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http://www.knockoutmouse.org/

Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.

Proper citation: International Knockout Mouse Consortium (RRID:SCR_005574) Copy   

•   Source: SciCrunch Registry

http://swissregulon.unibas.ch/fcgi/sr/swissregulon

A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.

Proper citation: SwissRegulon (RRID:SCR_005333) Copy   

•   Source: SciCrunch Registry

http://plantta.jcvi.org/

The TIGR database is a collection of plant transcript sequences. Transcript assemblies are searchable using BLAST and accession number. The construction of plant transcript assemblies (TAs) is similar to the TIGR gene indices. The sequences that are used to build the plant TAs are expressed transcripts collected from dbEST (ESTs) and the NCBI GenBank nucleotide database (full length and partial cDNAs). "Virtual" transcript sequences derived from whole genome annotation projects are not included. All plant species for which more than 1,000 ESTs or cDNA sequences are available are included in this project. TAs are clustered and assembled using the TGICL tool (Pertea et al., 2003), Megablast (Zhang et al., 2000) and the CAP3 assembler (Huang and Madan, 1999). TGICL is a wrapper script which invokes Megablast and CAP3. Sequences are initially clustered based on an all-against-all comparisons using Megablast. The initial clusters are assembled to generate consensus sequences using CAP3. Assembly criteria include a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched overhangs. Any EST/cDNA sequences that are not assembled into TAs are included as singletons. All singletons retain their GenBank accession numbers as identifiers. Plant TA identifiers are of the form TAnumber_taxonID, where number is a unique numerical identifier of the transcript assembly and taxonID represents the NCBI taxon id. In order to provide annotation for the TAs, each TA/singleton was aligned to the UniProt Uniref database. For release 1 TAs, a masked version of the Uniref90 database was used. For release 2 and onwards, a masked version of the UniRef100 database is used. Alignments were required to have at least 20% identity and 20% coverage. The annotation for the protein with the best alignment to each TA or singleton was used as the annotation for that sequence. Additionally, the relative orientation of each TA/singleton to the best matching protein sequence was used to determine the orientation of each TA/singleton. Some sequences did not have alignments to the protein database that met our quality criteria, and those sequences have neither annotation nor orientation assignments. The release number for the plant TAs refers to the release version for a particular species. For the initial build, all TA sets are of version 1. Subsequent TA updates for new releases will be carried out when the percentage increase of the EST and cDNA counts exceeds 10% of the previous release and when the increase contains more than 1,000 new sequences. New releases will also include additional plant species with more than 1,000 EST or cDNA sequences that have become publicly available.

Proper citation: TIGR Plant Transcript Assembly database (RRID:SCR_005470) Copy   

•   Source: SciCrunch Registry

http://bigg.ucsd.edu/

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

Proper citation: BiGG Database (RRID:SCR_005809) Copy   

•   Source: SciCrunch Registry

http://the_brain.bwh.harvard.edu/uniprobe/

Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.

Proper citation: UniPROBE (RRID:SCR_005803) Copy   

•   Source: SciCrunch Registry

http://tolweb.org/tree/

A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.

Proper citation: Tree of Life Web Project (RRID:SCR_005673) Copy   

•   Source: SciCrunch Registry

http://yh.genomics.org.cn

This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.

Proper citation: YanHuang Project (RRID:SCR_006077) Copy   

•   Source: SciCrunch Registry

https://www.clinicaltrialsregister.eu

Database of European clinical trials containing information on interventional clinical trials on medicines. The information available dates from 1 May 2004 when national medicine regulatory authorities began populating the EudraCT database, the application that is used by national medicine regulatory authorities to enter clinical trial data. The EU Clinical Trials Register website launched on 22 March 2011 enables users to search for information which has been included in the EudraCT database. Users are able to: * view the description of a phase II-IV adult clinical trial where the investigator sites are in European Union member states and the European Economic Area; * view the description of any pediatric clinical trial with investigator sites in the European Union and any trials which form part of a pediatric investigation plan (PIP) including those where the investigator sites are outside the European Union. * download up to 20 results (per request) in a text file (.txt). The details in the clinical trial description include: * the design of the trial; * the sponsor; * the investigational medicine (trade name or active substance identification); * the therapeutic areas; * the status (authorized, ongoing, complete).

Proper citation: EU Clinical Trials Register (RRID:SCR_005956) Copy   

•   Source: SciCrunch Registry

http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets.

Proper citation: IMG System (RRID:SCR_002965) Copy   

•   Source: SciCrunch Registry

http://www.whocc.no/atcddd/

The official compendium for the Anatomical Therapeutic Chemical Classification System (ATC)-code descriptions. The Centre's main tasks are development and maintenance of the ATC/DDD system, including: * To classify drugs according to the ATC system. * Priority will be given to the classification of single substances, while combination products available internationally (i.e. important fixed combinations) will be dealt with as far as possible. * To establish DDDs for drugs which have been assigned an ATC code. * To review and revise as necessary the ATC classification system and DDDs. * To stimulate and influence the practical use of the ATC system by co-operating with researchers in the drug utilization field. Support: The WHO Collaborating Centre for Drug Statistics Methodology was established in 1982. The Centre is situated in Oslo at the Norwegian Institute of Public Health. The Centre is funded by the Norwegian government.

Proper citation: WHO Collaborating Centre for Drug Statistics Methodology (RRID:SCR_000677) Copy   

•   Source: SciCrunch Registry

http://cmbi.bjmu.edu.cn/mirsnp

Database of human SNPs in predicted miRNA-mRNA binding sites, based on information from dbSNP135 and mirBASE18. MirSNP is highly sensitive and covers most experiments confirmed SNPs that affect miRNA function. MirSNP may be combined with researchers' own GWAS or eQTL positive data sets to identify the putative miRNA-related SNPs from traits/diseases associated variants. They aim to update the MirSNP database as new versions of mirBASE and dbSNP database become available.

Proper citation: MirSNP (RRID:SCR_001629) 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

http://spaserver.ridom.de/

Database of information of spa-typing of MRSA, or Staphylococcus aureus, that can be used to collate and harmonize data from various geographic regions.

Proper citation: Ridom SpaServer (RRID:SCR_001460) Copy   

•   Source: SciCrunch Registry

http://mint.bio.uniroma2.it/

A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.

Proper citation: MINT (RRID:SCR_001523) Copy   

•   Source: SciCrunch Registry

http://eyelab.biostr.washington.edu/repos/eyelab_repo/

The Image Repository contains a collection of images produced by the research of John Clark's Eye Lab. Experiments include: Irradiated CP49 KO and wildtype, Hypothesis: CP49 KO mice will be more sensitive to X-irradiation than controls Huntington Mice Cataract ID, Hypothesis: Individuals can be identified by the pattern of their cataract. Alpha-Synuclein Mice, Hypothesis: Mice transgenic for the EGFP-tagged, mutant and WT strains of human alpha-synuclein gene, will provide a model for the testing of drugs on aggregation of the protein. alpha B Crystallin/SPARC DKO, Hypothesis: The absence of the chaperone protein, alpha B-Crystallin, causes a greater intensity and earlier onset in the opacifying effects of an absence of the matricellular protein, SPARC. Survey of SPARC KO and WT Survey of SPARC KO and WT Mice The repository is being built through a collaboration between the University of Washington's Department of Biological Structure, led by John Clark, and the Structural Informatics Group, led by Jim Brinkley. As an aim of the Biomedical Information Sciences Technology Initiative (BISTI), members of the Structural Informatics Group have been talking with biomedical researchers to find out their informatics needs. Tools such as this repository are being created in response to those needs. This web tool allows the researchers to add their images to a repository facilitating the organization and management of their data.

Proper citation: The Eye Lab Image Database (RRID:SCR_002038) 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

https://enigma.lbl.gov/regprecise/

Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RegPrecise (RRID:SCR_002149) Copy   

•   Source: SciCrunch Registry

http://www.pubgene.org/

It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate.

Proper citation: PubGene (RRID:SCR_002119) Copy   

•   Source: SciCrunch Registry

http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy   

•   Source: SciCrunch Registry

http://greengenes.secondgenome.com/downloads

Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Greengenes (RRID:SCR_002830) Copy   

•   Source: SciCrunch Registry