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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | data processing software, alignment software, software application, software resource, image analysis software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-02-13 10:54:48 | 0 | ||||||
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Globin Gene Server Resource Report Resource Website 10+ mentions |
Globin Gene Server (RRID:SCR_001480) | Globin Gene Server | data analysis service, analysis service resource, resource, data or information resource, production service resource, source code, service resource, software resource, narrative resource, training material, database | Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles. | dna sequence, hemoglobin, mutation, globin gene cluster, sequence comparison, functional genomics, gene, alignment, genetic analysis, variant, gene expression, protein, thalassemia, globin gene, genome, pairwise alignment, multiple alignment, annotation, sequence analysis, dna |
is listed by: NIDDK Information Network (dkNET) has parent organization: Pennsylvania State University |
NLM R01LM05773; NLM R01LM05110; NIDDK DK27635 |
PMID:11857738 PMID:11480780 PMID:9799599 PMID:9576329 PMID:8088828 |
Free, Freely available | nlx_152723 | SCR_001480 | 2026-02-13 10:54:52 | 27 | ||||||
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International Mouse Strain Resource Resource Report Resource Website 10+ mentions |
International Mouse Strain Resource (RRID:SCR_001526) | IMSR | biomaterial supply resource, organism supplier, material resource | 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, RRID Community Authority |
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 | 2026-02-13 10:54:52 | 13 | ||||
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Biological Magnetic Resonance Data Bank (BMRB) Resource Report Resource Website 500+ mentions |
Biological Magnetic Resonance Data Bank (BMRB) (RRID:SCR_002296) | BioMagResBank, BMRB | data repository, storage service resource, data or information resource, service resource, database | Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. | magnetic resonance, data bank, depository, database, data repository, spectral data, quantitative data, nmr, spectroscopy, macromolecule, metabolite, metabolomics, FASEB list |
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: 3DVC is listed by: re3data.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Nucleic Acid Database is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: NRG-CING is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: CCPN Data Model has parent organization: University of Wisconsin-Madison; Wisconsin; USA is parent organization of: NMR Restraints Grid |
NLM LM05799 | PMID:18288446 PMID:17984079 PMID:12766409 PMID:36478084 |
Free, Freely available | nif-0000-21058 | SCR_002296 | BMRB, BioMagResBank, Biological Magnetic Resonance DataBank, BioMag Res Bank | 2026-02-13 10:55:00 | 752 | |||||
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Human Microbiome Compendium Resource Report Resource Website 1+ mentions |
Human Microbiome Compendium (RRID:SCR_026991) | data or information resource, portal, project portal | Project portal to build dataset of human microbiome. Provides dataset of human microbiome sequencing data processed and integrated via uniform pipelines. Sample metadata paired with amplicon and shotgun metagenomic datasets pulled from public databases. | microbiome, compendium, dataset, public data, amplicon, shotgun, metagenomics, | NLM R01LM013863 | PMID:39848248 | https://doi.org/10.5281/zenodo.8186993 | SCR_026991 | 2026-02-12 09:49:09 | 1 | |||||||||
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Michigan Molecular Interactions Resource Report Resource Website 1+ mentions |
Michigan Molecular Interactions (RRID:SCR_003521) | MiMI | web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu. | gene, interaction, molecule, protein, protein interaction, protein-protein interaction |
is related to: MiMI Plugin for Cytoscape has parent organization: National Center for Integrative Biomedical Informatics |
Michigan Center for Biological Information ; National Center for Integrative Biomedical Informatics ; Pfizer ; Medical and Academic Partnerships ; Howard Hughes Medical Institute ; Microsoft Corporation ; NLM R01 LM008106; NIDA U54 DA021519; NSF IIS 0219513 |
PMID:18978014 PMID:17130145 |
nif-0000-00214 | SCR_003521 | 2026-02-13 10:55:15 | 5 | |||||||
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PubMed Resource Report Resource Website 10000+ mentions |
PubMed (RRID:SCR_004846) | data or information resource, bibliography, database | Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut. | biomedical, literature, publication, open, access, bibliography, gold standard |
is used by: Knowledgebase for Addiction Related Genes is used by: Drug Related Gene Database is used by: ChannelPedia is used by: Molecular Imaging and Contrast Agent Database is used by: Colwiz is used by: Nowomics is used by: PINT is listed by: OMICtools is listed by: FORCE11 is listed by: LabWorm is related to: Chilibot: Gene and Protein relationships from MEDLINE is related to: ImpactStory is related to: Automated recognition of brain region mentions in neuroscience literature. is related to: Information Hyperlinked Over Proteins is related to: PubMed Central is related to: PIE the search is related to: Anne O'Tate is related to: PubBrain is related to: Europe PubMed Central is related to: ResearchGate is related to: CBioC is related to: CiteAb is related to: LitInspector is related to: RefMED is related to: Pubmed Commons is related to: iBIOFind is related to: Ensembl Variation is related to: MEDLINE is related to: XplorMed is related to: Linked Neuron Data is related to: NCBI Structure is related to: MeSH is related to: MEDLINE is related to: EBIMed is related to: Coremine Medical is related to: NIF Literature is related to: GoPubMed is related to: Integrated Auto-Extracted Annotation is related to: Polbase is related to: Integrated Manually Extracted Annotation is related to: DaTo is related to: NIF Registry Automated Crawl Data has parent organization: NCBI works with: Open Regulatory Annotation Database works with: rentrez |
NLM | Free, Freely available | nlx_82958, OMICS_01195 | http://www.force11.org/node/4652 http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed |
SCR_004846 | Pub Med | 2026-02-13 10:55:31 | 98390 | ||||||
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NCBI Sequence Read Archive (SRA) Resource Report Resource Website 5000+ mentions |
NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) | SRA | data repository, storage service resource, data or information resource, service resource, database | Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them. | sequence, blast, next-generation sequence, alignment, read placement, reference sequence, roche 454 gs system, illumina genome analyzer, applied biosystems solid system, helicos heliscope, complete genomics, pacific biosciences smrt, high-throughput sequencing, data analysis service, gold standard |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is listed by: OMICtools is related to: European Nucleotide Archive (ENA) is related to: RecountDB is related to: SRAdb is related to: DDBJ Sequence Read Archive is related to: Bgee: dataBase for Gene Expression Evolution is related to: NCBI BioSample is related to: DDBJ Sequence Read Archive is related to: METAGENOTE has parent organization: NCBI works with: SARS-CoV-2-Sequences works with: Signaling Pathways Project |
NLM | PMID:22009675 PMID:21062823 |
Free, Available for download, Freely available | OMICS_01031, nlx_86174, r3d100010775 | https://doi.org/10.17616/R31S69 | SCR_004891 | Sequence Read Archive, , SRA, NCBI SRA | 2026-02-13 10:55:31 | 6671 | ||||
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Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) Resource Report Resource Website 10+ mentions |
Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) | PDBP | material storage repository, biospecimen repository, storage service resource, service resource | Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders. | parkinson's, clinical neuroinformatics, magnetic resonance, diagnostic, progression, biomarker, clinical |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NINDS Repository is related to: MIPAV: Medical Image Processing and Visualization has parent organization: National Institute of Neurological Disorders and Stroke |
Parkinson's disease | nlm ; NINDS |
PMID:25976927 | Restricted | nlx_155919 | http://www.nitrc.org/projects/pdbp | http://pdbp.ninds.nih.gov/index.jsp | SCR_002517 | Parkinson's Disease Biomarkers Program, PDBP: Parkinsons Disease Biomarkers Program, Parkinson’s Disease Biomarkers Program Data Management Resource, PDBP DMR | 2026-02-13 10:55:03 | 24 | ||
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NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | data repository, storage service resource, data or information resource, service resource, database | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap https://bio.tools/dbgap https://doi.org/10.17616/R3GS4K |
SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-02-13 10:55:06 | 683 | ||||
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GenBank Resource Report Resource Website 10000+ mentions |
GenBank (RRID:SCR_002760) | GB | data repository, storage service resource, data or information resource, service resource, database | NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP. | genetic sequence, dna sequence, human genetics, human genome, nucleotide sequence, nucleotide, dna, dna data bank, gene mapping, genetics, gold standard |
is used by: Structural Genomics Consortium is used by: xFITOM is used by: Transcriptional Regulatory Element Database is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: CINERGI is related to: High Throughput Genomic Sequences Division is related to: DNA DataBank of Japan (DDBJ) is related to: HS3D - Homo Sapiens Splice Sites Dataset is related to: Influenza Virus Resource is related to: TPA is related to: Anopheles gambiae (African malaria mosquito) genome view is related to: Nucleotide database is related to: NCBI BioSample is related to: NCBI Nucleotide is related to: SpliceDB is related to: MaizeGDB is related to: NCBI Assembly Archive Viewer is related to: DNA DataBank of Japan (DDBJ) is related to: European Molecular Biology Laboratory is related to: INSDC is related to: NCBI Protein Database is related to: TrED is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: INSDC is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables has parent organization: NCBI is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: NCBI Genome Survey Sequences Database works with: OGDraw works with: A plasmid Editor works with: Webcutter works with: merge-gbk-records works with: PremierBiosoft Proteo IQ Software works with: SARS-CoV-2-Sequences works with: rentrez works with: MiMeDB |
NLM | PMID:24217914 PMID:23193287 PMID:21071399 |
Free, Freely available | nif-0000-02873, r3d100010528, OMICS_01650 | https://doi.org/10.17616/R3D31X | SCR_002760 | , Gen Bank, GenBank | 2026-02-13 10:55:07 | 61478 | ||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, atlas, service resource, image repository, database | 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, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb https://doi.org/10.17616/R3JC76 |
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 | 2026-02-13 10:55:06 | 13 | ||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | portal, data or information resource, atlas, narrative resource, database, topical portal, standard specification | 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 |
Free, Freely available | nif-0000-00019 | SCR_003142 | Brain Info | 2026-02-13 10:55:11 | 16 | ||||||
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FMA Resource Report Resource Website 1+ mentions |
FMA (RRID:SCR_003379) | FMA | ontology, data processing software, data or information resource, data analysis software, controlled vocabulary, software application, software resource, database | A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model. | anatomy, informatics, model, neuroanatomy, protg, reference, standard, structural, taxonomy, owl, phenotype |
is listed by: BioPortal is related to: T3DB is related to: HIV Brain Sequence Database is related to: CELDA Ontology has parent organization: University of Washington; Seattle; USA |
RSNA-NIBIB ; University of Washington; Washington; USA ; Murdock Charitable Trust ; Microsoft ; Intel Corporation ; NLM LM006822; NLM LM06316; NLM contract LM03528; NHLBI HL08770 |
PMID:18688289 PMID:18360535 PMID:16779026 |
Free, Freely available | nif-0000-00066 | http://bioportal.bioontology.org/ontologies/FMA | SCR_003379 | Foundational Model of Anatomy Ontology, Foundational Model of Anatomy | 2026-02-13 10:55:14 | 8 | ||||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | data visualization software, software resource, data processing software, software application | The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways. | protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, plugin |
is listed by: Biositemaps is related to: Cytoscape is related to: Michigan Molecular Interactions has parent organization: University of Michigan; Ann Arbor; USA has parent organization: National Center for Integrative Biomedical Informatics |
NIH ; NIDA U54 DA021519; NLM R01 LM008106; NCRR P41 RR018627 |
PMID:18812364 | nif-0000-33090 | http://mimiplugin.ncibi.org/index.html | SCR_003424 | Cytoscape Plugin for MiMI, MiMI Plugin - Cytoscape Plugin for MiMI | 2026-02-13 10:55:15 | 1 | |||||
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Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | software resource, authoring tool, software application | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-02-13 10:55:13 | 147 | |||||
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GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | data repository, storage service resource, web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-02-13 10:57:05 | 24 | ||||
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Informatics for Integrating Biology and the Bedside Resource Report Resource Website 10+ mentions |
Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) | i2b2 | training resource, portal, data set, data or information resource, organization portal, software resource | i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license. | genetic, biology, biomedical, computing, genomic, health, healthcare, informatic, origin, patient, therapy, predoctoral, postdoctoral |
is related to: National Centers for Biomedical Computing is parent organization of: i2b2 Cross-Institutional Clinical Translational Research project is parent organization of: Smoking NLP Challenge Data |
NLM U54LM008748 | Free, Public, Acknowledgement requested | nif-0000-33133 | SCR_013629 | 2026-02-13 10:57:10 | 27 | |||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | data processing software, software toolkit, software application, software resource, image analysis software | A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. | image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University; Indiana; USA |
NLM R01 LM011360; NSF IIS-1117335 |
http://www.iu.edu/~hdbig/ | SCR_014120 | High Dimensional Brain Imaging Genomics Toolkit | 2026-02-13 10:57:14 | 0 | ||||||||
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SCORE Resource Report Resource Website 100+ mentions |
SCORE (RRID:SCR_014165) | data or information resource, experimental protocol, narrative resource | A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. | experiment protocol, method, different image algorithm, quantitative score |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NLM HHSN276201000584P; NIBIB 1R41 EB011796 |
SCR_014165 | 2026-02-13 10:57:15 | 458 |
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