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http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

https://github.com/Ensembl

Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.

Proper citation: Ensembl Variation (RRID:SCR_001630) Copy   

•   Source: SciCrunch Registry

http://www.bioguo.org/AnimalTFDB/

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: AnimalTFDB (RRID:SCR_001624) Copy   

•   Source: SciCrunch Registry

https://www.bgee.org/

Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression.

Proper citation: Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) Copy   

•   Source: SciCrunch Registry

http://ratmap.gen.gu.se/

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 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.

Proper citation: Rat Gene Symbol Tracker (RRID:SCR_003261) Copy   

•   Source: SciCrunch Registry

http://www.peptideatlas.org

Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database.

Proper citation: PeptideAtlas (RRID:SCR_006783) Copy   

•   Source: SciCrunch Registry

https://database.riken.jp/sw/en/The_RIKEN_integrated_database_of_mammals/ria254i/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.
A database that integrates not only RIKEN''''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists'''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

Proper citation: RIKEN integrated database of mammals (RRID:SCR_006890) Copy   

•   Source: SciCrunch Registry

http://decipher.sanger.ac.uk/

Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes.

Proper citation: DECIPHER (RRID:SCR_006552) Copy   

•   Source: SciCrunch Registry

http://www.germonline.org/

Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: GermOnline (RRID:SCR_002807) Copy   

•   Source: SciCrunch Registry

http://www.vbase2.org/

Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed.

Proper citation: VBASE2 (RRID:SCR_007082) Copy   

•   Source: SciCrunch Registry

http://www.blueprint-epigenome.eu/

Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system.

Proper citation: Blueprint Epigenome (RRID:SCR_003844) Copy   

•   Source: SciCrunch Registry