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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | data analysis service, source code, analysis service resource, data set, web service, image repository, storage service resource, software resource, data access protocol, data repository, production service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01 |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me, http://www.nitrc.org/projects/ocp/ | SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-08-04 09:41:05 | 7 | ||||
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Clinical Outcomes Research Initiative Resource Report Resource Website 1+ mentions |
Clinical Outcomes Research Initiative (RRID:SCR_009010) | CORI | resource, software resource, service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5, 2022. Endoscopic Reporting Software, aggregated and individual research data and tailor-made services aimed to advance the overall practice of endoscopy. It was developed to study outcomes of gastrointestinal (GI) endoscopic procedures in real life settings, using data obtained from the CORI Endoscopic Reporting Software or from other endoscopic reporting software. Practice sites include hospitals, ambulatory care centers, private practices, universities, and Veteran''''s hospitals (VA''''s). The CORI v4 Endoscopic Reporting Software is a specialty Electronic Health Record used to document endoscopic procedures and provide reporting services to your practice. Data from participating providers is also sent to a central data repository to become part of the National Endoscopic Database (NED), which now contains data from over 2.7 million GI procedures. The CORI v4 Endoscopic Reporting Software offers significant benefits for participating practices, providers and patients, as well as for everyone who benefits from CORI''''s research efforts. You may actively participate in research with CORI. If you have ideas for research using the NED, their research team can help you evaluate those ideas, collect and analyze the data. In addition, you may choose to participate in one of the prospective research projects conducted by CORI research staff. | clinical, endoscopy, gastroenterology, gastrointestinal, endoscopic, endoscopy reporting software, outcome, report, electronic health record, aggregator |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: Oregon Health and Science University; Oregon; USA |
NIDDK | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152692 | SCR_009010 | 2026-08-04 09:42:15 | 6 | |||||||
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Renal Disease Portal Resource Report Resource Website |
Renal Disease Portal (RRID:SCR_009030) | Renal Disease Portal | portal, data set, topical portal, disease-related portal, data or information resource | An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms. | gene, quantitative trait locus, strain, renal hypertension, kidney neoplasm, phenotype, pathway, biological process, disease, kidney, genome, gviewer, chromosome, molecular function, cellular component, visualization, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Renal disease, Renal hypertension, Polycystic kidney disease, Renal insufficiency, Kidney neoplasm, Diabetes Insipidus, Hyperoxaluria, Renal hypertension, Nephritis, Nephrocalcinosis, Nephrolithiasis, Nephrosis, Renal Fibrosis, Inborn Error of Renal Tubular Transport, Uremia | nlx_153941 | SCR_009030 | RGD Renal Disease Portal | 2026-08-04 09:42:17 | 0 | |||||||
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GRDR Resource Report Resource Website 1+ mentions |
GRDR (RRID:SCR_008978) | GRDR, RaDaR | storage service resource, people resource, patient registry, data repository, service resource, database, data or information resource | Data repository of de-identified patient data, aggregated in a standardized manner, to enable analyses across many rare diseases and to facilitate various research projects, clinical studies, and clinical trials. The aim is to facilitate drug and therapeutics development, and to improve the quality of life for the many millions of people who are suffering from rare diseases. The goal of GRDR is to enable analyses of data across many rare diseases and to facilitate clinical trials and other studies. During the two-year pilot program, a web-based template will be developed to allow any patient organization to establish a rare disease patient registry. At the conclusion of the program, guidance will be available to patient groups to establish a registry and to contribute de-identified patient data to the GRDR repository. A Request for Information (RFI) was released on February 10, 2012 requesting information from patient groups about their interest in participating in a GRDR pilot project. ORDR selected 30 patient organizations to participate in this pilot program to test the different functionalities of the GRDR. Fifteen (15) organizations with established registries and 15 organizations that do not have patient registry. The 15 patient groups, each without a registry, were selected to assist in testing the implementation of the ORDR Common Data Elements (CDEs) in the newly developed registry infrastructure. These organizations will participate in the development and promotion of a new patient registry for their rare disease. The GRDR program will fund the development and hosting of the registry during the pilot program. Thereafter, the patient registry is expected to be self-sustaining.The 15 established patient registries were selected to integrate their de-identified data into the GRDR to evaluate the data mapping and data import/export processes. The GRDR team will assist these organizations in mapping their existing registry data to the CDEs. Participating registries must have a means to export their de-identified registry data into a specified data format that will facilitate loading the data into the GRDR repository on a regular basis. The GRDR will also develop the capability to link patients'''' data and medical information to donated biospecimens by using a Voluntary Global Unique Patient Identifier (GUID). The identifier will enable the creation of an interface between the patient registries that are linked to biorepositories and the Rare Disease Human Biospecimens/Biorepositories (RD-HUB) http://biospecimens.ordr.info.nih.gov/. | clinical, common data element, global unique patient identifier, clinical trial, drug development, therapy |
is related to: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) is related to: NIH Data Sharing Repositories has parent organization: Office of Rare Diseases Research |
Rare disease | NIH | Public, The community can contribute to this resource | nlx_152145 | http://www.grdr.info/ | SCR_008978 | Rare Diseases Registry Program (RaDaR), Global Rare Diseases Patient Registry and Data Repository | 2026-08-04 09:42:16 | 1 | ||||
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INVIZIAN Resource Report Resource Website 1+ mentions |
INVIZIAN (RRID:SCR_009549) | INVIZIAN | data processing software, data visualization software, software application, software resource | A visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once ?bringing together brain image data from some of the world?s best neuroscience research teams. INVIZIAN empowers both researchers and students of neuroscience to explore and understand the human brain using a simple yet powerful user interface for neuroimaging data exploration and discovery. See a beautiful example of a cloud of individual brains tumbling around in the INVIZIAN interface in Vimeo (http://vimeo.com/67984681). Visit often to see how we are making continuing progress to make Invizian even more amazing. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155775 | http://www.nitrc.org/projects/invizian | SCR_009549 | Informatics Visualization in Neuroimaging | 2026-08-04 09:42:25 | 1 | ||||||
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Mind Lab Resource Report Resource Website |
Mind Lab (RRID:SCR_009025) | Mind Lab | data or information resource, image collection, video resource | Interactive laboratory of the mind composed of 4 themed sessions housing four short introductory movies and sixteen trials with those you can experience visual phenomena and illusions used for study in psychological experiments. | visual illusion, sensory perception, visual phenomena, psychological experiment, vision | has parent organization: Japan Science and Technology Agency | nlx_153853 | http://jvsc.jst.go.jp/find/mindlab/english/ | SCR_009025 | JST Virtual Science Center Mind Lab | 2026-08-04 09:42:16 | 0 | |||||||
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Digital Ageing Atlas Resource Report Resource Website 10+ mentions |
Digital Ageing Atlas (RRID:SCR_009020) | DAA | storage service resource, data repository, service resource, database, data or information resource | Database of age-related changes covering different biological levels, including molecular, physiological, psychological and pathological age-related data, to create an interactive portal that serves as a centralized collection of human aging changes and pathologies. To facilitate integrative, system-level studies of aging, the DAA provides a centralized source for aging-related data as well as basic tools to query and visualize the data, including anatomical models. Data in the DAA is manually curated from the literature and retrieved from public databases. For more detailed analyses users are able to download the entire database. More information on how to use the DAA is available on the help page. The DAA primarily focuses on human aging, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human aging. If you would like to contribute to the database yourself, for instance if you have new data on aging, please use the contribute page to submit your data. | late adult human, anatomy, gene, molecular, pathological, physiological, psychological, tissue, reference, cellualar, gene expression | has parent organization: University of Liverpool; Liverpool; United Kingdom | Aging | The community can contribute to this resource, Creative Commons Attribution License, v3 Unported | nlx_153874 | SCR_009020 | Digital Aging Atlas | 2026-08-04 09:42:17 | 12 | ||||||
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Bionutrition Ontology Resource Report Resource Website 1+ mentions |
Bionutrition Ontology (RRID:SCR_010272) | BNO | ontology, data or information resource, controlled vocabulary | Ontology that relates concepts and terminologies used for human nutrition in a clinical and biomedical setting. | owl | is listed by: BioPortal | nlx_157337 | SCR_010272 | 2026-08-04 09:42:41 | 1 | |||||||||
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Ontology for Newborn Screening Follow-up and Translational Research Resource Report Resource Website |
Ontology for Newborn Screening Follow-up and Translational Research (RRID:SCR_010389) | ONSTR | ontology, data or information resource, controlled vocabulary | Application ontology covering the domain of newborn screening, follow-up and translational research pertaining to patients diagnosed with inheritable and congenital diseases mainly identified through newborn dried blood spot screening. ONSTR is a central component of the project Newborn Screening Follow-up Data Integration Collaborative (NBSDC), https://nbsdc.org. ONSTR uses the Basic Formal Ontology v2 (BFO2, v2012-07-20) as top-level ontology and extends the classes imported from OBO Foundry ontologies and candidate ontologies. | owl, newborn | is listed by: BioPortal | Inheritable disease, Congenital disease | nlx_157520 | SCR_010389 | 2026-08-04 09:42:40 | 0 | ||||||||
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Pediatric Terminology Resource Report Resource Website |
Pediatric Terminology (RRID:SCR_010395) | PEDTERM | ontology, data or information resource, controlled vocabulary | Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age; contributed by the National Institute of Child Health and Human Development. | owl | is listed by: BioPortal | Aging | nlx_157545 | SCR_010395 | 2026-08-04 09:42:40 | 0 | ||||||||
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Traditional Medicine Constitution Value Set Resource Report Resource Website |
Traditional Medicine Constitution Value Set (RRID:SCR_010435) | TM-CONST | ontology, data or information resource, controlled vocabulary | Ontology of the value set for the constitution property of the International Classification of Traditional Medicine (ICTM). | owl | is listed by: BioPortal | nlx_157612 | SCR_010435 | 2026-08-04 09:42:40 | 0 | |||||||||
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Manhattan HIV Brain Bank Resource Report Resource Website 1+ mentions |
Manhattan HIV Brain Bank (RRID:SCR_010520) | MHBB | biomaterial supply resource, brain bank, material resource, tissue bank | Biorepository of tissues and fluids relevant for the neurologic, neuropsychologic, psychiatric and neuropathologic manifestations of HIV infection, linked to medical records and an on-going clinical trial for research use by the scientific community. The MHBB conducts a longitudinal, observational study that follows a group of HIV-infected individuals who have agreed to be fluid and organ donors for the purposes of AIDS research. They are currently the largest, multidisciplinary neuroAIDS cohort in New York City, the epicenter of the US HIV epidemic. Research participants undergo regular neurologic, neuropsychologic, and psychiatric evaluations, and provide body fluid samples that are linked to clinical information. Upon their demise, study participants become organ donors. This program has supplied clinical information, tissue, and fluid samples to over 70 qualified AIDS researchers across America, Europe and Australia. In fulfilling its resource mission, the MHBB functions as part of the National NeuroAIDS Tissue Consortium (NNTC). MHBB provides a means by which people living with HIV can be engaged in the struggle to improve our knowledge about HIV infection and the damage it causes to the body. | human immunodeficiency virus, aids, body fluid, organ, clinical information, tissue, brain, liver disease, liver disorder, aids pathogenesis, clinical data |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: National NeuroAIDS Tissue Consortium has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Human immunodeficiency virus, AIDS, Liver disease, Liver disorder | NIH | nlx_19658 | http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Manhattan%20HIV%20Brain%20Bank | SCR_010520 | 2026-08-04 09:42:43 | 1 | ||||||
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Pathogenic Disease Ontology Resource Report Resource Website |
Pathogenic Disease Ontology (RRID:SCR_010405) | PDO | ontology, data or information resource, controlled vocabulary | An ontology for describing both human infectious disease caused by bacteria and the disease that is related to bacterial infection. | owl | is listed by: BioPortal | Infectious disease, (caused by bacteria), Bacterial infection related disease | nlx_157543 | SCR_010405 | 2026-08-04 09:42:40 | 0 | ||||||||
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Ontology for MicroRNA Target Prediction Resource Report Resource Website |
Ontology for MicroRNA Target Prediction (RRID:SCR_010387) | OMIT | ontology, data or information resource, controlled vocabulary | Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans'' various diseases and biological processes (usually through miRs'' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth. | obo | is listed by: BioPortal | nlx_157519 | SCR_010387 | 2026-08-04 09:42:39 | 0 | |||||||||
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Databrary Resource Report Resource Website 10+ mentions |
Databrary (RRID:SCR_010471) | Databrary | portal, storage service resource, software resource, software repository, data repository, service resource, project portal, database, data or information resource | Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data. | behavior, development, data, sharing, audio track, video |
is listed by: re3data.org is related to: Datavyu is related to: Datavyu has parent organization: New York University; New York; USA has parent organization: Pennsylvania State University |
NSF BCS-1238599; NICHD U01 HD076595 |
Restricted | nlx_157733, r3d100011023 | https://github.com/databrary | SCR_010471 | 2026-08-04 09:42:41 | 13 | ||||||
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Major Histocompatibility Complex Ontology Resource Report Resource Website |
Major Histocompatibility Complex Ontology (RRID:SCR_010354) | MHC | ontology, data or information resource, controlled vocabulary | Ontology that contains terms necessary for describing and categorizing concepts related to Major Histocompatibility Complex, in general, for a number of model species, and also for humans. | owl | is listed by: BioPortal | nlx_157463 | SCR_010354 | MaHCO, MaHCO - An MHC Ontology | 2026-08-04 09:42:39 | 0 | ||||||||
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Boston University Alzheimer's Disease Center Resource Report Resource Website 1+ mentions |
Boston University Alzheimer's Disease Center (RRID:SCR_010692) | BU ADC | portal, topical portal, training resource, disease-related portal, data or information resource | The goal of the Alzheimers Disease Center is to help reduce the human and economic costs associated with Alzheimers disease through the advancement of knowledge. The primary missions of the Center are to: conduct and facilitate cutting-edge Alzheimers disease research; enhance clinical care for Alzheimers disease patients and their families; and provide education regarding Alzheimers disease to both professional and lay audiences. The Center is made up of a multidisciplinary group of professionals dedicated to research, clinical care, and education. | alzheimers, research, patient, family, education, disease related portal, training resource |
has parent organization: Boston University School of Medicine; Massachusetts; USA is parent organization of: Boston University Alzheimer's Disease Center Neuropathology Core Facility |
Alzheimer's disease | NIA | Public | nlx_80502 | SCR_010692 | BU Alzheimers Disease Center | 2026-08-04 09:42:45 | 1 | |||||
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miRTar Resource Report Resource Website 50+ mentions |
miRTar (RRID:SCR_010851) | miRTar | data analysis service, analysis service resource, data set, production service resource, service resource, data or information resource | An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00410 | SCR_010851 | MicroRNA Target prediction | 2026-08-04 09:42:49 | 52 | |||||||||
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UBERON Resource Report Resource Website 50+ mentions |
UBERON (RRID:SCR_010668) | UBERON | ontology, data or information resource, controlled vocabulary | An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human. | anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, obo |
is used by: Neuroscience Information Framework is listed by: BioPortal is related to: Gene Ontology has parent organization: OBO |
ARRA ; NSF ; NHGRI 5R01HG004838; NHGRI P41HG002273; DOE DE-AC02-05CH11231; NCRR 1U24RR029825-01; NHGRI P41HG002273-09S1 |
PMID:22293552 | nlx_74404 | SCR_010668 | Uber anatomy ontology, Uber-anatomy ontology | 2026-08-04 09:42:48 | 59 | ||||||
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BCmicrO Resource Report Resource Website 1+ mentions |
BCmicrO (RRID:SCR_010838) | BCmicrO | web application, software resource | A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded. | mirna, microrna, bayesian, decision fusion algorithm, computational target prediction algorithm, web application, |
is listed by: OMICtools has parent organization: University of Texas at San Antonio; Texas; USA |
Public | OMICS_00393 | SCR_010838 | 2026-08-04 09:42:49 | 7 |
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