Tools   Select Another Resource Report Type

http://www.arabidopsis.org

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

Proper citation: TAIR (RRID:SCR_004618) Copy   

•   Source: SciCrunch Registry

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.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

http://www.drugbank.ca/

Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

Proper citation: DrugBank (RRID:SCR_002700) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/genomes/FLU/

Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more.

Proper citation: Influenza Virus Resource (RRID:SCR_002984) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gene

Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.

Proper citation: Entrez Gene (RRID:SCR_002473) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/genbank/tpa/

Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.

Proper citation: TPA (RRID:SCR_003593) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/proteinclusters

Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

Proper citation: Protein Clusters (RRID:SCR_003459) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/protein

Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Proper citation: NCBI Protein Database (RRID:SCR_003257) Copy   

•   Source: SciCrunch Registry

https://fairsharing.org/collections/

Web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with integrated view across all three types of resource. By registering your resource on FAIRsharing, you gain credit for your work, increase its visibility outside of your direct domain, reduce potential for unnecessary reinvention and proliferation of standards and databases.

Proper citation: FAIRsharing (RRID:SCR_004177) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry

http://www.data.gov/

Catalog of data sets that are generated and held by the Federal Government, including data, tools and resources to conduct research, develop web and mobile applications, design data visualizations, etc. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.

Proper citation: Data.gov (RRID:SCR_004712) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/structure

Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

Proper citation: NCBI Structure (RRID:SCR_004218) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/nucleotide

Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Proper citation: NCBI Nucleotide (RRID:SCR_004860) Copy   

•   Source: SciCrunch Registry