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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | data or information resource, database, service resource | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | Beta Cell Consortium ; NHGRI U54 HG 004558 |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-09-05 06:32:15 | 161 | |||||||||
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MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | data or information resource, database | Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. | Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list | Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Charles E. Culpeper Scholarship in Medical Science ; Howard Hughes Medical Institute ; NIDDK DK43351; NIDDK DK57521; NIGMS GM0077465 |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | MitoCarta2.0 | 2026-09-05 06:32:15 | 208 | ||||||||
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Geno2MP Resource Report Resource Website 1+ mentions |
Geno2MP (RRID:SCR_016872) | Geno2MP | data or information resource, database, service resource | Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community. | data, collection, Mendelian, phenotype, affected, individuals, profile, human, genetics |
is used by: MARRVEL is listed by: OMICtools |
University of Washington Center for Mendelian Genomics ; Seattle ; WA |
Free, Available for download, Freely available | SCR_016872 | Geno2MP, 2 Mendelian Phenotype, The Genotype 2 Mendelian Phenotype database | 2026-09-05 06:32:14 | 2 | |||||||
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GeneFriends Resource Report Resource Website 1+ mentions |
GeneFriends (RRID:SCR_021625) | data or information resource, database | Human RNA-seq-based gene and transcript co-expression database.Functional genomics tool based on gene co-expression map that describes which genes tend to be activated and deactivated simultaneously in large number of RNAseq data samples. | Human, RNA-seq-based gene, RNAseq data, gene co-expression network, candidate gene prioritization, functional genomics, | Biotechnology and Biological Sciences Research Council | Free, Freely available | SCR_021625 | 2026-09-05 06:32:17 | 6 | ||||||||||
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Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | atlas, data or information resource, portal, project portal | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-09-05 06:28:16 | 237 | ||||||||
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Italian Institute for Genomic Medicine; Turin; Italy Resource Report Resource Website |
Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) | IIGM, HuGeF | data or information resource, portal, topical portal | Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience. | institute, private, research, human, genetic, genomic, epigenomic, immunogenetic, quantitative, biology, computational, neuroscience | is parent organization of: HaTSPiL | SCR_017062 | 2026-09-05 06:28:18 | 0 | ||||||||||
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Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | data or information resource, data repository, service resource, storage service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-09-05 06:28:18 | 17 | |||||||
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SPARC Portal Resource Report Resource Website 100+ mentions |
SPARC Portal (RRID:SCR_017041) | SPARC.science | data repository, service resource, storage service resource | SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short. | Nervous system, periphery, organ, human, FASEB list, repository, curated |
uses: Protocols.io uses: Brain Imaging Data Structure (BIDs) uses: Physiome Model Repository uses: SciGraph uses: o²S²PARC uses: SODA uses: Blackfynn Discover uses: ApiNATOMY uses: Biolucida uses: TissueMaker uses: ScaffoldMaker uses: ScaffoldFitter uses: OpenCOR uses: Pennsieve Data Management Platform uses: InterLex uses: Neurolucida 360 uses: SciCrunch uses: Tissue Mapper uses: Vesselucida 360 uses: DataCite uses: TissueMaker is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is recommended by: National Library of Medicine is related to: SPARC Anatomy Working Group is related to: HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS is related to: NIH PRECISION Human Pain Network is related to: SCKAN Explorer is related to: SCKANNER works with: SPARC Data Standard has organization facet: o²S²PARC has organization facet: SODA has organization facet: SPARC Anatomy Working Group has organization facet: Blackfynn Discover has organization facet: ApiNATOMY has organization facet: Pennsieve Data Management Platform |
NIH Office of the Director OD023849; NIH Office of the Director OD024908; NIH Office of the Director OD025306; NIH Office of the Director OD025349; NIH Office of the Director OD026585; NIH Office of the Director OD030213; NIH Office of the Director OD030541; NIH Office of the Director OD032619 |
PMID:34248680 DOI:10.1101/2021.02.10.430563 |
Free, Freely available, | DOI:10.26275, r3d100013719 | https://commonfund.nih.gov/sparc, https://docs.sparc.science/, https://data.sparc.science/, https://doi.org/10.26275, https://doi.dx/10.26275, https://sparc.science/data?type=dataset, https://doi.org/10.17616/R31NJN2V | SCR_017041 | , SPARC Project, SPARC Repository, Stimulating Peripheral Activity to Relieve Conditions | 2026-09-05 06:28:17 | 119 | ||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, data processing software, software application, software resource | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | Carver Chair in Molecular Medicine ; Fraternal Order of Eagles Diabetes Research Center ; NHLBI R24 HL123482; NIDDK R01 DK115791; NIDDK R24 DK096518; NIGMS T32 GM082729; University of Iowa Center for Gene Therapy |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-09-05 06:28:16 | 5 | |||||||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NHGRI HG005998; NIGMS P50 GM071508; NIGMS R01 GM071966 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-09-05 06:28:23 | 8 | ||||||||
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TissueAtlas Resource Report Resource Website 10+ mentions |
TissueAtlas (RRID:SCR_017352) | atlas, data access protocol, data or information resource, database, software resource, web service | Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues. | Human, miRNA, tissue, atlas, data, distribution, expression | has parent organization: Saarland University; Saarbrucken; Germany | FP7 project BestAgeing ; Saarland University ; Germany ; Siemens Healthcare |
PMID:26921406 | Free, Freely available | SCR_017352 | 2026-09-05 06:28:23 | 37 | ||||||||
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Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | data analysis software, data processing software, simulation software, software application, software resource | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | 2026-09-05 06:28:24 | 13 | |||||
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Accessible Resource for Integrated Epigenomics Studies Resource Report Resource Website 50+ mentions |
Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) | data access protocol, data or information resource, portal, software resource, topical portal, web service | Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time. | Epigenomic, human, tissue, DNA, methylation, data, peripheral, blood | BBSRC ; Medical Research Council ; University of Bristol ; Wellcome Trust |
PMID:25991711 | Free, Freely available | http://www.bristol.ac.uk/alspac/ | SCR_017492 | ARIES | 2026-09-05 06:28:25 | 50 | |||||||
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Canadian Epigenetics, Environment and Health Research Consortium Network Resource Report Resource Website |
Canadian Epigenetics, Environment and Health Research Consortium Network (RRID:SCR_017491) | consortium, data or information resource, organization portal, portal | Network to connect Canadian epigenetics researchers and expand their reach to broader health research community in Canada and beyond. Curated epigenomics sequence focused on common human diseases. | Curated, epigenomic, sequence, human, disease | is related to: International Human Epigenome Consortium | Canadian Institutes of Health Research (CIHR) ; Genome Canada |
Free, Freely available | SCR_017491 | CEEHRC Network | 2026-09-05 06:28:25 | 0 | ||||||||
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HIRN Human Pancreas Analysis Consortium Resource Report Resource Website |
HIRN Human Pancreas Analysis Consortium (RRID:SCR_017583) | HIRN HPAC | consortium, data or information resource, organization portal, portal | Consortium is investigating physical and functional organization of human islet tissue environment, cell-cell relationships within pancreatic tissue ecosystem, and contributions of non endocrine components (acinar, ductal, vascular, perivascular, neuronal, lymphatic, immune) to islet cell function and dysfunction. HPAC consists of research grants as well as the Human Pancreas Analysis Program (HPAP). | Physical, functional, organization, human, islet, tissue, environment, cell, relationship, pancreatic, tissue, ecosystem, non, endocrine, HPAP, grant |
is parent organization of: HIRN Human Pancreas Analysis Program is organization facet of: Human Islet Research Network (HIRN) |
SCR_017583 | Human Pancreas Analysis Consortium | 2026-09-05 06:28:26 | 0 | |||||||||
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JWatcher Resource Report Resource Website 50+ mentions |
JWatcher (RRID:SCR_017595) | data acquisition software, data analysis software, data analytics software, data processing software, software application, software resource | Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer. | Quantitative, analysis, behavior, theoretical, problem, action, scored, human, observer |
has parent organization: University of California at Los Angeles; California; USA has parent organization: Macquarie University; Sydney; Australia |
Australian Research Council ; Macquarie University ; NIMH R21 MH065226 |
Free, Available for download, Freely available | SCR_017595 | 2026-09-05 06:28:26 | 53 | |||||||||
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MoTrPAC Data Hub Resource Report Resource Website 10+ mentions |
MoTrPAC Data Hub (RRID:SCR_017611) | MoTrPAC Data Hub | consortium, data or information resource, database, organization portal, portal | National research consortium designed to discover and perform preliminary characterization of range of molecular transducers that underlie effects of physical activity in humans. Used to study molecular changes that occur during and after exercise and to advance understanding of how physical activity improves and preserves health. Six year program into mechanisms of how physical activity improves health and prevents disease led by NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering. | Discover, premilinary, characterization, range, molecular, transducer, physical, activity, human, changes, health, prevent, disease | is listed by: NIDDK Information Network (dkNET) | NIH Common Fund | Restricted | SCR_017611 | Molecular Transducers of Physical Activity Consortium Data Hub | 2026-09-05 06:28:26 | 20 | |||||||
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Bio Resource for Array Genes Database Resource Report Resource Website |
Bio Resource for Array Genes Database (RRID:SCR_000748) | data or information resource, database | Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona. | drug, experiment, expression, fly, functional, gene, array, biological, biology, c. elegans, cluster, database, disease, human, microarray, mouse, protein, rat, target, tissue | has parent organization: University of Arizona; Arizona; USA | nif-0000-10165 | SCR_000748 | BioRag | 2026-09-05 06:31:12 | 0 | |||||||||
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Eide Neurolearning Blog Resource Report Resource Website |
Eide Neurolearning Blog (RRID:SCR_000680) | Eide Neurolearning Blog | blog, data or information resource, narrative resource | Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more. | learning, brain, learning style, problem-solving, creativity, child, family, parenting, gifted learner, visual learner, dyslexia, attention deficit disorder, autism, human, working memory | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144589 | SCR_000680 | 2026-09-05 06:31:11 | 0 | |||||||||
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Proteomics and Human Proteome: From Bench to Bedside Resource Report Resource Website |
Proteomics and Human Proteome: From Bench to Bedside (RRID:SCR_000285) | data or information resource, video resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This website contains lecture videos from the events and discussions of the SEProt congress meeting, the theme of which is Human proteome. From Bench to Bedside. Sponsors: These videos are supported by the University of Navarra. | congress, human, lecture, proteome | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10402 | SCR_000285 | Proteomics Meeting | 2026-09-05 06:31:10 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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