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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

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

https://mps.csb.pitt.edu/

Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects.

Proper citation: Microphysiology Systems Database (RRID:SCR_021126) Copy   

•   Source: SciCrunch Registry

http://www.marine-geo.org/portals/antarctic/

Accepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.

Proper citation: Antarctic and Southern Ocean Data Portal (RRID:SCR_002193) Copy   

•   Source: SciCrunch Registry

http://wwwn.cdc.gov/niosh-survapps/ables/

Interactive data set on lead exposure (Blood Lead Concentrations greater than or equal to 25 micrograms per deciliter) of adults in the United States. The data comes from laboratory-reported elevated blood lead levels. Recent research has led to increased concerns about the toxicity of lead at low doses. Reflecting this increased concern, the ABLES program updated its case definition for an elevated BLL to a blood lead concentration greater than or equal to 10 micrograms per deciliter in 2009. This new case definition has also been: (1) recommended by the Council of State and Territorial Epidemiologists in 2009; (2) included in CDC''s list of nationally notifiable conditions in 2010; and (3) adopted as the Healthy People 2020 Occupational Safety and Health Objective 7. Given this new case definition, NIOSH will update the ABLES Charts and Interactive Database to include lead exposures to blood lead level greater than or equal to 10 micrograms per deciliter in the near future.

Proper citation: Adult Blood Lead Epidemiology and Surveillance Interactive Database (RRID:SCR_006915) Copy   

•   Source: SciCrunch Registry

http://www.africacentre.ac.za/Default.aspx?tabid=69

Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present.

Proper citation: Africa Centre for Health and Population Studies (RRID:SCR_008964) Copy   

•   Source: SciCrunch Registry

http://tbdb.org

Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data.

Proper citation: Tuberculosis Database (RRID:SCR_006619) Copy   

•   Source: SciCrunch Registry

http://www.iiserpune.ac.in/~coee/histome/

Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune.

Proper citation: HIstome: The Histone Infobase (RRID:SCR_006972) Copy   

•   Source: SciCrunch Registry

http://www.hprd.org

Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.

Proper citation: HPRD - Human Protein Reference Database (RRID:SCR_007027) Copy   

•   Source: SciCrunch Registry

http://faostat.fao.org/

A multilingual database that provides large time-series and cross sectional data relating to hunger, food, agriculture, nutrition, fisheries, forestry and food aid by country and region from 1961 to present. Data can be searched, browsed, analyzed and downloaded.

Proper citation: FAOSTAT (RRID:SCR_006914) Copy   

•   Source: SciCrunch Registry

http://climate.gi.alaska.edu/

Archive of digital climate records, climate statistics, and monthly weather summaries on Alaska and the polar regions.

Proper citation: Alaska Climate Research Center (RRID:SCR_000913) Copy   

•   Source: SciCrunch Registry

http://www.cftri.com/pepdb/

Database of ~ 865 peptides where each record provides information on the food source, preparation, purification, reference(s) and any other additional information. The database provides a search and browsing option for a more personalized research experience.

Proper citation: ACEpepDB (RRID:SCR_010474) Copy   

•   Source: SciCrunch Registry

http://asterweb.jpl.nasa.gov/data.asp

An imaging instrument onboard Terra, the flagship satellite of NASA''s Earth Observing System (EOS) that collects and archives data to create detailed maps of land surface temperature, reflectance, and elevation. The ASTER project is a collaboration between NASA and the Japanese government to develop a scientific understanding of the Earth.

Proper citation: ASTER (RRID:SCR_010478) Copy   

•   Source: SciCrunch Registry

http://www.dsmz.de/

The DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures) is the most comprehensive biological resource center in Europe. With more than 18.000 microorganisms, 1.200 plant viruses, 600 human and animal cell lines, 770 plant cell cultures and more than 7.100 cultures deposited for the purposes of patenting, DSMZ has demonstrated their obligation to serve science for decades. Main functions of DSMZ are: - to collect, maintain and store microorganisms and cell lines, as well as other biological material of relevance for applied biology, biotechnology, microbiology, teaching and other areas of research and general application; - to keep the scientific and industrial community informed on the contents of the collections by the means of catalogs, special lists, databases or electronic media; - to supply scientists and institutions with DSMZ cultures, in accordance with national and international laws such as the Infektionsschutzgesetz (Act dealing with protection against infection), the Genetic Engineering Act, the Foreign Trade Laws, the Convention on Biological Diversity as well as the DSMZ terms of supply; - to function as an internationally recognized collection center for the deposit of microorganisms, cell lines, and other biological material which have been cited in scientific literature or which are used in national or international test procedures (e.g. type strains, reference strains for national and international quality control regulations or susceptibility tests, strains with special properties, such as the production of enzymes, degradation of pollutants, host strains for plasmids, etc.); - to act as an International Depositary Authority (IDA) for the deposit of biological material for patent purposes according to the Budapest Treaty; - to act, in a confidential manner, as a center for the safe deposit of biological material; - to act as an advisory center for the scientific community and to offer teaching and service facilities. The DSMZ collections contain over 26 000 cultures (including 6500 patent deposits) representing more than 16 000 cultures of microorganisms (Archaea, Bacteria, plasmids, phages, yeasts, fungi), 750 plant cell cultures, 600 plant viruses, 700 antisera and 580 human and animal cell lines. Unique subcollections are held in the prokaryotes groups of acidophiles, alkaliphiles, halophiles, methanogens, phototrophs, thermophiles, and sulfate reducers. The research is focused on collection related fields which include: - Taxonomy - Evolution - Phylogeny - Microbial diversity and molecular assessment of diversity - Molecular systematics - Research on pathobiological aspects of leukemia-lymphoma cell lines applying classical and molecular genetics, immunological and cell biological methods * Development of cultivation and preservation methods for biological material * Characterization and identification of biological material

Proper citation: German Collection of Microorganisms and Cell Cultures (RRID:SCR_001711) Copy   

•   Source: SciCrunch Registry

http://www.jcvi.org/mpidb

Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.

Proper citation: MPIDB (RRID:SCR_001898) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ecogene.org/

Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries.

Proper citation: EcoGene (RRID:SCR_002437) Copy   

•   Source: SciCrunch Registry

http://factfinder2.census.gov/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2025. Database that provides access to population, housing, economic, and geographic data from several censuses and surveys about the United States, Puerto Rico and the Island Areas. Census data may be compiled into tables, maps and downloadable files, which can be viewed or printed. A large selection of pre-made tables and maps satisfies many information requests. By law, no one is permitted to reveal information from these censuses and surveys that could identify any person, household, or business. The following data are available: * American Community Survey * ACS Content Review * American Housing Survey * Annual Economic Surveys * Annual Surveys of Governments * Census of Governments * Decennial Census * Economic Census * Equal Employment Opportunity (EEO) Tabulation * Population Estimates Program * Puerto Rico Community Survey

Proper citation: American FactFinder (RRID:SCR_002932) 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://zfin.org

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Proper citation: Zebrafish Information Network (ZFIN) (RRID:SCR_002560) Copy   

•   Source: SciCrunch Registry