Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | 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. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl https://sources.debian.org/src/ensembl/ https://doi.org/10.17616/R39K5B |
SCR_002344 | ENSEMBL | 2026-02-14 02:00:23 | 11652 | ||||||
|
dbSNP Resource Report Resource Website 5000+ mentions |
dbSNP (RRID:SCR_002338) | dbSNP | data repository, storage service resource, data or information resource, service resource, database | Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource. | insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standard, bio.tools |
is used by: ExAc is used by: GEMINI is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl Variation is related to: GWAS Central is related to: TopoSNP is related to: GWAS Central has parent organization: NCBI has parent organization: National Human Genome Research Institute works with: Open Regulatory Annotation Database |
NLM | PMID:21154707 | Free, Freely available | nif-0000-02734, biotools:dbsnp, OMICS_00264, r3d100010652 | http://www.ncbi.nlm.nih.gov/projects/SNP/ https://bio.tools/dbsnp https://doi.org/10.17616/R3XG81 |
SCR_002338 | dbSNP: Database for Short Genetic Variations, Entrez SNP - Single Nucleotide Polymorphism, SNV Database, NCBI SNV Database, NCBI Short Genetic Variations Database, NCBI Short Genetic Variations, NCBI Single Nucleotide Polymorphism, Entrez SNP, dbSNP, NCBI Short Genetic Variations (SNV) database | 2026-02-14 02:00:23 | 8619 | ||||
|
EOL - Encyclopedia of Life Resource Report Resource Website 100+ mentions |
EOL - Encyclopedia of Life (RRID:SCR_005905) | EOL | data or information resource, portal, database | Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise. | life, encyclopedia, environmental sciences, ecology, ecological survey, life sciences, specie, species diversity, diversity, taxon, image, video, audio, FASEB list |
is listed by: re3data.org is related to: Pensoft is related to: Biodiversity Heritage Library |
John D. and Catherine T. MacArthur Foundation ; Alfred P. Sloan Foundation |
PMID:24891832 | Creative Commons License, Acknowledgement requested, Note that a single page may be made up of many different data elements, Each covered by a different license, Http://eol.org/info/copyright_and_linking#using_content | r3d100010229, nlx_149476 | https://doi.org/10.17616/R35S3D | SCR_005905 | Encyclopedia of Life | 2026-02-14 02:05:21 | 138 | ||||
|
BOLD Resource Report Resource Website 100+ mentions |
BOLD (RRID:SCR_004278) | BOLD | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library. | protists, taxonomy, dna, barcode, dna barcode, gene sequence, primer, publication, barcode index number, unique identifier, annotation, platform, data management, data sharing, dna sequence, bioinformatics, molecular biology, biology, geography, species, sequence cluster, map, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Guelph; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada ; Ontario Innovation Trust ; NSERC ; Gordon and Betty Moore Foundation |
PMID:18784790 | Free, Public | DOI:10.17616/R3PP7J, nlx_29236, DOI:10.25504/FAIRsharing.en9npn, DOI:10.5883, r3d100010129 | http://www.boldsystems.org/ https://doi.org/10.17616/R3PP7J https://doi.org/10.17616/r3pp7j https://doi.org/10.5883/ https://dx.doi.org/10.5883/ https://fairsharing.org/10.25504/FAIRsharing.en9npn https://doi.org/10.17616/R3KG65 |
SCR_004278 | BOLD Systems, Barcode of Life Database Systems, Barcode of Life Database, Barcode of Life Data Systems, BOLD : The Barcode of Life Data System | 2026-02-14 02:04:46 | 298 | ||||
|
EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | data repository, storage service resource, data or information resource, atlas, service resource, database | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage https://doi.org/10.17616/R3860B |
SCR_005391 | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-02-14 02:04:31 | 23 | ||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data repository, storage service resource, data or information resource, service resource, database | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934 https://doi.org/10.48550/arxiv.1506.00272 https://doi.org/10.7303/ https://dx.doi.org/10.7303 https://doi.org/10.17616/R3B934 |
SCR_006307 | 2026-02-14 02:04:53 | 1002 | |||||
|
UK Data Archive Resource Report Resource Website 50+ mentions |
UK Data Archive (RRID:SCR_014708) | data or information resource, organization portal, portal | Organization which acquires, curates, and provides access to a collection of digital data in the social sciences and humanities in the United Kingdom. | data archive, digital data, social science, humanities, curator |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing |
ESRC ; JISC ; University of Essex |
grid.438826.3, DOI:10.25504/FAIRsharing.qtm44s, Wikidata: Q17039301, ISNI: 0000 0001 0377 8000, DOI:10.5255, DOI:10.17616/R3088K | https://ror.org/03fknw408 https://doi.org/10.17616/R3088K https://doi.org/10.17616/r3088k https://doi.org/10.5255/ https://dx.doi.org/10.5255/ https://fairsharing.org/10.25504/FAIRsharing.qtm44s |
SCR_014708 | 2026-02-14 02:05:34 | 88 | ||||||||
|
INPTDAT Resource Report Resource Website |
INPTDAT (RRID:SCR_022167) | data or information resource, data repository, storage service resource, service resource | Interdisciplinary data platform provides access to research data and information from all fields of applied plasma physics and plasma medicine. Aims at distributing, publishing and archiving of data and information, supporting findability, accessibility, interoperability and re-use of data, for low temperature plasma physics community.Most of data are freely available and can be used under terms of license listed on dataset description page. Each dataset can be identified, cited and shared by using Digital Object Identifier. | Leibniz Institute for Plasma Science and Technology, FAIR data, applied plasma physics, plasma medicine, low temperature plasma physics community |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing |
Federal Ministry of Education and Research BMBF | Free, Freely available | r3d100013120, DOI:10.34711, DOI:10.17616/R31NJMM8, DOI:10.25504/FAIRsharing.2VADoR | https://doi.org/10.17616/R31NJMM8 https://doi.org/10.17616/r31njmm8 https://doi.org/10.34711/ https://dx.doi.org/10.34711/ https://fairsharing.org/10.25504/FAIRsharing.2VADoR https://doi.org/10.17616/R31NJMM8 |
SCR_022167 | 2026-02-14 02:04:49 | 0 | |||||||
|
BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase https://doi.org/10.17616/R3G61K |
http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-02-14 02:04:50 | 82 | ||||
|
DataONE Resource Report Resource Website 10+ mentions |
DataONE (RRID:SCR_003999) | DataONE | data repository, storage service resource, portal, catalog, data or information resource, service resource, software resource, database | A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community. | earth, environment, data sharing, cyberinfrastructure, earth observational data, data management, data set, FASEB list |
uses: DataUp is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of New Mexico; New Mexico; USA |
NSF 0830944; NSF 1430508 |
Acknowledgement requested | DOI:10.25504/FAIRsharing.yyf78h, nlx_158410, DOI:10.17616/R3101G, r3d100010478, DOI:10.2586 | https://doi.org/10.17616/R3101G https://doi.org/10.17616/r3101g https://doi.org/10.2586/ https://dx.doi.org/10.2586/ https://fairsharing.org/10.25504/FAIRsharing.yyf78h https://doi.org/10.17616/R3TG83 |
SCR_003999 | Data Observation Network for Earth | 2026-02-14 02:04:30 | 44 | |||||
|
B2SHARE Eudat Resource Report Resource Website 1+ mentions |
B2SHARE Eudat (RRID:SCR_023135) | data repository, storage service resource, service resource | Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows. |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing |
Free, Freely available | r3d100011394, DOI:10.25504/FAIRsharing.da9307, DOI:10.17616/R3VK72, DOI:10.3473 | https://doi.org/10.3473 https://dx.doi.org/10.3473 http://doi.org/10.17616/R3VK72 https://fairsharing.org/10.25504/FAIRsharing.da9307 https://doi.org/10.17616/R3VK72 |
SCR_023135 | B2SHARE | 2026-02-14 02:05:07 | 1 | ||||||||
|
Polar Data Catalogue Resource Report Resource Website 1+ mentions |
Polar Data Catalogue (RRID:SCR_023131) | data repository, storage service resource, service resource | Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers. The metadata records follow ISO 19115 and Federal Geographic Data Committee (FGDC) standard formats to provide exchange with other data centres. The records cover a wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using a mapping interface and other parameters. | Arctic and Antarctic researcher data, Federal Geographic Data Committee standard format, |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.17616/R3QK86, r3d100010953, DOI:10.5884 | https://doi.org/10.5884 https://dx.doi.org/10.5884 http://doi.org/10.17616/R3QK86 https://doi.org/10.17616/R3QK86 |
SCR_023131 | ArcticNet | 2026-02-14 02:05:07 | 1 | |||||||
|
Aperta Turkey Open Archive Resource Report Resource Website 1+ mentions |
Aperta Turkey Open Archive (RRID:SCR_023128) | data repository, storage service resource, service resource | Aperta is the name of the Turkish Open Archive.You can upload your scientific studies within the scope of Aperta to this portal or you can easily access the uploaded studies. |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.48623, DOI:10.17616/r31njmv8, r3d100013444 | https://doi.org/10.48623 https://dx.doi.org/10.48623 https://doi.org/10.17616/r31njmv8 https://doi.org/10.17616/R31NJMV8 |
SCR_023128 | Aperta Turkey Open Archive | 2026-02-14 02:04:45 | 2 | ||||||||
|
Brown Digital Repository Resource Report Resource Website |
Brown Digital Repository (RRID:SCR_023144) | data repository, storage service resource, service resource | Collection contains open and publicly funded data sets created by Brown University faculty and student researchers. Increasingly, publishers, and funders are requiring that protocols, data sets, metadata, and code underlying published research be retained and preserved, their locations cited within publications, and shared with other researchers and the public. The deposits here endeavor to be in line with FAIR Principles (Findable, Accessible, Interoperable, Reusable). If you would like to deposit data set into this collection for the purposes of citation/linking within publication and public dissemination, then please log in, zip up and upload your file, and request digital object identifier (DOI) for your data citation. |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.17616/R3193B, r3d100011654, DOI:10.7301 | https://doi.org/10.7301 https://dx.doi.org/10.7301 http://doi.org/10.17616/R3193B https://doi.org/10.17616/R3193B |
SCR_023144 | Brown Digital Repository | 2026-02-14 02:04:45 | 0 | ||||||||
|
BioHeritage National Science Challenge Data Repository Resource Report Resource Website |
BioHeritage National Science Challenge Data Repository (RRID:SCR_023141) | data repository, storage service resource, service resource | Data catalogue and repository for New Zealand's Biological Heritage National Science Challenge. |
is listed by: DataCite is listed by: re3data.org |
Free, Freely available | DOI:10.17616/R31NJN01, DOI:10.34721, r3d100013617 | https://doi.org/10.34721 https://dx.doi.org/10.34721 http://doi.org/10.17616/R31NJN01 https://doi.org/10.17616/R31NJN01 |
SCR_023141 | BioHeritage National Science Challenge Data Repository | 2026-02-14 02:05:03 | 0 | ||||||||
|
NCBI Nucleotide Resource Report Resource Website 100+ mentions |
NCBI Nucleotide (RRID:SCR_004860) | NCBI Nucleotide, NCBI gi | data or information resource, database | 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. | gene expression, genomics, nucleic acid, biological assay, nucleotide, gold standard |
is listed by: re3data.org is related to: GenBank is related to: BioExtract is related to: DIG IT - Database of Immunoglobulins and Integrated Tools is related to: RefSeq is related to: TPA is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: NCBI |
nlx_84100, r3d100010778 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore http://www.ncbi.nlm.nih.gov/nuccore https://doi.org/10.17616/R3NG8J |
SCR_004860 | Nucleotide Database, Entrez Nucleotide, CoreNucleotide, Nucleotide | 2026-02-14 02:05:51 | 337 | |||||||
|
NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | data or information resource, database | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj https://bio.tools/bioproject https://doi.org/10.17616/R31NJMS2 |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | NCBI BioProject Database, BioProject | 2026-02-14 02:05:53 | 13968 | ||||
|
Tuberculosis Database Resource Report Resource Website 50+ mentions |
Tuberculosis Database (RRID:SCR_006619) | TBDB | data or information resource, database | 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. | genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list |
is listed by: re3data.org is related to: SMD is related to: BioCyc has parent organization: Broad Institute has parent organization: Stanford University School of Medicine; California; USA |
Tuberculosis | Bill and Melinda Gates Foundation | PMID:20488753 PMID:18835847 |
Acknowledgement requested, Public, (Published data) | nif-0000-03537, r3d100010930 | https://doi.org/10.17616/R39G8F | SCR_006619 | TB Database, TBDatabase | 2026-02-14 02:06:34 | 64 | |||
|
HIstome: The Histone Infobase Resource Report Resource Website 1+ mentions |
HIstome: The Histone Infobase (RRID:SCR_006972) | HIstome | data or information resource, database | 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. | histone, protein, enzyme, modifying enzyme, post-translational modification, variant, promoter region, gene, epigenetic regulation, india, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: ACTREC - Advanced Centre for Treatment Research and Education in Cancer |
Cancer | ACTREuropean Union - Advanced Centre for Treatment Research and Education in Cancer ; Government of India |
PMID:22140112 | Free, Public, Acknowledgement requested | biotools:histome, r3d100010977, nlx_151419 | http://www.actrec.gov.in/histome/ https://bio.tools/histome https://doi.org/10.17616/R3RD0R |
http://www.histome.net/ | SCR_006972 | 2026-02-14 02:05:57 | 1 | |||
|
HPRD - Human Protein Reference Database Resource Report Resource Website 1000+ mentions |
HPRD - Human Protein Reference Database (RRID:SCR_007027) | HPRD | data or information resource, database | 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. | protein, disease, network, post-translational, proteome, protein binding, protein s, protein c, pathway, protein-protein interaction, protein expression, subcellular localization, phosphorylation motif, signaling pathway, protein sequence, blast, molecule, domain, motif, post-translational modification, protein isoform, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEMINI is listed by: re3data.org is related to: Human Proteinpedia is related to: MatrixDB is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: Gene Ontology is related to: Agile Protein Interactomes DataServer has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18988627 PMID:16381900 PMID:14525934 |
Acknowledgement requested, Free, Non-commercial, Commercial requires license | nif-0000-00137, r3d100010978 | https://doi.org/10.17616/R3MK9N | SCR_007027 | Human Protein Reference Database | 2026-02-14 02:05:57 | 1266 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
