry various commercial cartridges exist that facilitate searching and analyzing chemical data. OrChem also provides functionality like this, but is not a cartridge. It doesn''t need Oracle''s extensibility architecture because its Java components run as Java stored procedures inside the Oracle standard JVM (Aurora). OrChem is suitable for Oracle 11G and onwards. Starting with Oracle 11g release 1 (11.1) there is a just-in-time(JIT) compiler for Oracle JVM environment. A JIT compiler for Oracle JVM enables much faster execution because it manages the invalidation, recompilation, and storage of code without an external mechanism. This new Oracle feature makes Java classes perform better than before.

Proper citation: OrChem (RRID:SCR_008865) Copy   

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http://www.ebi.ac.uk/Tools/

The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.

Proper citation: Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) Copy   

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http://www.hipsci.org/

A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation.

Proper citation: HipSci (RRID:SCR_003909) Copy   

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http://identifiers.org/

A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile.

Proper citation: Identifiers.org (RRID:SCR_003735) Copy   

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http://www.ebi.ac.uk/Tools/dbfetch/dbfetch

Dbfetch is an acronym for database fetch. Dbfetch provides an easy way to retrieve entries from various databases at the EBI in a consistent manner and allows you to retrieve up to 50 entries at a time from various up-to-date biological databases. It can be used from any browser as well as well as within a web-aware scripting tool that uses wget, lynx or similar. From the browser, follow these instructions... * Select a database: If you are using the first form to paste your search items: choose a database name from this form. If you are using the second form to upload your search items: the database name is included at the beginning of each line line of the upload file followed by a colon. * Enter search terms: These MUST BE in the appropriate database format, up to 200 search items can be queried in one run. If you are using the first form: separate search items with a comma or space. If you are using the second form: separate search items with a new line. * Choose an output format: Here you can choose the simpler fasta format, or the databases'''' default format for the chosen database. * Style: You can get your results as text or html. * Retrieve! - You are now ready to fetch your results, by pressing the Retrieve button.

Proper citation: EBI Dbfetch (RRID:SCR_004393) Copy   

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http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html

The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.

Proper citation: ProFunc (RRID:SCR_004450) Copy   

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http://www.ebi.ac.uk/biosamples/

Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI''''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples)

Proper citation: BioSample Database at EBI (RRID:SCR_004856) Copy   

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http://www.ebi.ac.uk/expressionprofiler/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.

Proper citation: Expression Profiler (RRID:SCR_005821) Copy   

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http://www.ebi.ac.uk/thornton-srv/databases/FunTree/

FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms.

Proper citation: FunTree (RRID:SCR_006014) Copy   

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http://www.ebi.ac.uk/thornton-srv/databases/drugport/

DrugPort provides an analysis of the structural information available in the Protein Data Bank (PDB) relating to drug molecules and their protein targets. The drug-target data comes from the DrugBank database. You can search the entries by identifier, test or by protein sequence, or you can use the browse options in the menu on the left.

Proper citation: DrugPort (RRID:SCR_006573) Copy   

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http://bioinformatics.oxfordjournals.org/content/21/19/3806.long

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 26, 2016. A data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CoGenT++ (RRID:SCR_000249) Copy   

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http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

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http://ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Protein_data/

FTP site to access Schizosaccharomyces pombe protein data.

Proper citation: Pompep (RRID:SCR_010536) Copy   

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