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http://www.ebi.ac.uk/ena/about/cram_toolkit

A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use.

Proper citation: CRAM (RRID:SCR_012975) Copy   

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

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

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

A database algorithm for generating protein backbone and side chain coordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.

Proper citation: MaxSprout (RRID:SCR_010687) Copy   

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http://purl.bioontology.org/ontology/GRO

Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of).

Proper citation: Gene Regulation Ontology (RRID:SCR_010590) Copy   

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http://phenomenal-h2020.eu/

Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.

Proper citation: PhenoMeNal (RRID:SCR_016605) Copy   

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http://www.mged.org/Workgroups/MAGE/mage.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. Group providing a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems.

Proper citation: MAGE (RRID:SCR_002313) Copy   

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http://www.biomart.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

Proper citation: BioMart Project (RRID:SCR_002987) Copy   

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

Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.

Proper citation: FASTA (RRID:SCR_011819) Copy   

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

Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.

Proper citation: GeneWise (RRID:SCR_015054) Copy   

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http://www.enfin.org/

ENFIN is a virtual institute to enable systems-level integration of experimental results. It is committed to provide a Europe-wide integration of computational approaches in systems biology. Its objectives are: - To develop a shared approach between traditionally dry and traditionally wet researchers in the area of systems-level interpretation of experimental results - To develop a distributed computational platform this integration and analysis of experimental data - To directly prove that such an approach has scientific value - To encourage and participate in the critical assessment of systems-level approaches - To disseminate knowledge and techniques to other academic researchers worldwide - To disseminate knowledge and techniques to commercial researchers, in particular European SMEs - To train young European researchers from a variety of backgrounds in system-level informatics techniques. The ENFIN Network runs four major platforms: A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling, a Provision of Analysis Tools - EnSUITE, a Platform for Data Integration - EnCORE, and training Courses and Workshops on Systems Biology. Sponsors: The ENFIN project is funded by the European Commission within its FP6 Programme, under the thematic area Life sciences, genomics and biotechnology for health,contract number LSHG-CT-2005-518254.

Proper citation: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology (RRID:SCR_001724) Copy   

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http://www.ebi.ac.uk/cgi-bin/sva/sva.pl/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The ENA Sequence Version Archive is a repository of all entries which have ever appeared in EMBL-Bank Sequence Database. You can browse the archive or use the batch retrieval form.

Proper citation: ENA Sequence Version Archive (RRID:SCR_000929) Copy   

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http://metazoa.ensembl.org/index.html

Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species.

Proper citation: Ensembl Metazoa (RRID:SCR_000800) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. 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. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.

Proper citation: The Alternatve Splicing Database (RRID:SCR_001883) Copy   

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https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) Copy   

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http://www.ebi.ac.uk/compneur-srv/LGICdb/

Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

Proper citation: Ligand-Gated Ion Channel Database (RRID:SCR_002418) Copy   

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

IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service.

Proper citation: IPI (RRID:SCR_003012) Copy   

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

A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines.

Proper citation: IPD - Immuno Polymorphism Database (RRID:SCR_003004) Copy   

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http://www.ebi.ac.uk/goldman-srv/pandit

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Proper citation: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees (RRID:SCR_003321) Copy   

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

IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. 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.

Proper citation: IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) Copy   

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http://ftp://ftp.ebi.ac.uk/pub/databases/taxonomy

The taxonomy database of the International Sequence Database Collaboration contains the names of all organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The database is available via the EBI SRS server of ftp.

Proper citation: Taxonomy (RRID:SCR_004299) Copy   

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