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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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BrainSpan Resource Report Resource Website 1+ mentions |
BrainSpan (RRID:SCR_004219) | atlas, data or information resource, expression atlas | 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 | SciCrunch Registry | BrainSpan: RNA-Seq exons, BrainSpan - Exon microarray summarized to genes | 2026-10-31 12:13:44 | 3 | ||||||
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All In The Mind Resource Report Resource Website |
All In The Mind (RRID:SCR_004240) | data or information resource, narrative resource, podcast | 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 | SciCrunch Registry | 2026-10-31 12:13:41 | 0 | ||||||||||
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dkCOIN Resource Report Resource Website 1+ mentions |
dkCOIN (RRID:SCR_004438) | dkCOIN | data or information resource, database, resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO). | gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cell |
is used by: NIF Data Federation is related to: Beta Cell Biology Consortium is related to: NIDDK Information Network (dkNET) is related to: National Mouse Metabolic Phenotyping Centers is related to: Nuclear Receptor Signaling Atlas is related to: Diabetic Complications Consortium is related to: T1DBase is related to: OBO has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIDDK 3U01DK072473-05S3; NIDDK 5U24DK076169; NIDDK U19DK062434 |
PMID:22734043 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44256 | SCR_004438 | SciCrunch Registry | NIDDKConsortium Interconnectivity Network | 2026-10-31 12:13:54 | 1 | |||||
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Biointeractive Resource Report Resource Website 10+ mentions |
Biointeractive (RRID:SCR_004388) | BioInteractive | data or information resource, narrative resource, podcast, training material, training resource, video resource | Collection of biology-focused teaching materials created and administered by the Howard Hughes Medical Institute including free lectures, videos and animations for science education. Many of the resources are also available on DVD and CD-ROM. In addition to the resources on the website, BioInteractive offers DVDs of HHMI''s annual Holiday Lectures on Science and CD-ROMs of the Virtual Lab series. These materials are available to educators for free and can be ordered from the catalog at http://catalog.hhmi.org. Each Holiday Lectures on Science is a set of four one-hour lectures presented each December at the headquarters of the Howard Hughes Medical Institute in Chevy Chase, Maryland . The lectures give students and teachers the opportunity to learn about cutting-edge biomedical research directly from some of the world''s leading scientists. Intended to inspire young students to pursue careers in science, the lectures bring the latest developments in a rapidly moving field of research into the classroom. The lectures are primarily geared to high school students in honors and Advanced Placement biology classes. Other high school students and undergraduates can certainly benefit from the content of the lectures. Some of the related materials on the biointeractive website (http://www.biointeractive.org/) are aimed at a broader audience. With a teacher''s guidance, middle school students can also enjoy learning about the topic. Holiday Lectures are webcast live at http://www.hhmi.org/biointeractive/hl/. Following the live event, they are available as on-demand streaming video at the same Web address. Webcasts of all past Holiday Lectures are available as on-demand streaming video at http://www.hhmi.org/biointeractive/lectures/index.html. Holiday Lectures are also available as podcasts from http://www.hhmi.org/biointeractive/podcast_popup.html | teaching, animation, lecture, evolution, infectious disease, biodiversity, stem cell, obesity, cancer, genomics, chemical genetics, sex determination, biological clock, cardiovascular, immunology, dna, rna, transgenic fly, bacterial identification, cardiology, neurophysiology, immunology, teacher guide, activity, poster |
is used by: NIF Data Federation is used by: Integrated Videos is related to: Integrated Podcasts has parent organization: Howard Hughes Medical Institute |
nlx_40070 | SCR_004388 | SciCrunch Registry | HHMI BioInteractive, Howard Hughes Medical Institute BioInteractive | 2026-10-31 12:13:53 | 12 | ||||||||
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Brain Science Podcast Resource Report Resource Website |
Brain Science Podcast (RRID:SCR_004491) | BSP | data or information resource, narrative resource, podcast | Podcast, hosted by Dr. Ginger Campbell, featuring the latest books about neuroscience as well as interviews with leading scientists from around the world. In this podcast, she shares recent discoveries from the world of neuroscience in a way that people of all backgrounds can enjoy. Dr. Campbell is an experienced emergency physician with a long-standing interest in mind-body medicine, the brain, and consciousness. She believes that understanding how the brain works gives us insight into what makes us human. She is also committed to showing how the scientific method has unraveled many long-standing mysteries. Brain Science Transcripts are also available. | neuroscience, brain, interview, consciousness, mind |
is used by: NIF Data Federation is related to: Integrated Podcasts |
nlx_47745 | SCR_004491 | SciCrunch Registry | 2026-10-31 12:13:56 | 0 | |||||||||
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UCSF Laboratory for Visual Neuroscience Resource Report Resource Website |
UCSF Laboratory for Visual Neuroscience (RRID:SCR_004913) | Laboratory for Visual Neuroscience | data or information resource, image, laboratory portal, organization portal, portal, video resource | Devise better ways to prevent and treat vision loss due to amblyopia and strabismus, and to advance medical science by understanding the human visual system. Various Images, Videos and Talks related to the research are available. In the Laboratory for Visual Neuroscience at the University of California, San Francisco, we are seeking to discover how visual perception occurs in the human brain. The function of the visual system is to guide our behavior by providing an efficient means for the rapid assimilation of information from the environment. As we navigate through our surroundings, a continuous stream of light images impinges on our eyes. In the back of each eye a light-sensitive tissue, the retina, converts patterns of light energy into electrical discharges known as action potentials. These signals are conveyed along the axons of retinal ganglion cells to the lateral geniculate body, a relay nucleus in the thalamus. Most of the output of the lateral geniculate body is relayed directly to the primary visual cortex (striate cortex, V1), and then to surrounding visual association areas. To understand the function of the visual pathways, our research is focused on 5 major themes: * Organization of Primary Visual Cortex * Mapping of Extrastriate Visual Cortex * Amblyopia and Visual Development * Strabismus and Visual Suppression * The Human Visual Cortex | amblyopia, strabismus, human, visual system, ophthalmology, monkey, eye, vision loss, patient, research, education, pediatric ophthalmology, neuro-ophthalmology, pediatric, primary visual cortex, vision |
is used by: NIF Data Federation is used by: Integrated Videos has parent organization: University of California at San Francisco; California; USA |
PMID:17898211 | nlx_143941 | SCR_004913 | SciCrunch Registry | University of California San Francisco Laboratory for Visual Neuroscience | 2026-10-31 12:14:05 | 0 | |||||||
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GeneDB Tbrucei Resource Report Resource Website 10+ mentions |
GeneDB Tbrucei (RRID:SCR_004786) | GeneDB_Tbrucei, GeneDB Tbrucei, GeneDB T. brucei | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries. | blast, sequence, annotation, genome |
is used by: NIF Data Federation is related to: AmiGO is related to: TriTrypDB has parent organization: GeneDB |
Wellcome Trust | PMID:16020726 | nlx_78417 | SCR_004786 | SciCrunch Registry | Trypanosoma brucei TREU927 homepage on GeneDB, Trypanosoma brucei TREU927 on GeneDB | 2026-10-31 12:14:02 | 17 | ||||||
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Integrated Podcasts Resource Report Resource Website |
Integrated Podcasts (RRID:SCR_004948) | data or information resource, database, narrative resource, podcast | A virtual database currently indexing multiple podcast resources including: The Brain Science Podcast, Nature Podcast, NeuroPod, Science Podcast, The American Journal of Psychiatry Podcast, 60-Second Mind, and Science Talk. | podcast, integrated, database |
is used by: NIF Data Federation is related to: Brain Science Podcast is related to: Nature Podcast is related to: NeuroPod is related to: Science Podcast is related to: American Journal of Psychiatry Podcasts is related to: 60-Second Mind is related to: Science Talk is related to: Gray Matters is related to: This Week In Science is related to: Neurology Podcast is related to: MNI Podcasts is related to: Biointeractive is related to: National Academy of Sciences Podcasts is related to: BrainPod is related to: Royal College of Psychiatrists Podcasts is related to: The Guardian: Science Weekly is related to: All In The Mind 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 | nlx_91615 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-9 http://neuinfo.org/nif/nifgwt.html?query=nlx_91615, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_91615-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-9 | SCR_004948 | SciCrunch Registry | NIF Integrated Podcasts, Integrated Podcasts View | 2026-10-31 12:14:01 | 0 | |||||||
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OpenNeuro Resource Report Resource Website 100+ mentions |
OpenNeuro (RRID:SCR_005031) | OpenNeuro, OpenfMRI | data or information resource, data repository, database, image repository, service resource, storage service resource | Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. | neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list |
uses: Brain Imaging Data Structure (BIDs) uses: HED Tags is used by: studyforrest.org is used by: DataLad is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is used by: Baby Open Brains is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing is affiliated with: NEMAR is related to: Integrated Manually Extracted Annotation has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Reproducible Neuroscience has parent organization: BRAIN Initiative is provided by: OpenNeuro |
BRAIN Initiative ; Laura and John Arnold Foundation ; NIDA ; NIMH ; NSF OCI1131441; Squishymedia ; Stanford |
Free, Freely available | DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 | http://www.nitrc.org/projects/openfmri, https://github.com/OpenNeuroDatasets, https://doi.org/10.17616/R33047, https://doi.org/10.17616/r33047, https://doi.org/10.18112/, https://dx.doi.org/10.18112/, https://fairsharing.org/10.25504/FAIRsharing.s1r9bw, https://doi.org/10.17616/R33047 | http://openfmri.org | SCR_005031 | SciCrunch Registry | OpenfMRI, Open fMRI, OpenNeuro | 2026-10-31 12:13:55 | 310 | ||||
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Protocol Online - Your labs reference book Resource Report Resource Website 10+ mentions |
Protocol Online - Your labs reference book (RRID:SCR_004937) | Protocol Online | data or information resource, experimental protocol, narrative resource | Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert). | bioinformatics, molecular biology, immunology, microbiology, proteomics, cell biology, database |
is used by: NIF Data Federation is used by: Integrated Blogs |
Eppendorf ; Invitrogen ; Chang Bioscience ; Mirus ; KPL ; Oligomaster ; Abcam ; Nature Publishing Group |
nlx_90492 | SCR_004937 | SciCrunch Registry | Protocol Online Your lab''s reference book, Protocol-Online | 2026-10-31 12:14:06 | 11 | |||||||
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studyforrest.org Resource Report Resource Website 10+ mentions |
studyforrest.org (RRID:SCR_003112) | studyforrest.org | data repository, image repository, service resource, storage service resource | 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 |
Free, Available for download, Freely available | r3d100011071, nlx_156710 | http://www.nitrc.org/projects/studyforrest, https://doi.org/10.17616/R3SW5S | SCR_003112 | SciCrunch Registry | study forrest, studyforrest | 2026-10-31 12:13:18 | 36 | |||||
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SciCrunch Resource Report Resource Website 10+ mentions |
SciCrunch (RRID:SCR_003115) | SciCrunch | community building portal, data or information resource, database, portal | 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 Portal 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 is related to: RRID Resolver 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 |
Free, Freely available | nlx_156715 | SCR_003115 | SciCrunch Registry | 2026-10-31 12:13:18 | 19 | ||||||||
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Developmental Therapeutics Program Resource Report Resource Website 500+ mentions |
Developmental Therapeutics Program (RRID:SCR_003057) | DTP | data or information resource, funding resource, portal, service resource, topical portal | 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., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 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 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30447 | https://medschool.cuanschutz.edu/colorado-cancer-center/research/research-programs/developmental-therapeutics | SCR_003057 | SciCrunch Registry | Developmental Therapeutics Program NCI/NIH | 2026-10-31 12:13:17 | 571 | ||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | atlas, data or information resource, database, narrative resource, portal, standard specification, topical portal | 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 | SciCrunch Registry | Brain Info | 2026-10-31 12:13:18 | 16 | ||||||
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Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource | 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 |
NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIDA ; NIDA DA028420; NIMH MH071984 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Free, Freely available | biotools:mpd, nif-0000-03160, r3d100010101 | https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F | http://www.jax.org/phenome | SCR_003212 | SciCrunch Registry | Mouse Phenome Database | 2026-10-31 12:13:20 | 230 | |||
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Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | data or information resource, data repository, database, image repository, service resource, storage service resource | 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, r3d100011601 | http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J | SCR_003510 | SciCrunch Registry | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-10-31 12:13:26 | 22 | ||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, data analysis service, data or information resource, database, production service resource, service 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 |
European Molecular Biology Laboratory ; European Union FP6 ENFIN LSHG-CT-2005-518254; NHGRI P41 HG003751; NIGMS GM080223; NIGMS R01 GM100039; Ontario Research Fund |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | SciCrunch Registry | Reactome Functional Interaction Network | 2026-10-31 12:13:27 | 4810 | |||||
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Royal College of Psychiatrists Podcasts Resource Report Resource Website |
Royal College of Psychiatrists Podcasts (RRID:SCR_003913) | RC PSYCH Podcasts | data or information resource, narrative resource, podcast | 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 | SciCrunch Registry | LetWisdomGuide, Let Wisdom Guide | 2026-10-31 12:13:37 | 0 | |||||||
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EEGbase Resource Report Resource Website 1+ mentions |
EEGbase (RRID:SCR_001452) | data or information resource, data repository, database, 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 | Free, Freely Available | nif-0000-08190 | http://eegdatabase.kiv.zcu.cz/ | SCR_001452 | SciCrunch Registry | 2026-10-31 12:12:51 | 7 | |||||||
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Integrated Animals Resource Report Resource Website |
Integrated Animals (RRID:SCR_001421) | biomaterial supply resource, material 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 |
Free, Freely Available | 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 | SciCrunch Registry | NIF Animals, NIF Integrated Animals, Integrated Animal | 2026-10-31 12:12:51 | 0 |
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