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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SpliceDB Resource Report Resource Website 1+ mentions |
SpliceDB (RRID:SCR_006262) | SpliceDB | data or information resource, data set | Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. | gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence |
is listed by: OMICtools is listed by: 3DVC is related to: GenBank has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11125105 PMID:11058137 |
nlx_151853, OMICS_01892 | http://linux1.softberry.com/berry.phtml?topic=splicedb | http://genomic.sanger.ac.uk/spldb/SpliceDB.htm | SCR_006262 | SpliceDB: canonical and non-canonical splice site sequences in mammalian genes | 2026-09-12 01:03:16 | 2 | |||||
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1000 Genomes Project and AWS Resource Report Resource Website 5000+ mentions |
1000 Genomes Project and AWS (RRID:SCR_008801) | 1000 Genomes Project and AWS | data or information resource, data set | A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow. | genomic data, genome, cloud computing, cloud, human, gene, genetic variation, research, dna |
is used by: HmtVar is related to: Broad Institute Genomics Platform has parent organization: Amazon Web Services |
nlx_144340 | SCR_008801 | 1000 Genomes Project and Amazon Web Services, 000 Genomes Project Amazon Web Services, 1000 Genomes Project AWS | 2026-09-12 01:03:18 | 7076 | ||||||||
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Sequence Tag Alignment and Consensus Knowledgebase Database Resource Report Resource Website |
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) | data or information resource, data processing software, data visualization software, database, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index | exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization | PMID:11125101 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20946 | SCR_002156 | STACKdb | 2026-09-12 01:00:07 | 0 | ||||||||
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UK Sheep Genome Mapping Project Resource Report Resource Website 1+ mentions |
UK Sheep Genome Mapping Project (RRID:SCR_002272) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The project aims to apply genome mapping research to sheep, utilizing previous research in sheep (in other countries) and in other species (in the UK and abroad) to the benefit of the UK sheep industry. The project itself uses existing breeding structures, knowledge of the sheep genome and experimental resources. It has three main aims: i) To use the Suffolk, Texel and Charollais Sire Referencing Schemes to detect and verify quantitative trait loci (QTLs) for growth and carcass composition traits ii) To investigate candidate genes and/or chromosomal regions for associations with production traits. iii) To investigate approaches for optimizing future genotyping strategies within the sire referencing schemes for practical and cost effective application of marker-assisted selection By using commercial breeding populations for the research, immediate application of beneficial results is possible. Potential benefits include increased genetic progress through marker assisted selection which utilizes the genotype information, correction of possible parentage errors (ultimately leading to additional genetic progress) and opportunities for using marker information for product certification. The project will benefit the UK sheep industry by the use of Marker Assisted Selection (MAS) utilizing QTL or gene variants identified in the project. Additional benefits may arise from parentage verification and correction of errors e.g. misallocation of lamb to ewe. In the longer term, opportunities may exist to use markers for quality control, tracing products to their source. The major advantage of the design of this project is that the results are immediately applicable to the breeding schemes within which the QTLs and/or genes are detected. The time lag in the application of the results that is often seen with experimental populations is minimized. The project requires close involvement with the Sire Reference Schemes, in return for their assistance the results have immediate benefit to animals within these groups. | gene, animal, breed, breeding, chromosomal, chromosome, genome, genotype, genotyping, lamb, map, mapping, marker, population, production, region, sheep, specie, structure, trait | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20995 | SCR_002272 | UKSGMP | 2026-09-12 01:00:08 | 1 | |||||||||
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VIRsiRNAdb Resource Report Resource Website 1+ mentions |
VIRsiRNAdb (RRID:SCR_006108) | VIRsiRNAdb | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development. | virus, sirna, shrna, gene, influenza, sars, hepatitis, sirna sequence, virus subtype, target gene, genbank accession, design algorithm, cell type, efficacy, target genome region, target object, experimental assay, off-target, sirna matching, reference viral sequence, influenza virus, hepatitis b virus, hpv, sars corona virus, viral genome, reference genome, align, sirna sequence, fasta, blast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
Influenza, SARS, Hepatitis, Infectious disease | Council of Scientific and Industrial Research; New Delhi; India | PMID:22139916 | Open unspecified license / Freely available | nlx_151610, biotools:virsirnadb | https://bio.tools/virsirnadb | SCR_006108 | VIRsiRNAdb - Database of Viral siRNA / shRNA, Viral siRNA Database, Viral siRNA Database (VIRsiRNAdb) | 2026-09-12 01:00:11 | 4 | |||
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SoyBase Resource Report Resource Website 500+ mentions |
SoyBase (RRID:SCR_005096) | SoyBase | analysis service resource, controlled vocabulary, data analysis service, data or information resource, data repository, database, ontology, production service resource, service resource, storage service resource | Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. | soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: Iowa State University; Iowa; USA is parent organization of: Soybean Ontologies is parent organization of: Soy Ontology |
USDA Agricultural Research Service | PMID:20008513 | The community can contribute to this resource | nif-0000-03483, r3d100010846, biotools:soybase | https://bio.tools/soybase, https://doi.org/10.17616/R3S032 | SCR_005096 | SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers | 2026-09-12 01:00:10 | 830 | ||||
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SNPeffect Resource Report Resource Website 50+ mentions |
SNPeffect (RRID:SCR_005091) | SNPeffect | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database for phenotyping human single nucleotide polymorphisms (SNPs)that primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. They provide a detailed variant analysis using their tools such as: * TANGO to predict aggregation prone regions * WALTZ to predict amylogenic regions * LIMBO to predict hsp70 chaperone binding sites * FoldX to analyse the effect on structure stability Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification. The meta-analysis tool enables scientists to carry out a large scale mining of SNPeffect data and visualize the results in a graph. It is now possible to submit custom single protein variants for a detailed phenotypic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, phenotyping, mutation, protein-coding variant, molecule, structure, phenotype, non-synonymous coding snp, allelic variation, gene, protein stability, functional site, protein phosphorylation, glycosylation, subcellular localization, protein turnover, protein aggregation, amyloidosis, chaperone interaction, protein variant, FASEB list |
is listed by: OMICtools has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
PMID:22075996 PMID:18086700 PMID:16809394 PMID:15608254 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00187, nif-0000-03480 | http://snpeffect.switchlab.org/ | SCR_005091 | SNPeffect 4 Phenotyping Human Mutations | 2026-09-12 01:00:10 | 62 | |||||
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Generic GO Term Mapper Resource Report Resource Website 10+ mentions |
Generic GO Term Mapper (RRID:SCR_005806) | GOTermMapper, GO Term Mapper | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms. The implementation of this Generic GO Term Mapper uses map2slim.pl script written by Chris Mungall at Berkeley Drosophila Genome Project, and some of the modules included in the GO-TermFinder distribution written by Gavin Sherlock and Shuai Weng at Stanford University, made publicly available through the GMOD project. GO Term Mapper serves a different function than the GO Term Finder. GO Term Mapper simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, GO Term Finder finds the GO terms significantly enriched in a submitted list of genes. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, gene association, slim ontology, slimmer-type tool, term enrichment, gene annotation, genomics, ontology, process, function, component, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA |
Free for academic use | nlx_149294, biotools:go_term_mapper | https://bio.tools/go_term_mapper | SCR_005806 | Generic Gene Ontology Term Mapper, Generic Gene Ontology (GO) Term Mapper | 2026-09-12 01:00:11 | 45 | ||||||
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ChEA Resource Report Resource Website 100+ mentions |
ChEA (RRID:SCR_005403) | ChEA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software application, software resource | Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes. | chip, transcription factor, interaction, mrna expression, gene, target gene, command-line, chip-chip, chip-seq |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20709693 | OMICS_00526 | SCR_005403 | ChIP Enrichment Analysis | 2026-09-12 01:00:11 | 280 | |||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1, https://bio.tools/source | SCR_005799 | 2026-09-12 01:00:11 | 69 | |||||
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Gene Class Expression Resource Report Resource Website 1+ mentions |
Gene Class Expression (RRID:SCR_005679) | Gene Class | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. Gene Class Expression allows functional annotation of SAGE data using the Gene Ontology database. This tool performs searches in the GO database for each SAGE tag, making associations in the selected GO category for a level selected in the hierarchy. This system provides user-friendly data navigation and visualization for mapping SAGE data onto the gene ontology structure. This tool also provides graphical visualization of the percentage of SAGE tags in each GO category, along with confidence intervals and hypothesis testing. Platform: Online tool | serial analysis of gene expression, functional annotation, annotation, gene expression, tag classification, gene ontology, gene, ontology, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Sao Paulo; Sao Paulo; Brazil |
Center for Cell-Based Therapy/FAPESP ; CNPq |
PMID:16755502 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149119 | http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl | SCR_005679 | GC Browser, Gene Classification Browser Tool, Gene Class expression: analysis tool of Gene Ontology terms with gene expression data | 2026-09-12 01:00:11 | 1 | ||||
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Onto-Compare Resource Report Resource Website 1+ mentions |
Onto-Compare (RRID:SCR_005669) | Onto-Compare | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool | microarray, gene, ontology, gene expression, data-mining, browser, visualization, analysis, compare, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, compare commercially available microarrays based on go |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:12664686 PMID:15215428 |
Free for academic use | nlx_149108 | SCR_005669 | 2026-09-12 01:00:11 | 1 | |||||||
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | controlled vocabulary, data access protocol, data or information resource, data repository, database, image collection, image repository, ontology, service resource, software resource, storage service resource, web service | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-09-12 01:00:11 | 11 | |||
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TreeBASE Resource Report Resource Website 500+ mentions |
TreeBASE (RRID:SCR_005688) | TreeBASE | data or information resource, data repository, database, service resource, storage service resource | Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review. | taxonomy, matrix, tree, topology, phylogeography, cladistic analysis, amino acid sequence, animal behavior, morphology, nucleotide sequence, genetics, dna, phylogeny, evolution, gene, population, web service, FASEB list |
is listed by: re3data.org is listed by: SoftCite has parent organization: NESCent - National Evolutionary Synthesis Center |
NSF DEB 9318325; NSF EF 0331654 |
Public, The community can contribute to this resource | r3d100010170, nif-0000-03587 | https://doi.org/10.17616/R3DK58 | SCR_005688 | TreeBASE - A Database of Phylogenetic Knowledge | 2026-09-12 01:00:11 | 813 | |||||
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Allen Institute for Brain Science Resource Report Resource Website 500+ mentions |
Allen Institute for Brain Science (RRID:SCR_006491) | atlas, data or information resource, portal, topical portal | Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain. | Institute, embryonic, gene, expression, data, neuroscience, medical, research, neuroanatomy |
is listed by: Brain Architecture Project is related to: VisiGene Image Browser is related to: Recombinase (cre) Activity is related to: Cytosplore Viewer is related to: Mozak is related to: Microns Explorer is related to: CellLocator is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: Atlasplot is related to: Atlas Ontology Model is related to: Allen Brain Atlas-Driven Visualizations is related to: Brain heatmap is related to: Brainmapr is related to: ABAEnrichment is related to: Hippo-ATESC is related to: AllenDigger is related to: Cocoframer is related to: Process Genes List is related to: AIDAhisto is related to: MeshGen is related to: PET-CT mouse brain toolbox is related to: Multimodal Environment for Neuroimaging and Genomic Analysis is related to: goi2roimapping is related to: Spatiotemporal pattern Exploration of Brain is related to: Allen Mouse Brain ImageLoader is related to: ARA Tools is related to: allenCCF is related to: CutNII is related to: Genomic-and-High-Dimensional-Data is related to: Mouse_abi_tool is related to: Abagen is related to: VoxHunt is related to: ABI-expression-data-generator is related to: GCEA_FalsePositives is related to: Atlas Splitter is related to: ABAnnotate is related to: JuGEx is related to: Alleninf is related to: Atlas Alignment Meter is related to: Pinpoint is related to: Atlas Densities is related to: Atlas Direction Vectors is related to: SageBionetworks Portals is related to: brain-mapping is related to: BrainModules is related to: BrainRegionMarkers is related to: AP-histology is related to: Brainreg-segment is related to: Segmenting Brain Regions is related to: DeepSlice is related to: Cell Type Analysis Toolbox is related to: BrainGlobe Atlas API is related to: QUINT is related to: BRain area Input Output is related to: Brainreg is related to: MorphAPI is related to: Aligning Big Brains and Atlases is related to: Allen Brain Atlas Tools is related to: Brain Gene Expression Analysis toolbox is related to: Blue Brain Cell Atlas is related to: 3DBar is related to: Brainrender is related to: QuickNII is related to: Brain Architecture Project is related to: NeuroInfo is related to: Azimuth is related to: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas is related to: Integrated Brain Gene Expression is related to: MIRACL is related to: Linked Neuron Data is related to: BrainStars is related to: MouseLight Project is related to: Distributed Archives for Neurophysiology Data Integration is related to: Open Source Brain is related to: VisuAlign is related to: NS-Forest is related to: SHARCQ is related to: ModelDB is related to: Gene Expression Omnibus (GEO) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: CellFinder is related to: Nutil - Neuroimaging utilities is related to: NeuroMorpho.Org is related to: Semi-Manual Alignment to Reference Templates is related to: MeshView is related to: Single Cell Portal is related to: Brain Image Library is related to: UCSC Cell Browser is related to: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is related to: cellxgene is related to: Atlas Ontology Model has parent organization: Allen Institute is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Institute for Brain Science Sleep Study is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Institute for Brain Science Transgenic Mouse Study is parent organization of: Allen Institute Neurowiki is parent organization of: Ivy Glioblastoma Atlas Project is parent organization of: Allen Brain Atlas API is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: Allen Institute Mouse Diversity Study is parent organization of: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: ABA Adult Mouse Brain Ontology is parent organization of: NIH Blueprint NHP Atlas is parent organization of: Aging Dementia and Traumatic Brain Injury Study is parent organization of: ACQ4 is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas is parent organization of: BRAIN Cell Data Center is parent organization of: BICCN Cell Registry is parent organization of: ABA Mouse Brain: Atlas is parent organization of: Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Allen Mouse Reference Atlas Ontology is parent organization of: BICCN is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: Brain Knowledge Platform |
nif-0000-00146 | SCR_006491 | The Allen Institute for Brain Science, Allen Mouse Brain | 2026-09-12 01:00:12 | 803 | |||||||||
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VMD Resource Report Resource Website 1+ mentions |
VMD (RRID:SCR_004905) | PAMGO_VMD, VMD | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. | microbial genome sequence, genome, genome sequence, genome model, gene, image, oomycete, fungus, bacteria, phytophthora sojae, phytophthora ramorum, hyaloperonospora arabidopsidis, plant |
is used by: NIF Data Federation is related to: AmiGO has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
USDA Cooperative State Research Education and Extension Service 2002-35600-12747; USDA Cooperative State Research Education and Extension Service 2004-35600-15055; NSF MCB-0242131; NSF EF-0412213; NSF DBI-0211863 |
PMID:16381891 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_87328 | http://phytophthora.vbi.vt.edu | SCR_004905 | VBI Microbial Database, Virginia Bioinformatics Institute Microbial Database | 2026-09-12 01:00:10 | 8 | ||||
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GeneTalk Resource Report Resource Website 10+ mentions |
GeneTalk (RRID:SCR_005231) | GeneTalk | blog, community building portal, data or information resource, data repository, database, narrative resource, portal, service resource, storage service resource | A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations. | sequence variant, annotation, exome sequencing, genetic variant, gene, data sharing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22826540 | The community can contribute to this resource, Free, (during beta period) | OMICS_00270, biotools:genetalk | https://bio.tools/genetalk | SCR_005231 | GeneTalk - The Professional Network and Online Tool for Geneticists | 2026-09-12 01:00:10 | 31 | |||||
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Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology Resource Report Resource Website 1000+ mentions |
Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) | data acquisition software, data or information resource, data processing software, database, software application, software resource | Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013. | function, gene, bioinformatics, data, database, human, meta search engine, prediction, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Karlsruhe Institute of Technology; Karlsruhe; Germany |
biotools:harvester, nif-0000-10169 | https://bio.tools/harvester | SCR_008017 | Harvester IV | 2026-09-12 01:00:13 | 1480 | ||||||||
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CLC Genomics Workbench Resource Report Resource Website 100+ mentions |
CLC Genomics Workbench (RRID:SCR_011853) | data analysis software, data processing software, data visualization software, software application, software resource | Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program. | ngs, next, generation, sequencing, gene, rna, visualisation, analysis |
is listed by: OMICtools is listed by: SoftCite works with: CLC Genomics Server |
Restricted | SCR_016245, OMICS_01124 | SCR_011853 | 2026-09-12 01:00:15 | 187 | |||||||||
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SNPFILE Resource Report Resource Website 1+ mentions |
SNPFILE (RRID:SCR_009402) | software application, software library, software resource, software toolkit | Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, unix | is listed by: Genetic Analysis Software | nlx_154641 | SCR_009402 | 2026-09-12 01:00:14 | 1 |
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