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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gene Ontology Resource Report Resource Website 5000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | portal, knowledge environment resource, project portal, organization portal, data or information resource, consortium | Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases. | gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: GreenPhylDB is used by: LIPID MAPS Proteome Database is used by: Aging Portal is used by: ChannelPedia is used by: Open PHACTS is used by: CoPub is used by: PhenoGO is used by: Database for Annotation Visualization and Integrated Discovery is used by: MitoMiner is used by: dcGO is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: barleyGO is used by: SynGO is used by: Functional Annotation is used by: SwissLipids is listed by: BioPortal is listed by: OBO is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: Mouse Genome Informatics: The Gene Ontology Project is related to: GenNav is related to: SynaptomeDB is related to: High-Throughput GoMiner is related to: Onto-Design is related to: OnEx - Ontology Evolution Explorer is related to: Avadis is related to: GONUTS is related to: PiNGO is related to: Automated Microarray Pipeline is related to: categoryCompare is related to: globaltest is related to: Semantic Measures Library is related to: WegoLoc is related to: AnimalTFDB is related to: MEME Suite - Motif-based sequence analysis tools is related to: Arabidopsis Hormone Database is related to: DAVID is related to: Arabidopsis thaliana Protein Interactome Database is related to: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is related to: pSTIING is related to: GoMiner is related to: FunSimMat is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Centre for Modeling Human Disease Gene Trap Resource is related to: Patterns of Gene Expression in Drosophila Embryogenesis is related to: Babelomics is related to: BioPerl is related to: GeneCruiser is related to: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool is related to: GOToolBox Functional Investigation of Gene Datasets is related to: Cotton EST Database is related to: MouseNET is related to: PLANTTFDB is related to: T-profiler is related to: Physico-Chemical Process is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: GOCat is related to: Quantitative Enrichment of Sequence Tags is related to: Neural-Immune Gene Ontology is related to: INMEX is related to: StRAnGER is related to: QuickGO is related to: Repository of molecular brain neoplasia data is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PANTHER is related to: Short Time-series Expression Miner (STEM) is related to: DATFAP is related to: GORetriever is related to: Gene Ontology Browsing Utility (GOBU) is related to: GeneTools is related to: GOSlimViewer is related to: go-moose is related to: Network Ontology Analysis is related to: Onto-Compare is related to: Onto-Express is related to: OntoVisT is related to: STRAP is related to: CGAP GO Browser is related to: COBrA is related to: Gene Class Expression is related to: GeneInfoViz is related to: GOfetcher is related to: GoFish is related to: GOProfiler is related to: GOanna is related to: Manatee is related to: Pandora - Protein ANnotation Diagram ORiented Analysis is related to: TAIR Keyword Browser is related to: Wandora is related to: GOTaxExplorer is related to: Onto-Miner is related to: Onto-Translate is related to: ToppGene Suite is related to: DBD - Slim Gene Ontology is related to: ONTO-PERL is related to: Blip: Biomedical Logic Programming is related to: OWL API is related to: CLENCH is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: CateGOrizer is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is related to: ProteInOn is related to: GeneMerge is related to: GraphWeb is related to: ClueGO is related to: CLASSIFI - Cluster Assignment for Biological Inference is related to: GOHyperGAll is related to: FuncAssociate: The Gene Set Functionator is related to: GOdist is related to: FuncExpression is related to: FunCluster is related to: FIVA - Functional Information Viewer and Analyzer is related to: GARBAN is related to: GOEx - Gene Ontology Explorer is related to: SGD Gene Ontology Slim Mapper is related to: GOArray is related to: SNPsandGO is related to: GoSurfer is related to: GOtcha is related to: MAPPFinder is related to: GoAnnotator is related to: MetaGeneProfiler is related to: OntoGate is related to: ProfCom - Profiling of complex functionality is related to: SerbGO is related to: SOURCE is related to: Ontologizer is related to: THEA - Tools for High-throughput Experiments Analysis is related to: Generic GO Term Mapper is related to: GREAT: Genomic Regions Enrichment of Annotations Tool is related to: GoBean - a Java application for Gene Ontology enrichment analysis is related to: TXTGate is related to: GO-Module is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools is related to: MalaCards is related to: FSST - Functional Similarity Search Tool is related to: Expression Profiler is related to: GOChase is related to: GoPubMed is related to: Whatizit is related to: REViGO is related to: WEGO - Web Gene Ontology Annotation Plot is related to: Blast2GO is related to: InterProScan is related to: PubSearch is related to: TrED is related to: CharProtDB: Characterized Protein Database is related to: VirHostNet: Virus-Host Network is related to: Pathbase is related to: GO Online SQL Environment (GOOSE) is related to: Neurobehavior Ontology is related to: InterSpecies Analysing Application using Containers is related to: KOBAS is related to: ConceptWiki is related to: GeneTerm Linker is related to: Bioconductor is related to: ErmineJ is related to: Gene Ontology For Functional Analysis (GOFFA) is related to: MGI GO Browser is related to: Comparative Toxicogenomics Database (CTD) is related to: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is related to: Ontology Lookup Service is related to: LexGrid is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: g:Profiler is related to: OwlSim is related to: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool is related to: YeTFaSCo is related to: FastSemSim is related to: RamiGO is related to: AutismKB is related to: GeneCodis is related to: FunSpec is related to: FunNet - Transcriptional Networks Analysis is related to: PhenoM - Phenomics of yeast Mutants is related to: agriGO is related to: GOblet is related to: DynGO is related to: SeqExpress is related to: ProbeExplorer is related to: ECgene: Gene Modeling with Alternative Splicing is related to: Organelle DB is related to: Gemma is related to: Candidate Genes to Inherited Diseases is related to: Proteome Analyst PA-GOSUB is related to: Network Analysis, Visualization and Graphing TORonto is related to: GOstat is related to: Onto-Express To Go (OE2GO) is related to: Tk-GO is related to: EGAN: Exploratory Gene Association Networks is related to: Spotfire is related to: GOMO - Gene Ontology for Motifs is related to: GFINDer: Genome Function INtegrated Discoverer is related to: Generic GO Term Finder is related to: Agile Protein Interactomes DataServer is related to: AgingDB is related to: UBERON is related to: Algal Functional Annotation Tool is related to: gsGator is related to: Flash Gviewer is related to: Cerebellar Development Transcriptome Database is related to: PlantNATsDB - Plant Natural Antisense Transcripts DataBase is related to: EASE: the Expression Analysis Systematic Explorer is related to: PiGenome is related to: L2L Microarray Analysis Tool is related to: MeGO is related to: CELDA Ontology is related to: Diabetes Disease Portal is related to: MatrixDB is related to: Kidney and Urinary Pathway Knowledge Base is related to: MouseCyc is related to: Candida Genome Database is related to: Honey Bee Brain EST Project is related to: ECO is related to: FlyMine is related to: Gramene is related to: 3D-Interologs is related to: Biomine is related to: UniProtKB is related to: NCBI BioSystems Database is related to: EBIMed is related to: Coremine Medical is related to: EMAGE Gene Expression Database is related to: GeneMANIA is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: GeneTrail is related to: Magic is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: InterPro is related to: InnateDB is related to: canSAR is related to: HPRD - Human Protein Reference Database is related to: CRCView is related to: Integrated Manually Extracted Annotation is related to: LegumeIP is related to: Renal Disease Portal is related to: PhenoGO is related to: DOAF is related to: OBO is related to: biomaRt is related to: OncoboxPD is parent organization of: AmiGO is parent organization of: GOlr is parent organization of: RefGenome is parent organization of: OBO-Edit is parent organization of: OWLTools is parent organization of: Gene Ontology Tools is parent organization of: Gene Ontology Extension is parent organization of: SO is parent organization of: go-db-perl is parent organization of: go-perl works with: topGO works with: DIANA-mirPath works with: GOnet |
European Union QLRI-CT-2001-0098; European Union QLRI-CT-2001-00015; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
The community can contribute to this resource, Acknowledgement required | biotools:go, OMICS_02278, nif-0000-02915 | http://bioportal.bioontology.org/ontologies/GO https://bio.tools/go |
SCR_002811 | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2025-04-02 11:02:30 | 9965 | ||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, production service resource, atlas, database, data repository, data or information resource, service resource, data analysis service, storage service resource, image repository | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2025-04-02 11:02:28 | 13 | ||||
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EEGbase Resource Report Resource Website 1+ mentions |
EEGbase (RRID:SCR_001452) | database, data repository, data or information resource, service resource, storage service resource | EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework. | eeg, erp, experiments, data storage and management, EEG/ERP data, EEG/ERP experiments, |
uses: NIX uses: Open metadata mark up language is used by: NIF Data Federation has parent organization: University of West Bohemia; Pilsen; Czech Republic |
Ministry of Education Czech Science Foundation | nif-0000-08190 | http://eegdatabase.kiv.zcu.cz/ | SCR_001452 | 2025-04-02 11:00:47 | 7 | ||||||||
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Intestinal Stem Cell Consortium Resource Report Resource Website 10+ mentions |
Intestinal Stem Cell Consortium (RRID:SCR_001555) | ISCC | portal, database, resource, catalog, organization portal, data or information resource, consortium, narrative resource, experimental protocol | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh. | intestinal, epithelial stem cell, development, homeostasis, regeneration, disease, intestine, stem cell, intestinal stem cell, intestinal epithelium, stem cell, antibody, epithelium, data set |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
NIDDK U01DK085532 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152862 | SCR_001555 | ISCC - Intestinal Stem Cell Consortium | 2025-04-02 11:00:53 | 19 | ||||||
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International Mouse Strain Resource Resource Report Resource Website 10+ mentions |
International Mouse Strain Resource (RRID:SCR_001526) | IMSR | material resource, biomaterial supply resource, organism supplier | Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known. | RIN, Resource Information Network, mouse, strain, stock, inbred, mutant, genetically engineered, embryo, embryonic stem cell line, database, knockout mouse, mutant mouse strain, transgenic mouse, embryonic mouse, live mouse, gamete, ovary, sperm, germplasm, model organism |
uses: Vanderbilt Cryopreserved Mouse Repository uses: Janvier Labs uses: Korea Mouse Phenotyping Center uses: CLEA Japan, Inc. uses: genOway uses: Inotiv uses: Cyagen Biosciences uses: Cam-Su Genomic Resource Center is used by: BioSample Database at EBI is used by: Integrated Animals lists: Oak Ridge Collection at JAX lists: National Resource Center for Mutant Mice lists: JAX Mice and Services lists: National Applied Research Laboratories lists: Oriental BioService Inc. is listed by: Resource Information Network is related to: NIF Data Federation is related to: Recombinase (cre) Activity is related to: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines is related to: Mouse Genome Informatics (MGI) has parent organization: MRC Mammalian Genetics Unit works with: Shanghai Model Organisms Center works with: European Mouse Mutant Archive works with: Texas A and M Institute for Genomic Medicine works with: JAX Mice and Services works with: CMMR - Canadian Mouse Mutant Repository works with: RIKEN BioResource Center works with: Center for Animal Resources and Development works with: National Institute of Genetics; Shizuoka; Japan works with: NHMRC Australian PhenomeBank works with: Taconic Biosciences works with: Charles River Laboratories works with: Medical Research Council Harwell: An International Centre for Mouse Genetics |
NLM LM009693 | PMID:10098412 PMID:26373861 |
Restricted | nif-0000-09876 | http://www.findmice.org/ | SCR_001526 | IMSR, International Mouse Strain Resource | 2025-04-02 11:00:51 | 10 | ||||
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Integrated Animals Resource Report Resource Website |
Integrated Animals (RRID:SCR_001421) | material resource, biomaterial supply resource, organism supplier | Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish). | non human animal, mutant, database, integrated, nif, FASEB list |
uses: Mouse Genome Informatics (MGI) uses: Beta Cell Biology Consortium uses: Zebrafish Information Network (ZFIN) uses: International Mouse Strain Resource uses: Bloomington Drosophila Stock Center uses: Rat Genome Database (RGD) uses: Zebrafish International Resource Center uses: Ambystoma Genetic Stock Center uses: Kyoto Stock Center uses: FlyBase uses: Mutant Mouse Resource and Research Center uses: National Swine Resource and Research Center uses: National Xenopus Resource uses: CWRU In Vivo Animal Facilities uses: Sperm Stem Cell Libraries for Biological Research uses: Tetrahymena Stock Center uses: WormBase uses: Xiphophorus Genetic Stock Center is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nif-0000-08137 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_154697-1 http://neuinfo.org/nif/nifgwt.html?query=nif-0000-08137, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-08137-1 | SCR_001421 | NIF Animals, NIF Integrated Animals, Integrated Animal | 2025-04-02 11:00:45 | 0 | |||||||
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BrainSpan Resource Report Resource Website |
BrainSpan (RRID:SCR_004219) | expression atlas, atlas, data or information resource | Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis. | brain, development, brain development, exon, microarray, gene, rna-seq, expression value, expression |
is used by: NIF Data Federation has parent organization: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) |
Free, Freely available | nlx_98194, nlx_86215, SCR_004877, SCR_005029, SCR_004344, nlx_37081, nlx_2397 | http://brainspan.org/rnaseq/downloads.html?format=html http://brainspan.org/docs.html |
http://brainspan.org/docs.html | SCR_004219 | BrainSpan: RNA-Seq exons, BrainSpan - Exon microarray summarized to genes | 2025-04-02 11:03:20 | 0 | ||||||
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Royal College of Psychiatrists Podcasts Resource Report Resource Website |
Royal College of Psychiatrists Podcasts (RRID:SCR_003913) | RC PSYCH Podcasts | narrative resource, podcast, data or information resource | Each month our podcast team will be broadcasting the very latest breakthroughs and discoveries in neurosciences, psychiatry and psychology. | neuroscience, psychiatry, psychology |
is used by: NIF Data Federation is related to: Integrated Podcasts |
For personal, Non-commercial use | nlx_15826 | SCR_003913 | LetWisdomGuide, Let Wisdom Guide | 2025-04-02 11:03:09 | 0 | |||||||
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All In The Mind Resource Report Resource Website |
All In The Mind (RRID:SCR_004240) | narrative resource, podcast, data or information resource | Radio National''s weekly foray into all things mental a program (podcast) about the mind, brain and behavior, hosted by Lynne Malcolm (previously by Natasha Mitchell). From dreaming to depression, addiction to artificial intelligence, consciousness to coma, psychoanalysis to psychopathy, free will to forgetting ��All in the Mind��explores the human condition through the mind''s eye. All in the Mind brings together unexpected voices, themes and ideas and engages with both leading thinkers and personal stories. Psychology and human behavior are only part of the equation. The program''s scope is considerably broader and explores themes in science, religion, health, philosophy, education, history and pop culture, with the mind as the key focus. | mental, mind, brain, behavior, dream, depressive disorder, addiction, artificial intelligence, consciousness, coma, psychoanalysis, psychopathy, free will, forget, human, psychology, human behavior, science, religion, health, philosophy, education, history, pop culture |
is used by: NIF Data Federation is related to: Integrated Podcasts |
nlx_25223 | SCR_004240 | 2025-04-02 11:03:21 | 0 | ||||||||||
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studyforrest.org Resource Report Resource Website 10+ mentions |
studyforrest.org (RRID:SCR_003112) | studyforrest.org | service resource, data repository, storage service resource, image repository | An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data. | neuroimaging, open data, brain, brain scan, fmri, stimulus material, participant demographic, stimulus, demographic, experimental protocol, structure mri, mri, 7-tesla, data set, auditory system, language, perception |
uses: OpenNeuro uses: rsync uses: XNAT - The Extensible Neuroimaging Archive Toolkit is used by: NIF Data Federation is listed by: NITRC-IR is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
BMBF 01GQ1112; BMBF 01GQ1411; NSF 1129855; DFG PO 548/15-1 |
ODC Public Domain Dedication and License, Acknowledgement requested | nlx_156710 | http://www.nitrc.org/projects/studyforrest | SCR_003112 | study forrest, studyforrest | 2025-04-02 11:02:38 | 33 | |||||
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SciCrunch Resource Report Resource Website 10+ mentions |
SciCrunch (RRID:SCR_003115) | SciCrunch | community building portal, database, portal, data or information resource | Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation. | Data sharing, community, data, RRID, portal, data discovery, data accessibility, data visibility, data interoperability, scientific publication data, data access |
uses: NIF Data Federation uses: SciBot uses: SciGraph is used by: SPARC Project is related to: Neuroscience Information Framework is related to: SciScore is related to: SciBot is related to: SPARC Anatomy Working Group is related to: PRECISE Traumatic Brain Injury Model Catalog has parent organization: University of California at San Diego; California; USA is parent organization of: Aging Portal is parent organization of: NIDDK Information Network (dkNET) is parent organization of: Resource Identification Portal is parent organization of: Integrated Datasets is parent organization of: Integrated is parent organization of: InterLex |
Restricted | nlx_156715 | SCR_003115 | 2025-04-02 11:02:38 | 18 | ||||||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | standard specification, topical portal, atlas, portal, database, data or information resource, narrative resource | Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. | brain, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is related to: INIA19 Primate Brain Atlas has parent organization: University of Washington; Seattle; USA has parent organization: University of California at San Diego; California; USA |
The Human Brain Project ; NIBIB ; NLM LM/OD-06243; NIH Office of the Director LM/OD-06243; NIMH MHO69259; NCRR RR-00166 |
PMID:21789500 PMID:21163300 PMID:18368361 PMID:15055392 |
Contents of this work may be downloaded, Copied, Cited and disseminated provided that proper attribution is given: BrainInfo (1991-present), National Primate Research Center, University of Washington, Http://www.braininfo.org. | nif-0000-00019 | SCR_003142 | Brain Info | 2025-04-02 11:02:38 | 16 | ||||||
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ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | database, data repository, catalog, service resource, data or information resource, storage service resource | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Union ; SLING 226073; European Commission ; Gen2Phen 200754; NHGRI P41 HG003619 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123 | http://www.ebi.ac.uk/microarray-as/ae | SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2025-04-02 11:02:33 | 7192 | ||||
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Developmental Therapeutics Program Resource Report Resource Website 500+ mentions |
Developmental Therapeutics Program (RRID:SCR_003057) | DTP | topical portal, portal, data or information resource, service resource, funding resource | Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example. | cell line, drug discovery, drug development, drug, treatment, therapy, biopharmaceutical, bortezomib, paclitaxel, romidepsin, eribulin, sipuleucel-t, anticancer therapeutic, compound, natural product extract, animal model, in vivo, in vitro, chemical structure, chemical, structure, anti-hiv, anticancer, molecular structure, database, chemotherapeutic agent, testing, drug synthesis, chemistry, grant, contract, information technology, molecular pharmacology, natural product, pharmaceutical, screening technology, toxicology, pharmacology, screening, FASEB list |
is used by: NIF Data Federation is related to: Integrated Cell Lines has parent organization: National Cancer Institute |
Cancer, Tumor | NCI | Public | nif-0000-30447 | SCR_003057 | Developmental Therapeutics Program NCI/NIH | 2025-04-02 11:02:36 | 539 | |||||
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Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | database, data repository, data or information resource, service resource, storage service resource, narrative resource, experimental protocol | Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. | female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Special Mouse Strains Resource is related to: Vertebrate Trait Ontology is related to: GenomeMUSter has parent organization: Jackson Laboratory |
NIDA ; NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIMH MH071984; NIDA DA028420 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Restricted | biotools:mpd, nif-0000-03160 | https://bio.tools/mpd | http://www.jax.org/phenome | SCR_003212 | Mouse Phenome Database | 2025-04-02 11:02:40 | 215 | |||
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Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | database, data repository, data or information resource, service resource, storage service resource, image repository | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation 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: re3data.org is listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639 | http://www.cellimagelibrary.org/pages/about https://bio.tools/cellimagelibrary |
SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2025-04-02 11:02:52 | 17 | ||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, production service resource, database, data analysis service, service resource, data or information resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | nif-0000-03390, biotools:reactome | https://bio.tools/reactome | SCR_003485 | Reactome Functional Interaction Network | 2025-04-02 11:02:51 | 3580 | |||||
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Animal QTLdb Resource Report Resource Website 10+ mentions |
Animal QTLdb (RRID:SCR_001748) | Animal QTLdb | database, data repository, data or information resource, service resource, storage service resource | Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome. | chromosome, comparative genomics, dna sequence, genome, livestock, quantitative trait locus, non-human animal, structural genomics, single-nucleotide polymorphism, gene association, genomics, trait, copy number variation, trait, phenotype, expression, eqtl, genome wide association study, candidate gene, genotype |
uses: Entrez Gene uses: Ensembl is used by: NIF Data Federation is used by: MONARCH Initiative is listed by: re3data.org is related to: Ensembl Variation is related to: Vertebrate Trait Ontology has parent organization: Iowa State University; Iowa; USA has parent organization: NAGRP Bioinformatics Coordination Program |
USDA NRSP-8; USDA 2007-04187 |
PMID:23180796 PMID:17245610 |
Free, Freely available | nif-0000-02550 | http://www.animalgenome.org/QTLdb/ | SCR_001748 | Animal QTL database, Animal Quantitative Trait Loci database, AnimalQTLdb, Animal Quantitative Trait Loci (QTL) database | 2025-04-02 11:01:08 | 48 | ||||
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AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | analysis service resource, production service resource, database, data analysis service, service resource, data or information resource | Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium. | search, sort, analyze, visualize, data, ontology, gene, annotation, FASEB list |
uses: GOlr is used by: NIF Data Federation is listed by: OMICtools is listed by: Gene Ontology Tools is related to: ASAP is related to: Candida Genome Database is related to: Berkeley Bioinformatics Open-Source Projects is related to: ECO is related to: Zebrafish Information Network (ZFIN) is related to: Gramene is related to: WormBase is related to: NCBI Protein Database is related to: UniProtKB is related to: GeneDB Lmajor is related to: TAIR is related to: SGD is related to: GeneDB Tbrucei is related to: VMD is related to: JCVI CMR is related to: go-db-perl is related to: Mouse Genome Informatics (MGI) is related to: NCBI is related to: FlyBase is related to: GeneDB Pfalciparum is related to: PomBase is related to: Pseudomonas Genome Database is related to: Dictyostelium discoideum genome database is related to: Plant Ontology is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: MeGO is related to: ASPGD is related to: EcoCyc is related to: Reactome is related to: SGN is related to: GO-Module is related to: Songbird Brain Transcriptome Database is related to: Rat Genome Database (RGD) is related to: RamiGO has parent organization: Gene Ontology |
NHGRI P41 HG002273 | PMID:19033274 | Free, Available for download, Freely available | nif-0000-20935, OMICS_02266 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2025-04-02 11:01:39 | 1187 | ||||
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ASPGD Resource Report Resource Website 100+ mentions |
ASPGD (RRID:SCR_002047) | ASPGD, ASPGD LOCUS, ASPGD REF | database, data repository, data or information resource, service resource, storage service resource | Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. | function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Candida Genome Database is related to: AmiGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Broad Institute |
NIAID R01 AI077599 | PMID:19773420 | Free, Public | nif-0000-12244, biotools:aspgd | http://www.aspergillusgenome.org/ https://bio.tools/aspgd |
SCR_002047 | Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS | 2025-04-02 11:01:30 | 211 |
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