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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
DataLad
 
Resource Report
Resource Website
50+ mentions
DataLad (RRID:SCR_003931) DataLad data or information resource, portal, software resource Project to adapt model of open source software distributions to address technical limitations of data sharing and develop all components of data distribution. Builds on top of git-annex and extends it with intuitive command line interface. Enables users to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. Can create DataLad datasets using any data files published on the web. Data sharing, aggregator, federated platform, distributed version control system, data set uses: OpenNeuro
uses: CRCNS
uses: NeuroImaging Tools and Resources Collaboratory (NITRC)
uses: NIH Human Connectome Project
uses: Mind Research Network - COINS
uses: 1000 Functional Connectomes Project
uses: Git
uses: git-annex
is related to: datasets.datalad.org
has parent organization: Dartmouth College; New Hampshire; USA
has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany
has parent organization: Research Center Jülich; Jülich; Germany
works with: ReproIn: The ReproNim image input management system (featuring DataLad)
NSF 1429999;
BMBF 01GQ1411;
NSF 1912266;
BMBF 01GQ1905;
NIH 1P41EB019936-01A1;
European Union’s Horizon 2020 research and innovation programme 945539;
European Union’s Horizon 2020 research and innovation programme 826421;
Deutsche Forschungsgemeinschaft SFB1451-INF;
German federal state of Saxony-Anhalt and the European Regional Development Fund ;
NIH 1R24MH117295-01A1
DOI:10.21105/joss.03262 Free, Freely available nlx_158300 https://github.com/datalad/datalad.org SCR_003931 DataGit, Data Lad 2026-08-10 09:32:08 58
Pedianet
 
Resource Report
Resource Website
10+ mentions
Pedianet (RRID:SCR_004107) data or information resource, portal, database Independent network and system used to collect epidemiological information for clinical research from family paediatricians in Italy. It is based on the transmission of specific data from computerised clinical files. Such data is collected anonymously by a central server in Padua, where it is validated and elaborated. pediatric, clinical, epidemiology, child, young human, pharmacovigilance, primary care, pediatrician is related to: EMIF Wellcome Glaxo nlx_158583 SCR_004107 Pedianet project 2026-08-10 09:32:11 18
Neural ElectroMagnetic Ontologies (NEMO) Project
 
Resource Report
Resource Website
10+ mentions
Neural ElectroMagnetic Ontologies (NEMO) Project (RRID:SCR_002001) NEMO data or information resource, project portal, portal THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. annotation, classification, labeling, eeg, event-related potential, meg, rdf, metadata standard, decomposition, segmentation, extraction, brain, electromagnetic, electrocorticography, information specification, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Oregon; Oregon; USA
is parent organization of: NEMO Ontology
PMID:22180824 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10899 http://www.nitrc.org/projects/nemo, https://sourceforge.net/projects/nemoontologies/ http://nemo.nic.uoregon.edu SCR_002001 Neural ElectroMagnetic Ontologies 2026-08-10 09:31:35 25
GoMiner
 
Resource Report
Resource Website
100+ mentions
GoMiner (RRID:SCR_002360) GoMiner software application, data processing software, software resource GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. experiment, expression, function, gene, genomics, biological, genomic, microarray, omic, process, gene expression, gene ontology, biological process, biological function, biological component, proteomic, database, FASEB list is related to: Gene Ontology
is related to: High-Throughput GoMiner
has parent organization: Georgia Institute of Technology; Georgia; USA
has parent organization: Emory University; Georgia; USA
has parent organization: National Cancer Institute
NCI ;
Georgia Institute of Technology; Georgia; USA ;
Emory University; Georgia; USA
PMID:12702209 nif-0000-21181 SCR_002360 2026-08-10 09:31:42 115
PlantCyc
 
Resource Report
Resource Website
1000+ mentions
PlantCyc (RRID:SCR_002110) PMN data or information resource, project portal, portal, database Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. enzyme, gene, biochemical pathway, compound, metabolism, plant metabolic, reaction, database is listed by: Plant Metabolic Network
has parent organization: Carnegie Institution for Science
NSF 1026003;
NSF 0640769
PMID:20522724 Free, Available for download, Freely available , nif-0000-20890, nlx_15806 plant http://www.plantcyc.org/ SCR_002110 2026-08-10 09:31:37 3659
Drug Development Tools Qualification Programs
 
Resource Report
Resource Website
1+ mentions
Drug Development Tools Qualification Programs (RRID:SCR_003714) DDT Qualification Programs data or information resource, portal To support Drug Development Tools development efforts, FDA established qualification programs for animal models for use under Animal Rule, biomarkers, and clinical outcome assessments. DDTs are methods, materials, or measures that have potential to facilitate drug development. Examples of DDTs may include, but are not limited to biomarker2 used for clinical trial enrichment, clinical outcome assessment used to evaluate clinical benefit, and animal model used for efficacy testing of medical countermeasures under regulations commonly referred to as Animal Rule3. Drug1 Development Tools, FDA established qualification programs, animal models for use under Animal Rule, gold standard has parent organization: U.S. Food and Drug Administration
is parent organization of: PSTC Nephrotoxicity Biomarkers
is parent organization of: ILSI HESI Drug-induced Nephrotoxicity Biomarkers
is parent organization of: O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers
is parent organization of: Exacerbations of Chronic Pulmonary Disease Tool
Public nlx_157888 SCR_003714 Drug Development Tools (DDT) Qualification Programs 2026-08-10 09:32:05 1
FGED
 
Resource Report
Resource Website
10+ mentions
FGED (RRID:SCR_001897) FGED data or information resource, knowledge environment, portal Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications. gene expression, gene modification, biological, biologist, biomedical, computer scientist, data analyst, genomic, integration, life science, microarray, technology, functional genomics, annotate, data sharing, genome, data integration, software is listed by: OMICtools
is parent organization of: MINSEQE
is parent organization of: MAGE
is parent organization of: MIAME
OMICS_01778, nif-0000-10466 http://www.mged.org/ SCR_001897 Functional Genomics Data Society, MGED Society, The Microarray Gene Expression Data Society, The Functional Genomics Data Society, MGED 2026-08-10 09:31:33 24
FIVA - Functional Information Viewer and Analyzer
 
Resource Report
Resource Website
1+ mentions
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) FIVA software application, data processing software, software resource Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: MolGen
Netherlands Organization for Scientific Research ;
industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ;
Center IOP Genomics ;
European Union QLK3-CT-2001-01473
PMID:17237043 Free for academic use nlx_149245 SCR_005776 FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer 2026-08-10 09:32:39 1
GoBean - a Java application for Gene Ontology enrichment analysis
 
Resource Report
Resource Website
10+ mentions
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) GoBean software application, data processing software, software resource GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Gachon University of Medicine and Science; Incheon; South Korea
PMID:22360891 Free for academic use nlx_149296 http://neon.gachon.ac.kr/GoBean/ SCR_005808 2026-08-10 09:32:40 22
Neural Simulation Language
 
Resource Report
Resource Website
Neural Simulation Language (RRID:SCR_007308) software application, data processing software, software resource NSL, Neural Simulation Language, is a simulation system for large-scale general neural networks. NSL provides a simulation environment simplifying the task of modeling neural networks. In particular, NSL supports neural models having as basic data structure neural layers with similar properties and similar connection patterns, where neurons are modeled as leaky integrators with connections subject to diverse learning rules. Development of NSL has gone hand in hand with modeling of neural mechanisms underlying visuomotor coordination, with special emphasis on the analysis of data from anurans, monkeys, and humans. NSL follows an object-oriented design, providing higher level programming abstraction corresponding to neural elements. NSL provides system development tools, such as visualization capabilities and a run-time interpreter, which give the user powerful tools in developing and analyzing models. NSL has been widely used throughout the world for both teaching and research. simulation; software nif-0000-00164 SCR_007308 NSL 2026-08-10 09:33:06 0
ALSPAC
 
Resource Report
Resource Website
100+ mentions
ALSPAC (RRID:SCR_007260) ALSPAC data or information resource, project portal, portal A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally. longitudinal, study, parent, child, health, research, mother, development, research, disease, genetic, environmental has parent organization: University of Bristol; Bristol; United Kingdom UK Medical Research Council ;
Wellcome Trust ;
University of Bristol
Available to the research community nif-0000-30224 SCR_007260 The Avon Longitudinal Study of Parents and Children, Avon Longitudinal Study of Parents and Children 2026-08-10 09:33:13 485
Colorado Assessment Tests - Card Sort
 
Resource Report
Resource Website
Colorado Assessment Tests - Card Sort (RRID:SCR_007331) software application, data processing software, software resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. CATs Card Sort is a free, general purpose card sorting program which allows the user to design sorting tasks similar to those described by Vigotsky (1934), Weigel (1941), and Grant and Berg (1948). Card sorting tasks have been shown to be particularly sensitive to frontal lobe dysfunction, but have also shown sensitivity to motor disorders, schizophrenia, chronic alcoholism, aging, and attention deficit disorder. The CATs Card Sort package provides extensive flexibility in the development of stimulus cards, allowing the experimenter to define the relevant dimensions of cards in terms of figures, letters or words, figure/letter/word color, card color, figure/letter numerosity, and a user defined dimension. Considerable flexibility is also provided in designing lists of to be sorted cards, sort criteria, and the criteria for sort classification shift. The package also provides limited analysis capabilities as described by Grant and Berg (1948). However, as with all CATs packages raw data can be copied to the clipboard in a format acceptable for import into commonly available spreadsheets such as Excel allowing the user to design analysis routines appropriate to their needs. frontal lobe, alcoholism, attention deficit disorder, card sorting task, disfunctional, human, motor disorder, schizophrenia has parent organization: University of Colorado; Colorado Springs; USA Aging THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00210 SCR_007331 Card Sort 2026-08-10 09:33:06 0
Orphanet
 
Resource Report
Resource Website
100+ mentions
Orphanet (RRID:SCR_006628) Orphanet data or information resource, portal European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases. drug, clinical, diagnostic, test, rare, disease, molecule, gene, orphan, drug is used by: NIF Data Federation
is used by: HmtPhenome
is listed by: OMICtools
is related to: Disease core ontology applied to Rare Diseases
is related to: phenomeNET
has parent organization: National Institute of Health and Medical Research; Rennes; France
is parent organization of: Orphanet Rare Disease Ontology
National Institute of Health and Medical Research ;
Rennes ;
France ;
French Directorate General for Health ;
European Union
Free, Freely available nif-0000-21306, grid.458406.b, Wikidata: Q1515833 https://ror.org/03d3kf570 SCR_006628 2026-08-10 09:32:53 474
Compartment Model Kinetic Analysis Tool
 
Resource Report
Resource Website
Compartment Model Kinetic Analysis Tool (RRID:SCR_007359) software application, data processing software, software resource COMKAT is a software package for compartmental modeling oriented for biomedical image quantification. Free for academic research use, COMKAT has various functions for modeling and imaging analysis in both command-line function and GUIs. COMKAT is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user. has parent organization: Case Western Reserve University; Ohio; USA nif-0000-00281 http://comkat.case.edu/comkat/comkat_wiki/index.php?title=Home SCR_007359 COMKAT: COmpartment Model Kinetic Analysis Tool, COMKAT 2026-08-10 09:33:07 0
CLEAVE
 
Resource Report
Resource Website
10+ mentions
CLEAVE (RRID:SCR_007113) CLEAVE software application, data processing software, software resource A UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use (without loading all of the data into memory). It has been used for fMRI analysis, e.g. CLEAVE adds the following to the standard ANOVA analyses: # Unlimited numbers of factors can be analyzed. # Factor Correlation and Unequal Variance Corrections # Treatment Magnitudes: omega^2, partial eta^2, and R^2 # A convenient Ranking of Factors based upon treatment magnitudes and significance levels. # Post-Hoc Significance Tests # Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. # Allows the use of Random Factors. # A Configuration File to make the program more tunable # A Histogram and Cell Line Diagrams: which help the user to detect outliers. # Associated MATLAB functions: port CLEAVE-style data sets in or out of MATLAB. c, console (text based), macos, microsoft, magnetic resonance, posix/unix-like, statistical operation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of California at Davis; California; USA
Creative Commons Attribution License nlx_155530 http://www.nitrc.org/projects/cleave SCR_007113 2026-08-10 09:33:02 17
SeqExpress
 
Resource Report
Resource Website
SeqExpress (RRID:SCR_007075) software application, data processing software, software resource A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Gene Expression Omnibus
PMID:14988116 Free nlx_149285, biotools:seqexpress https://bio.tools/seqexpress SCR_007075 2026-08-10 09:33:01 0
OwlSim
 
Resource Report
Resource Website
1+ mentions
OwlSim (RRID:SCR_006819) OwlSim software application, data processing software, software resource Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible functional similarity, semantic similarity, ontology, phenotype, annotation, windows, mac os x, linux, unix is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Berkeley Bioinformatics Open-Source Projects
has parent organization: OWLTools
Biomedical Information Science and Technology Initiative ;
National Center for Biomedical Ontology ;
NHGRI U54 HG004028;
NHGRI HG002659
PMID:19956802 Open unspecified license - Free for academic use nlx_149312 SCR_006819 2026-08-10 09:32:57 5
International Stroke Database/Software
 
Resource Report
Resource Website
International Stroke Database/Software (RRID:SCR_007348) software application, data processing software, software resource Diffusion tensor imaging (DTI) tractography: An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke DTI Task Card for Siemens systems, DTI Visualization platform independent tool kit, PWI analysis tools for bolus-tracking data has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
has parent organization: Harvard University; Cambridge; United States
nif-0000-00253 SCR_007348 International Stroke Database/Software 2026-08-10 09:33:07 0
BrainColor: Collaborative Open Labeling Online Resource
 
Resource Report
Resource Website
1+ mentions
BrainColor: Collaborative Open Labeling Online Resource (RRID:SCR_006377) BrainCOLOR data or information resource, knowledge environment This resource was created to host descriptions of protocols, definitions and rules for the reliable identification and localization of human brain anatomy and discussions of best practices in brain labeling. Project for manual anatomical labeling of human brain MRI data, and the visual presentation of labeled brain images. atlas, curation, map, mapping, mri, image, brain, label, neurolabel, neuroanatomy is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Neuromorphometrics
has parent organization: Columbia University; New York; USA
NIMH R43 MH084358;
NIMH MH084029
Free, Available for download, Freely available nif-0000-07727 https://www.binarybottle.com/braincolor/, https://github.com/binarybottle/braincolor http://www.braincolor.org/ SCR_006377 Neurolabels, Collaborative Open Labeling Online Resource, Neuroanatomical Labeling Methods 2026-08-10 09:32:49 3
Brain Computer Interface 2000 Software Package
 
Resource Report
Resource Website
100+ mentions
Brain Computer Interface 2000 Software Package (RRID:SCR_007346) software application, data processing software, software resource BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: National Institutes of Health
NIBIB R01 EB026439;
NINDS U24 NS109103;
NIBIB P41 EB018783
nif-0000-00251 http://www.nitrc.org/projects/bci2000, http://www.bci2000.org, https://www.neurotechcenter.org/software SCR_007346 BCI2000 2026-08-10 09:33:06 180

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