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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Open Science Framework Resource Report Resource Website 500+ mentions |
Open Science Framework (RRID:SCR_003238) | OSF | service resource, data repository, storage service resource | Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research. | workflow, cloud, data management, provenance, network, collaboration, data sharing, interdisciplinary research, FASEB list |
is used by: NIH Heal Project is listed by: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: DataCite is listed by: FAIRsharing has parent organization: Center for Open Science |
Free, Freely available | DOI:10.25504/FAIRsharing.g4z879, DOI:10.17605, nlx_157292, DOI:10.17616/R3N03T, r3d100011268, SCR_017419 | http://openscienceframework.org, https://doi.org/10.17616/R3N03T, https://doi.org/10.17616/r3n03t, https://doi.org/10.17605/, https://dx.doi.org/10.17605/, https://fairsharing.org/10.25504/FAIRsharing.g4z879, https://doi.org/10.17616/R35G9K | SCR_003238 | 2026-08-12 10:48:45 | 938 | |||||||
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Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | authoring tool, software resource, software application | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-08-12 10:48:46 | 165 | |||||
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Mouse Biomedical Informatics Research Network Resource Report Resource Website |
Mouse Biomedical Informatics Research Network (RRID:SCR_003392) | MouseBIRN, mBIRN | data or information resource, atlas, reference atlas, data set | Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more. | electron microscopy, expression, functional, gene, 3-dimentional, brain, cellular, disorder, genomic, genotype, mouse, neurodegenerative disease, phenotype, molecular neuroanatomy resource, mri, light microscopy, model organism, gene expression, atlas data, imaging genomics, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse BIRN Atlasing Toolkit is related to: Mouse Connectome Project has parent organization: Biomedical Informatics Research Network |
Normal, Neurodegenerative disease, Multiple Sclerosis, Alzheimer's disease, Parkinson's disease | NIH ; Collaborative Tools Support Network Award ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
Free, Available for download, Freely available | nif-0000-00200 | https://loni.usc.edu/research/software?name=MBATWA | http://www.loni.ucla.edu/BIRN/Projects/Mouse/index.shtml | SCR_003392 | Mouse BIRN | 2026-08-12 10:48:47 | 0 | |||
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PSTC Nephrotoxicity Biomarkers Resource Report Resource Website |
PSTC Nephrotoxicity Biomarkers (RRID:SCR_003709) | PSTC Nephrotoxicity Biomarkers | data or information resource, narrative resource, standard specification | Urinary kidney biomarkers (KIM-1, albumin, total protein, 2-microglobulin, cystatin C, clusterin and trefoil factor-3) that are considered acceptable biomarkers for the detection of acute drug-induced nephrotoxicity in rats and can be included along with traditional clinical chemistry markers and histopathology in toxicology studies. These biomarkers may be used voluntarily as additional evidence of nephrotoxicity in nonclinical safety assessment studies to complement the standard data (BUN and sCr). In ROC analyses, some of these biomarkers showed better sensitivity and specificity than BUN and sCr relative to histopathological alterations considered to be the gold standard when tested with a limited number of nephrotoxicant and control compounds. | biomarker, drug development, drug, urinary, urinary biomarker, gold standard, kim-1, albumin, total protein, beta2-microglobulin, cystatin c, clusterin, trefoil factor-3, kidney, nonclinical |
is recommended by: U.S. Food and Drug Administration has parent organization: Drug Development Tools Qualification Programs has parent organization: Predictive Safety Testing Consortium |
Nephrotoxicity, Drug-induced nephrotoxicity | Public | nlx_157890 | SCR_003709 | Predictive Safety and Testing Consortium Drug-induced Nephrotoxicity Biomarkers, PSTC NWG Drug-induced Nephrotoxicity Biomarkers | 2026-08-12 10:48:51 | 0 | ||||||
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Mindtouch DekiWiki Resource Report Resource Website 1+ mentions |
Mindtouch DekiWiki (RRID:SCR_003425) | MindTouch | commercial organization, software resource, source code | A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more. | authoring, publishing, standard, web service, cloud |
is listed by: FORCE11 is listed by: Biositemaps has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Free, Freely available | nif-0000-33097 | http://sourceforge.net/projects/dekiwiki/, https://www.force11.org/node/4733 | SCR_003425 | MindTouch Core, DekiWiki, MindTouch Deki Wiki, Deki Wiki, MindTouch (frmly deki wiki) | 2026-08-12 10:48:47 | 2 | ||||||
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nSolver Analysis Software Resource Report Resource Website 100+ mentions |
nSolver Analysis Software (RRID:SCR_003420) | nSolver Analysis Software | data processing software, software resource, software application | Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages. | normalization, analysis, ncounter, os x, windows, quality control | is listed by: OMICtools | Restricted | OMICS_02309 | https://nanostring.app.box.com/v/nSolver-AdvancedAnalysis, https://nanostring.com/products/ncounter-analysis-system/ncounter-analysis-solutions/nsolver-data-analysis-support/ | SCR_003420 | 2026-08-12 10:48:48 | 405 | |||||||
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Alaska Satellite Facility Resource Report Resource Website 1+ mentions |
Alaska Satellite Facility (RRID:SCR_003610) | ASF, ASF SAR DAAC | service resource, data repository, storage service resource | Satellite facility that downlinks, processes, archives, and distributes remote-sensing data to scientific users around the world. Three major components: * Satellite Tracking Ground Station: Part of NASA?s Near Earth Network system of ground stations around the world. * Synthetic Aperture Radar Distributed Active Archive Center (SAR DAAC): ASF maintains the NASA archive of SAR data from a variety of satellites and aircraft, and provides these data and associated specialty support services to U.S. Government-approved researchers in support of NASA?s Earth Science Data and Information System project. * ASF Enterprise Center (ASFE): In support of UAF?s mission to be a student-centered research university, the ASF-E focuses on applications of remote-sensing data, specifically for UAF research. The ASF-E includes the GeoData Center (GDC), which provides data management and archive services for UAF principal investigators and maintains a variety of geophysical data collections in support of scientific research. | remote sensing, earth resources technology satellite, earth, satellite, synthetic aperture radar |
is listed by: re3data.org has parent organization: University of Alaska Fairbanks; Alaska; USA |
Acknowledgement requested, Account required, (for some), Approval required, (for some), Open unspecified license, (some) | nlx_157757, r3d100013015 | https://doi.org/10.17616/R31NJMJB | SCR_003610 | Alaska Satellite Facility - Synthetic Aperture Radar Distributed Active Archive Center | 2026-08-12 10:48:50 | 8 | ||||||
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National Renal Administrators Association Resource Report Resource Website |
National Renal Administrators Association (RRID:SCR_003991) | NRAA | data or information resource, community building portal, portal | A nonprofit organization representing dialysis facilities and centers throughout the United States. It supports members from all types of providers including freestanding, hospital-based and national chains through the weekly e-mail newsletter, Renal Watch, the Annual Meeting, periodic workshops and other meetings. NRAA members include dialysis provider companies and management consulting companies and other companies involved in the End Stage Renal Disease (ESRD) industry and supportive of the purposes of NRAA. Individuals not directly employed or otherwise involved in companies that are NRAA members may join as individual Associate Members. The purposes for which the NRAA is organized are as follows: # To provide renal administrators the opportunity for gaining continuing education, obtaining peer recognition and expanding development in the profession. # To promote and encourage education and training for renal administrators. # To recognize individuals who have done or are doing noteworthy service in the field of renal administration. # To educate the public and members of governing bodies of health care organizations to understand the issues surrounding the practice of renal administration. # To represent the professional interests of renal administrators as a national representative spokesperson for the development and implementation of public policy. # To act as a resource on local and national ESRD issues. | kidney, dialysis | is related to: Kidney Health Initiative | Kidney disease, End Stage Renal Disease | nlx_158405 | SCR_003991 | 2026-08-12 10:48:55 | 0 | ||||||||
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European Biotechnology Network Resource Report Resource Website |
European Biotechnology Network (RRID:SCR_003908) | EBN | data or information resource, community building portal, portal | Non-profit organization that facilitates co-operation between professionals in biotechnology and the life sciences all over Europe bringing research groups, universities, SMEs, large companies and indeed all actors in biotechnology together to build and deliver partnerships. | biotechnology, life science | is related to: European Gram Negative AntiBacterial Engine | Individual membership:, Free, Corporate membership:, Fee | nlx_158528 | SCR_003908 | European Biotechnology Network AISBL | 2026-08-12 10:48:54 | 0 | |||||||
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ERA-EDTA Resource Report Resource Website 10+ mentions |
ERA-EDTA (RRID:SCR_003982) | ERA-EDTA | data or information resource, community building portal, portal | An association of European kidney specialists whose objective is advancement of medical science and of clinical work in nephrology, dialysis, renal transplantation, hypertension and related subjects. They aim at providing up-to-date knowledge, exclusively based on scientific data, independent from governments'' policies and from any influence of the industry. It is registered in England and Wales, but its area of activity mainly covers Europe and the Mediterranean area. | kidney, dialysis, transplant, nephrology, medical, clinical, renal transplantation, hypertension | is related to: Kidney Health Initiative | Kidney disease | nlx_158389 | SCR_003982 | European Renal Association - European Dialysis and Transplant Association, European Renal Association - European Dialysis & Transplant Association | 2026-08-12 10:48:54 | 22 | |||||||
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Minimum Information About a Simulation Experiment Resource Report Resource Website 1+ mentions |
Minimum Information About a Simulation Experiment (RRID:SCR_003800) | MIASE | data or information resource, narrative resource, standard specification | A set of guidelines (community effort) suitable for use with any structured format for simulation experiments to identify the Minimal Information About a Simulation Experiment necessary to enable the reproducible simulation experiments. The Guidelines list the information that a modeller needs to provide to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models. MIASE is designed to help modelers and software tools to exchange their simulation settings and to foster collaboration. In 2011, he MIASE guidelines were accepted by researchers from 19 different institutes. | simulation |
is used by: Simulation Experiment Description Markup Language is listed by: Minimum Information for Biological and Biomedical Investigations |
PMID:21552546 | nlx_158097 | SCR_003800 | MIASE Guidelines | 2026-08-12 10:48:52 | 2 | |||||||
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MIAPA Resource Report Resource Website 1+ mentions |
MIAPA (RRID:SCR_003777) | MIAPA | data or information resource, narrative resource, standard specification | Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard. | phylogeny, dna, amino acid sequence |
is listed by: Minimum Information for Biological and Biomedical Investigations is listed by: GitHub is listed by: SourceForge |
PMID:16901231 | nlx_158100 | https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md, http://mibbi.sourceforge.net/projects/MIAPA.shtml | SCR_003777 | Minimal Information for a Phylogenetic Analysis | 2026-08-12 10:48:52 | 1 | ||||||
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7T Structural MRI scans ATAG Resource Report Resource Website 1+ mentions |
7T Structural MRI scans ATAG (RRID:SCR_014084) | data or information resource, atlas, data set | Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases. | 7t mri, data set, atlas, basal ganglia, structural mri scan, brain, human brain, probabilistic atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Available for download | SCR_014084 | 2026-08-11 09:42:42 | 7 | ||||||||||
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Rhesus Macaque Brain Atlases Resource Report Resource Website |
Rhesus Macaque Brain Atlases (RRID:SCR_017533) | data or information resource, atlas, data set | Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque. | Collection, atlas, data, scan, functional, structural, imaging, rhesus macaque | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | http://brainmap.wisc.edu/monkey.html | SCR_017533 | 2026-08-11 09:43:31 | 0 | |||||||||
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IconBAZAAR Resource Report Resource Website |
IconBAZAAR (RRID:SCR_002376) | data or information resource, database, 3d molecular model | This website contains animated 3D molecular models for amino acids, carbohydrates, and drugs. The amino acids listed are: -Alanine -Arginine -Asparagine -Aspartate -Cysteine -Glutamine -Glutamate -Glycine -Histidine -Isoleucine -Leucine -Lysine -Methionine -Phenylalanine -Proline -Serine -Threonine -Tryptophan -Tyrosine -Valine The categories of drugs included are: -Analgesics -Mood Elevators -Antacids -Psychedelics -Aphrodisiacs -Depressants -Stimulants -Intoxicants The carbohydrates listed are: -Fructose -Glucosamine -Glucose -Glyceraldehyde -Glycerol -Lactose -Maltose -Mannitol -Ribose -Ribulose -Sorbitol -Sucrose | drug, fructose, 3d molecular structures, alanine, amino acid, analgesics, antacid, aphrodisiac, arginine, asparagine, aspartate, carbohydrate, cysteine, depressant, glucosamine, glucose, glutamate, glutamine, glyceraldehyde, glycerol, glycine, histidine, intoxicant, isoleucine, lactose, leucine, lysine, maltose, mannitol, methionine, model, molecular, mood elevator, phenylalanine, proline, psychedelic, ribose, ribulose, serine, sorbitol, stimulant, structure, sucrose, threonine, tryptophan, tyrosine, valine | nif-0000-21212 | SCR_002376 | 2026-08-11 09:40:36 | 0 | |||||||||||
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Human Gene Mutation Database Resource Report Resource Website 1000+ mentions |
Human Gene Mutation Database (RRID:SCR_001621) | HGMD | data or information resource, database | Curated database of known (published) gene lesions responsible for human inherited disease. | gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: BIOBASE Corporation has parent organization: Cardiff University; Wales; United Kingdom |
Inherited disease | PMID:22948725 PMID:20368137 PMID:20038494 PMID:19348700 PMID:18428754 PMID:18245393 PMID:12754702 PMID:10612821 PMID:9399854 PMID:9066272 PMID:8882888 |
Free, Freely available | nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 | http://www.hgmd.cf.ac.uk/ac/index.php, https://bio.tools/hgmd, | SCR_001621 | The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff | 2026-08-11 09:40:23 | 2682 | ||||
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Brodmann's Interactive Atlas Resource Report Resource Website 1+ mentions |
Brodmann's Interactive Atlas (RRID:SCR_006368) | data or information resource, atlas, mri d image | An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded. | neuroanatomy, fmri, interactive, mri, pet, brain, brodmann's areas, brodmann partition scheme region, cerebral cortex, function, brain activation, atlas | fMRI consulting | nlx_152117 | SCR_006368 | Broadmann's Interactive Atlas | 2026-08-12 10:49:27 | 3 | |||||||||
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EasyOpenData Resource Report Resource Website |
EasyOpenData (RRID:SCR_006354) | EasyOpenData | authoring tool, software resource, software application | Software application to create Open Data from your Google Drive spreadsheets. # Create a spreadsheet in Google Drive. Share, collaborate and refine your data as usual. # Design the template in EasyOpenData. Format your data the way you want it - any markup, any schema. # Publish your Open Data feed. Feeds update automatically when your spreadsheet is changed. | author, publish | nlx_152087 | SCR_006354 | easy open data | 2026-08-12 10:49:26 | 0 | |||||||||
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EZID Resource Report Resource Website 1+ mentions |
EZID (RRID:SCR_006473) | EZID | production service resource, service resource | A production service that gives researchers the ability to create and manage long-term identifiers so that they can to track usage, get credit for their work, share their data, and have the data reused for additional research. As a result, EZID identifiers also make it possible to increase citations, to build on previous work, to conduct new research, and avoid duplicating previous efforts. EZID identifiers provide a simple but powerful way to track research materials, including datasets, throughout their life cycle. In this way, researchers can share their data, get more citations, and track their results. | data citation, data management, open citation, digital object identifier |
is listed by: FORCE11 has parent organization: California Digital Library |
Subscription | nlx_156045 | http://www.force11.org/node/4793 | SCR_006473 | easy-eye-dee | 2026-08-12 10:49:28 | 1 | ||||||
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ResearchGate Resource Report Resource Website 100+ mentions |
ResearchGate (RRID:SCR_006505) | ResearchGate | data or information resource, database, community building portal, portal | A professional, social network and publication database geared to researchers where the latest field specific publications can be read, publications with other specialists can be discussed, and collaboration with colleagues is facilitated. They provide researchers with access to around 40 million abstracts and tens of thousands of Full texts, uploaded by the authors themselves. Researchers can search through 7 of the largest databases simultaneously, such as PubMed, IEEE & CiteSeer. | social network, biology, literature, publication, bibliographic, abstract, collaborate, statistics, citation, FASEB list |
is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: PubMed is parent organization of: ResearchGate: Research Jobs is parent organization of: ResearchGate: Research Conferences |
Free, Account required, The community can contribute to this resource | nlx_143849, DOI:10.1314, DOI:10.17616/R36H16, r3d100012227 | https://doi.org/10.17616/R36011, https://doi.org/10.17616/r36H16, https://doi.org/10.1314/, https://dx.doi.org/10.1314/, https://doi.org/10.17616/R36H16 | SCR_006505 | Research Gate, Research gate | 2026-08-12 10:49:27 | 432 |
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