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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
Experimental Factor Ontology
 
Resource Report
Resource Website
10+ mentions
Experimental Factor Ontology (RRID:SCR_003574) EFO ontology, data or information resource, controlled vocabulary An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome. gene expression, owl, experimental factor, disease, cell line, cell type, anatomy, gold standard is listed by: BioPortal
is related to: ArrayExpress
is related to: ArrayExpress
is related to: Gene Expression Atlas
has parent organization: European Bioinformatics Institute
European Molecular Biology Laboratory ;
European Union FELICS contract 021902;
European Union EMERALD LSHG-CT-2006-037686;
European Union Gen2Phen contract 200754
PMID:20200009 The community can contribute to this resource nlx_11363 SCR_003574 2026-08-08 11:58:03 19
RAREMETAL
 
Resource Report
Resource Website
10+ mentions
RAREMETAL (RRID:SCR_003573) RAREMETAL software resource A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing. bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Michigan; Ann Arbor; USA
PMID:24894501 biotools:raremetal, OMICS_00243 https://bio.tools/raremetal SCR_003573 2026-08-08 11:58:00 22
Adverse Event Reporting Ontology
 
Resource Report
Resource Website
1+ mentions
Adverse Event Reporting Ontology (RRID:SCR_003571) AERO ontology, data or information resource, controlled vocabulary An ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. owl, rdf, aero, bfo, ogms, iao, adverse event, clinician, health is listed by: BioPortal
is listed by: OBO
is listed by: Google Code
is related to: Information Artifact Ontology
New BSD License (code), Creative Commons Attribution License (content) nlx_11209 http://bioportal.bioontology.org/ontologies/1580, http://www.obofoundry.org/cgi-bin/detail.cgi?id=AERO, http://purl.obolibrary.org/obo/aero.owl, http://purl.obolibrary.org/obo/aero SCR_003571 2026-08-08 11:58:02 1
Karma
 
Resource Report
Resource Website
50+ mentions
Karma (RRID:SCR_003732) Karma data management software, software resource, software application An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database. integration, FASEB list is related to: GitHub
has parent organization: University of Southern California; Los Angeles; USA
Air Force Research Laboratory FA8750-14-C-0240;
NCRR 1 U24 RR025736-01;
NCRR 1 UL1 RR031986-01;
NSF IIS-1117913;
NSF CMMI-0753124
PMID:15215426 Apache License, v2 nlx_157923 https://github.com/InformationIntegrationGroup/Web-Karma SCR_003732 Karma A Data Integration Tool, Karma - A Data Integration Tool 2026-08-08 11:58:05 83
Alaska Satellite Facility
 
Resource Report
Resource Website
1+ mentions
Alaska Satellite Facility (RRID:SCR_003610) ASF, ASF SAR DAAC storage service resource, data repository, 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 2026-08-08 11:58:01 8
Polyester
 
Resource Report
Resource Website
100+ mentions
Polyester (RRID:SCR_003602) software resource, software application, simulation software, data analysis software, data processing software An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code standalone software, unix/linux, mac os x, windows, r, rna-seq is listed by: OMICtools OMICS_04272 SCR_003602 2026-08-08 11:58:01 491
Myelin Repair Foundation
 
Resource Report
Resource Website
1+ mentions
Myelin Repair Foundation (RRID:SCR_003723) MRF institution A non-profit foundation that funds basic research and is focused on accelerating the development of myelin repair therapeutics for multiple sclerosis. They have defined a 15-year research plan to develop a drug or drugs and believes its Accelerated Research Collaborative (ARC) model can subsequently be used to accelerate the treatment for all diseases. The ARC framework coordinates and manages the entire therapeutic development continuum from discovery biology to FDA approval. The model works by coordinating multi-disciplinary basic research from academic and government laboratories, systematically validating and derisking potential compounds/targets, and collaborating with pharma partners to increase the probability of successful programs. consortium, drug, myelin repair, therapeutic, myelin, drug development is listed by: Consortia-pedia Multiple Sclerosis, Neurological disease nlx_157901, grid.429475.9, Wikidata: Q6947290 https://ror.org/05yb6xa82 SCR_003723 2026-08-08 11:58:04 3
Tocris Bioscience
 
Resource Report
Resource Website
100+ mentions
Tocris Bioscience (RRID:SCR_003689) commercial organization An Antibody supplier nlx_152479 SCR_003689 2026-08-08 11:58:01 393
TransCelerate BioPharma
 
Resource Report
Resource Website
1+ mentions
TransCelerate BioPharma (RRID:SCR_003728) TransCelerate nonprofit organization Non-profit research organization aiming to accelerate drug development by increasing the quality and efficiency of clinical studies through the development of shared tools, methods, and platforms. Consortium partnerships are limited to pharmaceutical and biotechnology companies with research & development operations, although there are collaborations with external organizations such the Clinical Data Interchange Standards Consortium (CDISC). Its current focus is to collaborate on: * Standardizing risk-based monitoring * Development of methods to qualify and train clinical trial sites * Development of a common investigator web portal * Development of clinical data standards on efficacy, and methods for comparator drug trials It currently has 5 projects: # Standardized Approach for High-Quality, Risk-Based Monitoring program aims to develop an industry-wide standard and approach for risk-based monitoring of clinical trials in order to enhance patient safety and ensure the quality of clinical trial data. # Shared Site Qualification and Training program aims to standardize GCP training and site qualification credentials in order to realize efficiencies and accelerate study start-up timelines. # Common Investigator Site Portal is a platform designed to streamline investigator and site access through harmonized delivery of content and services. # Data Standards project is a partnership with CDISC to develop industry-wide data standards in priority therapeutic areas to support the exchange and submission of clinical research and meta-data, improving patient safety and outcomes. # Comparator Drugs project aims to establish reliable, rapid sourcing of quality products for use in clinical trials through a comparator supply model enabling accelerated trial timelines and enhanced patient safety. drug, clinical trial, multipharma, data sharing, drug development, consortium, medicine, clinical, standard specification is listed by: Consortia-pedia Member companies financial contributions ;
Member companies in-kind contributions ;
GlaxoSmithKline
nlx_157913 SCR_003728 TransCelerate BioPharma Inc. 2026-08-08 11:58:02 6
Project Data Sphere
 
Resource Report
Resource Website
10+ mentions
Project Data Sphere (RRID:SCR_003726) PDS data or information resource, database, consortium, portal, organization portal Initiative to advance oncology research by enabling collaborative sharing of historical oncology clinical trial data through a universal platform (database). The initiative aims to network all stakeholders in the cancer community researchers, industry, academia, advocacy, and other organizations to share insights and collaborate on issues that could not be solved individually. To do this, they have made efforts to address issues of data privacy, security, intellectual property, resources, and incentives as part of its effort to maximize participation. Data contributions include control arms of clinical trials, and the platform uses data-security precautions and analytics to pool multiple studies associated with the same diagnosis in a manner that seeks to protect the privacy of patients and the security of the data contributed. drug, oncology, clinical trial, data sharing, consortium, phase iii is listed by: DataCite
is listed by: re3data.org
PMID:25876994 nlx_157911, DOI:10.34949, DOI:10.17616/R31NJMJB, r3d100010760 https://doi.org/10.17616/R36H16, https://doi.org/10.17616/r31NJMJB, https://doi.org/10.34949/, https://dx.doi.org/10.34949/, https://doi.org/10.17616/R3KP67 SCR_003726 DataSphere, Project Data Sphere Initiative, Project DataSphere, Project Data Sphere LLC 2026-08-08 11:58:04 43
NCI Thesaurus
 
Resource Report
Resource Website
10+ mentions
NCI Thesaurus (RRID:SCR_003563) NCIt ontology, data or information resource, controlled vocabulary A reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP). thesaurus, clinical, treatment, prevention, biomedical, owl, health, drug, chemotherapy is listed by: OBO
is listed by: BioPortal
is related to: NCI Metathesaurus
is related to: OnEx - Ontology Evolution Explorer
has parent organization: National Cancer Institute
Cancer See license, http://evs.nci.nih.gov/ftp1/NCI_Thesaurus/NCI_THESAURUS_license.txt nlx_157698 ftp://ftp1.nci.nih.gov/pub/cacore/EVS/, https://cabig.nci.nih.gov/concepts/EVS/, https://wiki.nci.nih.gov/display/EVS/NCI+Thesaurus+%28NCIt%29, http://nciterms.nci.nih.gov, http://purl.bioontology.org/ontology/NCIT http://ncicb.nci.nih.gov/core/EVS SCR_003563 ncithesaurus 2026-08-08 11:58:07 10
MMRF CoMMpass Study
 
Resource Report
Resource Website
1+ mentions
MMRF CoMMpass Study (RRID:SCR_003721) CoMMpass data or information resource, topical portal, consortium, portal, organization portal, disease-related portal A personalized medicine initiative to discover biomarkers that can better define the biological basis of multiple myeloma to help stratify patients. This effort hopes to obtain samples from approximately 1,000 multiple myeloma patients and follow them over time to identify how a patient's genetic profile is related to clinical progression and treatment response. As a partnership between 17 academic centers, 5 pharmaceuticals and the Department of Veterans Affairs, the goal of this eight year study is to create a database that can accelerate future clinical trials and personalized treatment strategies. MMRF's CoMMpass Study has the following goals: * Create a guide to which treatments work best for specific patient subgroups. * Share data with researchers to accelerate drug development for specific subtypes of multiple myeloma patients. In order to facilitate discoveries and development related to targeted therapies, the comprehensive data from CoMMpass is placed in an open-access research portal. The data will be part of the Multiple Myeloma Research Foundation's (MMRF) Personalized Medicine Platform combines CoMMpass data with those collected from MMRF's Genomics Initiative. It is hoped that the longitudinal data, combined with the annotated bio-specimens will help provide insights that can accelerate personalized therapies. consortium, biomarker, molecular, genetic, blood, cancer, clinical, data sharing uses: Multiple Myeloma Genomics Portal
is listed by: Consortia-pedia
has parent organization: Multiple Myeloma Research Foundation
United States Department of Veterans Affairs ;
Multiple Myeloma Research Foundation
nlx_157899 SCR_003721 Relating Clinical Outcomes in MM to Personal Assessment of Genetic Profile, Relating Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile Study, Multiple Myeloma Research Foundation (MMRF) - CoMMpass Study 2026-08-08 11:58:02 1
Cure Alzheimers Fund
 
Resource Report
Resource Website
1+ mentions
Cure Alzheimers Fund (RRID:SCR_003564) CAF data or information resource, narrative resource, blog, topical portal, portal, funding resource Cure Alzheimer's Fund is a 501(c)(3) public charity. At Cure Alzheimer's Fund, our mission is to fund research with the highest probability of slowing, stopping or reversing Alzheimer's disease. This topical portal has a lot of information including news and blog. Cure Alzheimer's Fund is governed by a board of directors; administered by a small, full-time staff; and guided scientifically by a Research Consortium. A Scientific Advisory Board audits the research program to make sure it is consistent with the objectives of the foundation. Cure Alzheimer's Fund is a doing business as name for the Alzheimer's Disease Research Foundation, federal tax ID # 52-2396428. nlx_11948 SCR_003564 2026-08-08 11:58:00 3
MetaCore
 
Resource Report
Resource Website
1000+ mentions
MetaCore (RRID:SCR_008125) software resource, software application, data analysis software, data processing software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. An integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression. expression, gene, dna, interaction, metabolomics, microarray, pathway, protein, proteomic, software is listed by: Metabolomics Workbench THIS RESOURCE IS NO LONGER IN SERVICE. nif-0000-20874 http://www.genego.com/metacore.php SCR_008125 2026-08-08 11:59:12 1182
MedGene
 
Resource Report
Resource Website
1+ mentions
MedGene (RRID:SCR_008122) software resource An algorithm that generates lists of genes associated with a gene or one or more disorders. The algorithm can be used in high-throughput screening experiments, can create disease-specific micro-arrays, and can sort the results of gene profiling data. Based on the co-citations of all Medline records, MedGene can retrieve the following relationships: 1. A list of human genes associated with a particular human disease in ranking order 2. A list of human genes associated with multiple human diseases in ranking order 3. A list of human diseases associated with a particular human gene in ranking order 4. A list of human genes associated with a particular human gene in ranking order 5. The sorted gene list from other disease related high-throughput experiments, such as micro-array 6. The sorted gene list from other gene related high-throughput experiments, such as micro-array gene, disease, human order, microarray has parent organization: Harvard University; Cambridge; United States nif-0000-20869 SCR_008122 MedGene 2026-08-08 11:58:57 4
BraInSitu: A homepage for molecular neuroanatomy
 
Resource Report
Resource Website
1+ mentions
BraInSitu: A homepage for molecular neuroanatomy (RRID:SCR_008081) BraInSitu expression atlas, data or information resource, atlas, narrative resource, image, database, experimental protocol Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE. function, gene expression, gene, anatomical structure, brain, central nervous system, cerebral cortex, in situ hybridization, mammalian, neocortex, pcr cloning, probe, molecular neuroanatomy resource, neuroanatomy, in situ hybridization protocol has parent organization: National Institute for Basic Biology; Okazaki; Japan nif-0000-11633 SCR_008081 2026-08-08 11:59:12 4
University of Washington Integrated Brain Project
 
Resource Report
Resource Website
1+ mentions
University of Washington Integrated Brain Project (RRID:SCR_008075) ontology, data or information resource, controlled vocabulary, software resource The UW Integrated Brain Project is one project within the national Human Brain Project, a national multi-agency effort to develop informatics tools for managing the exploding amount of information that is accumulating about the human brain. The objective of the UW Integrated Brain Project effort is to organize and integrate distributed functional information about the brain around the structural information framework that is the long term goal of our work. This application therefore extends the utility of the Digital Anatomist Project by using it to organize non-structural information. The initial driving neuroscience problem that is being addressed is the management, visualization and analysis of cortical language mapping data. In recent years, advances in imaging technology such as PET and functional MRI have allowed researchers to observe areas of the cortex that are activated when the subject performs language tasks. These advances have greatly accelerated the amount of data available about human language, but have also emphasized the need to organize and integrate the sometimes contradictory sources of data, in order to develop theories about language organization. The hypothesis is that neuroanatomy is the common substrate on which the diverse kinds of data can be integrated. A result of the work done by this project is a set of software tools for generating a 3-D reconstruction of the patient''s own brain from MRI, for mapping functional data to this reconstruction, for normalizing individual anatomy by warping to a canonical brain atlas and by annotating data with terms from an anatomy ontology, for managing individual lab data in local laboratory information systems, for integrating and querying data across separate data management systems, and for visualizing the integrated results. Sponsors: This Human Brain Project research is funded jointly by the National Institute on Deafness and Other Communication Disorders, the National Institute of Mental Health, and the National Institute on Aging. functional mri, anatomy, brain, imaging, neuroanatomy, neuroscience, open source license, pet, technology Aging nif-0000-10536 SCR_008075 UW Brain Project 2026-08-08 11:59:04 1
Gladstone Institute of Neurological Disease
 
Resource Report
Resource Website
1+ mentions
Gladstone Institute of Neurological Disease (RRID:SCR_008072) data or information resource, training resource, portal, organization portal, job resource GIND provides a highly interactive academic environment and state-of-the-art research facilities that are ideal for training in neuroscience and biomedical research. GIND Investigators hold university appointments at UCSF and participate in educational activities, including the teaching and training of graduate students and postdoctoral fellows. Additionally, GIND is actively engaged in efforts to translate scientific discoveries into better treatments for major diseases of the nervous system. Sponsors: Support for GIND comes from the University of California at San Francisco. biomedical, disease, nervous system, neuroscience, research, treatment is related to: Collaboratory of AIDS Researchers for Eradciation (CARE) nif-0000-10522 SCR_008072 GIND 2026-08-08 11:59:12 2
Cellular Open Resource
 
Resource Report
Resource Website
10+ mentions
Cellular Open Resource (RRID:SCR_008022) database, data or information resource, software resource Cellular Open Resource is a Microsoft Windows environment for cellular modeling that is built around CellML (except for reactions and metadata which are not supported). It offers, through CellML, an ''out of the box'' access to a large database of single cell models. COR was among the early adopters of this standard, eventually forming the first publicly available CellML-based modeling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modelers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential. Sponsors: This study has been supported by a grant from the UK Biotechnology and Biological Sciences Research Council (BB/E024955/1). Keyword: Cell, Model, Cellular, Modeling, Open resource, Microsoft, Environment, Database, Experimentalist, Teacher, Student, Modeler, Computationally, Development, has parent organization: University of Oxford; Oxford; United Kingdom nif-0000-10187 SCR_008022 COR 2026-08-08 11:59:03 15
Bacterial Genomes
 
Resource Report
Resource Website
10+ mentions
Bacterial Genomes (RRID:SCR_008141) data or information resource, software resource, software application, database, data analysis software, data processing software This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences. bacteria, bacterial, classification, description, disease, genomic, model, organism, pathogen, sequence, sequencing, model is listed by: 3DVC
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
nif-0000-20963 SCR_008141 Bacterial Genomes 2026-08-08 11:59:12 12

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