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http://www.findmice.org/index.jsp

Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.

Proper citation: International Mouse Strain Resource (RRID:SCR_001526) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-1/search?q=*&l=

Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish).

Proper citation: Integrated Animals (RRID:SCR_001421) Copy   

•   Source: SciCrunch Registry

http://www.animalgenome.org/cgi-bin/QTLdb/index

Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome.

Proper citation: Animal QTLdb (RRID:SCR_001748) Copy   

•   Source: SciCrunch Registry

http://www.aspgd.org/

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

Proper citation: ASPGD (RRID:SCR_002047) Copy   

•   Source: SciCrunch Registry

http://amigo.geneontology.org/

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

Proper citation: AmiGO (RRID:SCR_002143) Copy   

•   Source: SciCrunch Registry

http://gara.bio.uci.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.

Proper citation: Glomerular Activity Response Archive (RRID:SCR_002089) Copy   

•   Source: SciCrunch Registry

http://www.genenetwork.org/

Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.

Proper citation: GeneNetwork (RRID:SCR_002388) Copy   

•   Source: SciCrunch Registry

http://biodbcore.org

A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: bioDBcore (RRID:SCR_002781) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry

http://uwaging.org/genesdb/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.

Proper citation: Aging Genes and Interventions Database (RRID:SCR_002701) Copy   

•   Source: SciCrunch Registry

http://www.pharmgkb.org/

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Proper citation: PharmGKB (RRID:SCR_002689) Copy   

•   Source: SciCrunch Registry

http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

•   Source: SciCrunch Registry

http://studyforrest.org

An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.

Proper citation: studyforrest.org (RRID:SCR_003112) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation.

Proper citation: SciCrunch (RRID:SCR_003115) Copy   

•   Source: SciCrunch Registry

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

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://www.dtp.nci.nih.gov

Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Developmental Therapeutics Program (RRID:SCR_003057) Copy   

•   Source: SciCrunch Registry

http://braininfo.rprc.washington.edu

Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

Proper citation: BrainInfo (RRID:SCR_003142) Copy   

•   Source: SciCrunch Registry

http://phenome.jax.org/

Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility.

Proper citation: Mouse Phenome Database (MPD) (RRID:SCR_003212) Copy   

•   Source: SciCrunch Registry

http://www.cellimagelibrary.org/

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

Proper citation: Cell Image Library (CIL) (RRID:SCR_003510) Copy   

•   Source: SciCrunch Registry

http://www.reactome.org

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Proper citation: Reactome (RRID:SCR_003485) Copy   

•   Source: SciCrunch Registry