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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-11 10:56:26 | 11652 | ||||||
|
Alzforum Antibody Directory for Neuroscience Research Resource Report Resource Website |
Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) | data or information resource, database | The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations. | alzheimer, antibody, clinical trail, community, data, disease, disorder, molecule, neurodegenerative, protein, reagent, research, science, scientific, technology | has parent organization: Alzheimer's Research Forum | nif-0000-00129 | SCR_013601 | Alzforum Antibody Directory | 2026-02-11 10:58:55 | 0 | |||||||||
|
Brain RNA-Seq Resource Report Resource Website 100+ mentions |
Brain RNA-Seq (RRID:SCR_013736) | data or information resource, database | Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. | RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain, FASEB list | has parent organization: Stanford University; Stanford; California | NIMH R01MH09955501; NINDS R01NS08170301; NIGMS T32GM007365 |
PMID:25186741 PMID:26687838 |
Free, Freely available | SCR_017483 | http://www.brainrnaseq.org/ | SCR_013736 | Barres Brain RNA-Seq | 2026-02-11 10:58:49 | 109 | |||||
|
PhenoDB Resource Report Resource Website 1+ mentions |
PhenoDB (RRID:SCR_016551) | data or information resource, database | Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease. | store, standardized, phenotype, genotype, Mendelian disease, mutation, next, generation, sequencing, data | has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA | Mendelian disease | NHGRI | PMID:25684268 | Free, Registration required, Freely available for non commercial users | SCR_016551 | 2026-02-11 10:59:32 | 5 | |||||||
|
Danish Twin Registry Resource Report Resource Website |
Danish Twin Registry (RRID:SCR_017482) | DTR | data or information resource, database | Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years. | Twin, cancer, data, gene, environment | Restricted | SCR_017482 | 2026-02-11 10:59:38 | 0 | ||||||||||
|
Diversity Outbred Database Resource Report Resource Website 1+ mentions |
Diversity Outbred Database (RRID:SCR_018180) | data or information resource, database | Database provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full studies or subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data. | JAX, genetic diversity, genotype data, phenotype data, diversity outbred mice, genotype, clinical phenotype, molecular phenotype, proteomic, metabolomic, data | has parent organization: JAX Mice and Services | Free, Freely available | https://www.jax.org/research-and-faculty/genetic-diversity-initiative/tools-data/diversity-outbred-database | SCR_018180 | 2026-02-11 10:59:51 | 8 | |||||||||
|
Codon and Codon-Pair Usage Tables Resource Report Resource Website 1+ mentions |
Codon and Codon-Pair Usage Tables (RRID:SCR_018504) | CoCoPUTs | data or information resource, database | Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data. | Codon-pair, codon, nucleotide, gene, genomic codon pair, dinucleotide statistic, sequence, genetic variation, recombinant gene design, data |
is related to: GenBank is related to: RefSeq |
PMID:31029701 | Free, Freely available | SCR_018504 | 2026-02-11 10:59:46 | 5 | ||||||||
|
Database of Antimicrobial Activity and Structure of Peptides Resource Report Resource Website 10+ mentions |
Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) | DBAASP | data or information resource, database | Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index. | data, collection, structure, antimicrobial, activity, natural, synthetic, peptide, sequence | NIAID G2102; Shota Rustaveli National Science Foundation FR397718014; International Science and Technology Center |
PMID:26578581 PMID:27060142 |
Free, Freely available | SCR_016600 | DataBase of Antimicrobial Activity and Structure of Peptides, Database of Antimicrobial Activity and Structure of Peptides | 2026-02-11 10:59:27 | 42 | |||||||
|
p300db Resource Report Resource Website 1+ mentions |
p300db (RRID:SCR_017063) | data or information resource, database | Data collection of CBP/p300 regulated acetylome, proteome, and transcriptome in murine embryonic fibroblasts. Composed of Symbol search for quantified acetylation sites, proteins and transcripts abundance in CBP/p300, Domain search for batch query of proteins by specific domain and Conserved sites for acetylation sites that are conserved between mouse and human, and their regulation in KATi treated cells. | data, collection, CBP, p300, regulated, acetylome, proteome, transcriptome, murine, embryonic, fibroblast, domain, protein, acetylation, site, dataset |
is related to: Ensembl is related to: UniProt has parent organization: University of Copenhagen; Copenhagen; Denmark |
Free, Available for download, Freely available | SCR_017063 | 2026-02-11 10:59:33 | 1 | ||||||||||
|
miRTarBase Resource Report Resource Website 100+ mentions |
miRTarBase (RRID:SCR_017355) | data or information resource, database | Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. | Manually, curated, experimentally, validated, database, microRNA, target, interaction, collection, data, MTI, FASEB list | is listed by: OMICtools | Ministry of Science and Technology ; Taiwan |
PMID:29126174 | Free, Available for download, Freely availabe | http://mirtarbase.mbc.nctu.edu.tw/php/index.php | SCR_017355 | microRNA-Target interactions Base | 2026-02-11 10:59:41 | 321 | ||||||
|
MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | data or information resource, database | Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. | Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list | NIGMS GM0077465; NIDDK DK43351; NIDDK DK57521; Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Howard Hughes Medical Institute ; Charles E. Culpeper Scholarship in Medical Science |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | MitoCarta2.0 | 2026-02-11 10:59:47 | 183 | ||||||||
|
VA Phenomics Library Resource Report Resource Website 1+ mentions |
VA Phenomics Library (RRID:SCR_019107) | VAPheLib | data or information resource, database | Shared knowledgebase of VA EHR-based phenotype algorithms, definitions and data curation metadata. | Phenomics library, centralized phenomics VA library, data, curation metadata, phenotype | https://www.hsrd.research.va.gov/for_researchers/cyber_seminars/archives/3814-notes.pdf | SCR_019107 | 2026-02-11 10:59:55 | 1 | ||||||||||
|
Primate Cell Type Database Resource Report Resource Website |
Primate Cell Type Database (RRID:SCR_017963) | data or information resource, database | Database of intracellular recordings of non-human primates (NHP) cells sampled from the lateral prefrontal cortex. 249 patch clamp recordings for 2 protocols: 1 second current pulse and 3 millisecond pulse. Morphology obtained by biocytin injections and confocal imaging at 63x magnification. | Intracellular, recording, non human, primate, NHP, cell, sampled, lateral, perfrontal, cortex, data, collection, electrophysiology, morphology, transcriptomics | has parent organization: Western University; Ontario; Canada | Free, Freely available | r3d100013202 | https://doi.org/10.17616/R31NJMOI | SCR_017963 | 2026-02-11 10:59:43 | 0 | ||||||||
|
ChemokineDB Resource Report Resource Website |
ChemokineDB (RRID:SCR_016593) | data or information resource, database | Resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt public databases. | data, chemokine, receptor, taxonomy, nomenclature, structure, physiological, function, phenotype, collection | is listed by: NIAID | NIH | Free, Freely available | SCR_016593 | 2026-02-11 10:59:33 | 0 | |||||||||
|
GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | data or information resource, database | Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases. | geroprotector, data, collection, current, thearpeutic, prevention, aging, disease, geriatic |
uses: PubChem uses: ChemSpider uses: DrugBank uses: ChEMBL uses: CHEBI uses: UniProt uses: GenAge |
Wellcome Trust ; Israel Ministry of Science and Technology ; Fund in Memory of Dr. Amir Abramovich |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-02-11 10:59:31 | 11 | |||||||
|
COLLECT database Resource Report Resource Website 1+ mentions |
COLLECT database (RRID:SCR_018366) | data or information resource, database | Collaborative database for pregnancy and placental research studies worldwide by Global Pregnancy Collaboration CoLab . Database for collecting data for pregnancy studies in preeclampsia and other fields. Database has web based data entry platform with study specific user access. Data can also be entered offline using formatted spreadsheet template that can be uploaded to database in bulk or stored locally. Data is property of investigator but with permission can be combined into larger studies across centers and countries. Collaboration is enabled but not required. | Placenta, preeclampsia, obstetrics, perinatal research, data, data set, pregnancy, Global Pregnancy Collaboration, CoLab | preeclampsia | Bill and Melinda Gates Foundation | PMID:29978556 PMID:28864015 |
Restricted | SCR_018366 | 2026-02-11 10:59:49 | 1 | ||||||||
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Molecular Signatures Database Resource Report Resource Website 500+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NCI ; NIH ; NIGMS |
Free, Freely available, Registration required to download GSEA software | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-02-11 10:59:31 | 762 | |||||||
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Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes Resource Report Resource Website 1+ mentions |
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) | data or information resource, data set | Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. | molecular, taxonomy, lung, carcinoma, cancer, death, mrna, expression, sequence, data, adenocarcinoma, neuroendocrine, gene, type ii pneumocyte, analysis, metastasis, integration, mrna expression profiling | has parent organization: Broad Institute | Lung cancer | NCI U01 CA84995 | PMID:11707567 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30292 | SCR_003010 | Cancer Genomics Publication | 2026-02-11 10:56:35 | 2 | |||||
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EyeBrowse Resource Report Resource Website 1+ mentions |
EyeBrowse (RRID:SCR_008000) | data or information resource, data set |
EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation. |
est, expressed sequence tag, eye, gene, genome, cataract, cdna, chicken, clone, cluster, cornea, cornea disease, cow, data, disease, dog, human, locus, maturation, mouse, myopia, photoreceptor, rat, retina, rhesus, rna polymerase-ii, tag, zebrafish, data analysis software, eye tracking device |
is listed by: 3DVC has parent organization: University of California at Santa Cruz; California; USA |
Retinal disease, Cataract, Myopia, Cornea disease | NEIBank | nif-0000-07733 | SCR_008000 | EyeBrowse | 2026-02-11 10:57:44 | 3 | |||||||
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CellTax vignette Resource Report Resource Website 1+ mentions |
CellTax vignette (RRID:SCR_017000) | data or information resource, data set | Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. | data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region |
is related to: Allen Brain Atlas API is related to: Allen Mouse Brain Reference Atlas is related to: Allen Cell Types Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science ; NEI R01 EY023173; NIMH U01 MH105982 |
PMID:26727548 | Free, Public | SCR_017000 | Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science | 2026-02-11 10:59:37 | 3 |
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