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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Genedata Expressionist Resource Report Resource Website 10+ mentions |
Genedata Expressionist (RRID:SCR_003298) | data analysis software, data processing software, data management software, software application, software resource | Software that provides data processing, analysis, management, and reporting of metabolomics, proteomics and biotherapeutics characterization studies based on mass spectrometry. It can process raw data from various MS instruments, serve MS processing, analysis and reporting needs, and ensure reproducibility and traceability of results. | mass spectrometry data processing, mass spectrometry data analysis, mass spectrometry data management, omics software | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00761 | SCR_003298 | Genedata Expressionist for Genomic Profiling | 2026-08-09 09:03:43 | 10 | ||||||||
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eDoctoring Resource Report Resource Website 1+ mentions |
eDoctoring (RRID:SCR_003336) | eDoctoring | training resource, data or information resource, service resource, narrative resource, continuing medical education, training material, training service resource | Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making | clinical, medical education, medical, clinical medicine, ethics, clinical management, epidemiology, communication, legal, social, implication, genetic testing, palliative care, end-of-life care, prostate cancer screening, decision-making, prostate cancer, medicine, tutorial, article, video, fact, training material |
has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom has parent organization: University of California; California; USA |
NCI ; NIH ; CDC ; NHGRI ; Health Resources and Services Administration ; Paul G. Allen Family Foundation ; Robert Wood Johnson Foundation |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31964 | http://edoctoring.ncl.ac.uk/System_Check/psa_detect_html;clickonRouletteWheels | SCR_003336 | 2026-08-09 09:03:43 | 1 | ||||||
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Chemical Methods Ontology Resource Report Resource Website 1+ mentions |
Chemical Methods Ontology (RRID:SCR_003286) | CHMO, RSC CMO | data or information resource, controlled vocabulary, ontology | An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). | obo, chemistry, analytical chemistry, physical chemistry, material chemistry, method, health, mass spectrometry, electron microscopy, chemical experiment, sample ionization, chromatography, electrophoresis, instrument |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is listed by: Ontobee is related to: Information Artifact Ontology is related to: Ontology for Biomedical Investigations has parent organization: Royal Society of Chemistry |
Free, Available for download, Freely available | nlx_157363 | http://purl.bioontology.org/ontology/CHMO, http://purl.obolibrary.org/obo/chmo.owl, http://www.ontobee.org/browser/index.php?o=CHMO | https://code.google.com/p/rsc-cmo/ | SCR_003286 | RSC Chemical Methods Ontology | 2026-08-09 09:03:42 | 1 | |||||
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Michigan State University Brain Biodiversity Bank Resource Report Resource Website 1+ mentions |
Michigan State University Brain Biodiversity Bank (RRID:SCR_003289) | database, data or information resource, atlas, narrative resource, training material | The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. Atlases and brain sections are available for a variety of mammals, and we are also developing a series of labeled atlases of stained sections for educators, students, and researchers. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan. What we are doing currently at Michigan State is a series of demonstration projects for publicizing the contents of the collections and ways in which they can be used. For example, the images from the collection can be used for comparative brain study. We have prepared databases of the contents of the collections for presentation and use on this site, as well as for downloading by users in several formats. We are also developing a series of labeled atlases of stained sections for educators, students, and researchers. This internet site is associated with the Comparative Mammalian Brain Collections site. All of the images are in JPEG or GIF format. | echidna, anatomy, axolotl, brain, brainstem, cat, cerebellum, chimpanzee, cortex, cow, dolphin, histology, human, hyena, hypothalamus, images, imaging, lion, llama, loris, manatee, mandrill, mongoose, morphology, movies, mri, nissl, owl monkey, pig, polar bear, red kangaroo, rhesus monkey, sea lion, sheep, subcortical, tasmanian devil, weasel, white matter, zebra | has parent organization: Michigan State University; Michigan; USA | Free, Available for download, Freely available | nif-0000-00059, r3d100012667 | https://doi.org/10.17616/R31F77 | SCR_003289 | Brain Biodiversity Bank | 2026-08-09 09:03:43 | 1 | |||||||
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Yale Rudd Center for Food Policy and Obesity Resource Report Resource Website 1+ mentions |
Yale Rudd Center for Food Policy and Obesity (RRID:SCR_003283) | Rudd Center | portal, data or information resource, topical portal | A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma. | diet, nutrition | has parent organization: Yale University; Connecticut; USA | Obesity | Free, Freely available | nif-0000-31473 | https://medicine.yale.edu/internal-medicine/drc/resources/institutional/ruddcenter/ | SCR_003283 | Rudd Center for Food Policy & Obesity | 2026-08-09 09:03:43 | 1 | |||||
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Harvard Brain Tissue Resource Center Resource Report Resource Website 10+ mentions |
Harvard Brain Tissue Resource Center (RRID:SCR_003316) | HBTRC | brain bank, tissue bank, material resource, biomaterial supply resource | Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens. | biomaterial supply resource, brain tissue, brain, tissue, Huntington's disease, Parkinson's disease, mental disease, neurological disorder, Alzheimer's disease, schizophrenia, bipolar disorder, relative, parent, sibling, child, lewy body variant Alzheimer's disease, amyotrophic lateral sclerosis, dementia, unipolar depressive disorder, diffuse lewy body disease, dyt-1 dystonia, progressive supranuclear palsy, rett syndrome, Tourette's syndrome, restless legs syndrome, autism, post-mortem |
is listed by: One Mind Biospecimen Bank Listing is listed by: Multiple Sclerosis Discovery Forum is related to: One Mind Biospecimen Bank Listing is related to: Multiple Sclerosis Discovery Forum has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: National Brain Databank is parent organization of: Autism Tissue Program is parent organization of: RLS Foundation Brain Bank |
Huntington's disease, Parkinson's disease, Mental disease, Neurological disorder, Normal control, Alzheimers disease, Schizophrenia, Bipolar Disorder, Lewy Body Variant Alzheimer's disease, Amyotrophic Lateral Sclerosis, Dementia, Unipolar Depressive Dissorder, Diffuse Lewy Body Disease, DYT-1 Dystonia, Progressive Supranuclear Palsy, Rett Syndrome, Tourette's Syndrome | National Institutes of Health ; Private organizations ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00192 | https://rarediseases.org/organizations/harvard-brain-tissue-resource-center/ | SCR_003316 | Harvard Brain Bank, The Brain Bank | 2026-08-09 09:03:44 | 25 | ||||
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Biological Biochemical Image Database Resource Report Resource Website 10+ mentions |
Biological Biochemical Image Database (RRID:SCR_003474) | BBID | database, data or information resource, service resource, image collection, storage service resource, image repository, data repository | Database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. The rationale for this collection is that: # Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. # Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. # The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. # Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. # All images are attributable to the original authors. All pathways or other biological systems described are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. Image/pathway submissions are welcome. | eukaryota, gene, gene family, biochemical, biological role, cdna, cdna array, cellular relationship, genomics, macromolecule, protein, proteomics, image, pathway, structure, annotation, cell, macromolecular structure, protein, functional genomics, proteomics | has parent organization: Intramural Research Program | NIH Blueprint for Neuroscience Research | PMID:11099263 | IMAGES MAY NOT BE USED WITHOUT BOTH THE WRITTEN PERMISSION FROM THE ORIGINAL PUBLISHER AND THE BBID DATABASE ADMINISTRATOR., The community can contribute to this resource | nif-0000-00205 | http://bbid.grc.nia.nih.gov/ | SCR_003474 | BBID-Biological Biochemical Image Database | 2026-08-09 09:03:44 | 11 | ||||
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Structural Biology Grid Resource Report Resource Website 50+ mentions |
Structural Biology Grid (RRID:SCR_003511) | SBGrid | data or information resource, service resource, storage service resource, data set, computational hosting, data repository | Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application. | structure, x-ray crystallography, nuclear magnetic resonance, electron microscopy, structural biology, software application, computation, chemistry, meeting, software service, molecule, data sharing, biomedical |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: Harvard Medical School; Massachusetts; USA |
NSF | PMID:22514186 | Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, Tomography and other experimental structural biology technologies in their research., The community can contribute to this resource | nif-0000-37641, r3d100010234 | https://doi.org/10.17616/R3NS3R | http://sbgrid.org/index.php | SCR_003511 | SBGrid Software Consortium, SBGrid Science Portal, SBGrid Consortium | 2026-08-09 09:03:45 | 60 | |||
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Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | database, data or information resource, service resource, storage service resource, image repository, data repository | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J | SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-08-09 09:03:44 | 22 | ||||
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DTU Center for Biological Sequence Analysis Resource Report Resource Website 1000+ mentions |
DTU Center for Biological Sequence Analysis (RRID:SCR_003590) | CBS, DTU CBS | service resource, production service resource, web service, analysis service resource, software resource, data access protocol | Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics. | nucleotide, sequence, amino acid, dna, microarray, molecule, immunology, protein function, protein structure, protein, post-translational, whole genome, sequence analysis |
has parent organization: Technical University of Denmark; Lyngby; Denmark is parent organization of: NESbase is parent organization of: O-GLYCBASE is parent organization of: OligoWiz is parent organization of: SignalP |
Danish National Research Foundation ; Danish Research Councils ; Danish Center for Scientific Computing ; Villum Kann Rasmussen Foundation ; Novo Nordisk Foundation ; European Union ; NIH |
nlx_12329 | http://www.cbs.dtu.dk/index.shtml | SCR_003590 | 2026-08-09 09:03:46 | 1475 | |||||||
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Solstice Resource Report Resource Website 1+ mentions |
Solstice (RRID:SCR_003463) | Solstice | software development tool, software application, software resource, software development environment | A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development. | perl |
is listed by: Biositemaps has parent organization: University of Washington; Seattle; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33380 | SCR_003463 | 2026-08-09 09:03:45 | 2 | ||||||||
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Eton Bioscience Resource Report Resource Website 50+ mentions |
Eton Bioscience (RRID:SCR_003533) | organization portal, portal, data or information resource, department portal | An Antibody supplier | nlx_152359 | SCR_003533 | Eton Bioscience Inc. | 2026-08-09 09:03:45 | 87 | |||||||||||
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Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | database, data or information resource, service resource, storage service resource, data repository | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 | SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-08-09 09:03:44 | 811 | ||||
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caTRIP Resource Report Resource Website 1+ mentions |
caTRIP (RRID:SCR_003409) | caTRIP | data analysis software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity. | element, clinical, patient, structure, tissue, trial, tumor, common data element, clinician, data technician, java, outcomes research, ctsa | has parent organization: Cancer Biomedical Informatics Grid | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33400 | SCR_003409 | 2026-08-09 09:03:47 | 2 | |||||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | database, data or information resource, service resource, data analysis service, analysis service resource, production service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-08-09 09:03:45 | 4810 | |||||
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Michigan Molecular Interactions Resource Report Resource Website 1+ mentions |
Michigan Molecular Interactions (RRID:SCR_003521) | MiMI | database, data or information resource, service resource, web service, data access protocol, data analysis service, analysis service resource, software resource, production service resource | MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu. | gene, interaction, molecule, protein, protein interaction, protein-protein interaction |
is related to: MiMI Plugin for Cytoscape has parent organization: National Center for Integrative Biomedical Informatics |
Michigan Center for Biological Information ; National Center for Integrative Biomedical Informatics ; Pfizer ; Medical and Academic Partnerships ; Howard Hughes Medical Institute ; Microsoft Corporation ; NLM R01 LM008106; NIDA U54 DA021519; NSF IIS 0219513 |
PMID:18978014 PMID:17130145 |
nif-0000-00214 | SCR_003521 | 2026-08-09 09:03:45 | 5 | |||||||
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L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | service resource, image processing software, data processing software, software application, image analysis software, software resource | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure | SCR_003487 | 2026-08-09 09:03:44 | 30 | |||||
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NIH Blueprint for Neuroscience Research Resource Report Resource Website 10+ mentions |
NIH Blueprint for Neuroscience Research (RRID:SCR_003670) | NIH Blueprint, Blueprint, | training resource, data or information resource, topical portal, portal, funding resource | Collaborative framework that includes the NIH Office of the Director and the 14 NIH Institutes and Centers that support research on the nervous system. By pooling resources and expertise, the Blueprint identifies cross-cutting areas of research, and confronts challenges too large for any single Institute or Center. The Blueprint makes collaboration a day-to-day part of how the NIH does business in neuroscience, complementing the basic missions of Blueprint partners. During each fiscal year, the partners contribute a small percentage of their funds to a common pool. Since the Blueprint's inception in 2004, this pool has comprised less than 1 percent of the total neuroscience research budget of the partners. In 2009, the Blueprint Grand Challenges were launched to catalyze research with the potential to transform our basic understanding of the brain and our approaches to treating brain disorders. * The Human Connectome Project is an effort to map the connections within the healthy brain. It is expected to help answer questions about how genes influence brain connectivity, and how this in turn relates to mood, personality and behavior. The investigators will collect brain imaging data, plus genetic and behavioral data from 1,200 adults. They are working to optimize brain imaging techniques to see the brain's wiring in unprecedented detail. * The Grand Challenge on Pain supports research to understand the changes in the nervous system that cause acute, temporary pain to become chronic. The initiative is supporting multi-investigator projects to partner researchers in the pain field with researchers in the neuroplasticity field. * The Blueprint Neurotherapeutics Network is helping small labs develop new drugs for nervous system disorders. The Network provides research funding, plus access to millions of dollars worth of services and expertise to assist in every step of the drug development process, from laboratory studies to preparation for clinical trials. Project teams across the U.S. have received funding to pursue drugs for conditions from vision loss to neurodegenerative disease to depression. Since its inception in 2004, the Blueprint has supported the development of new resources, tools and opportunities for neuroscientists. For example, the Blueprint supports several training programs to help students pursue interdisciplinary areas of neuroscience, and to bring students from underrepresented groups into the neurosciences. The Blueprint also funds efforts to develop new approaches to teaching neuroscience through K-12 instruction, museum exhibits and web-based platforms. From fiscal years 2007 to 2009, the Blueprint focused on three major themes of neuroscience - neurodegeneration, neurodevelopment, and neuroplasticity. These efforts enabled unique funding opportunities and training programs, and helped establish new resources including the Blueprint Non-Human Primate Brain Atlas. | animal model, collaboration, computational biology, imaging tool, initiative, neurodegeneration, neurodevelopment, neuroinformatics, brain, brain disorder, pain, drug, nervous system disorder, neurotherapeutics, neuroplasticity, neuroscience |
has parent organization: National Institutes of Health is parent organization of: CRE Driver Network is parent organization of: Blueprint Neurotherapeutics Network is parent organization of: National Center for Complementary and Alternative Medicine is parent organization of: National Eye Institute (NEI) Commons is parent organization of: National Institute of Biomedical Imaging and Bioengineering is parent organization of: National Institute of Nursing Research is parent organization of: National Institute on Alcohol Abuse and Alcoholism is parent organization of: National Institute on Drug Abuse is parent organization of: National Institute on Deafness and Other Communication Disorders is parent organization of: National Institute of General Medical Sciences is parent organization of: National Institute of Dental and Craniofacial Research is parent organization of: Office of Behavioral and Social Sciences Research is parent organization of: National Institute of Child Health and Human Development is parent organization of: National Institute of Environmental Health Sciences is parent organization of: National Institute of Mental Health is parent organization of: National Institute on Aging is parent organization of: National Institute of Neurological Disorders and Stroke is parent organization of: NeuroImaging Tools and Resources Collaboratory (NITRC) |
nif-0000-00219 | SCR_003670 | Neuroscience Blueprint | 2026-08-09 09:03:52 | 10 | ||||||||
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Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | data or information resource, controlled vocabulary, ontology | Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles. | adverse event, health, pathological, molecular, cellular, organismal, multi-organismal |
is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Ontology of Vaccine Adverse Events has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:25093068 | Free, Freely available | nlx_157522 | http://purl.bioontology.org/ontology/OAE, http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl | SCR_003428 | 2026-08-09 09:03:47 | 2 | ||||||
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Mindtouch DekiWiki Resource Report Resource Website 1+ mentions |
Mindtouch DekiWiki (RRID:SCR_003425) | MindTouch | commercial organization, source code, software resource | 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) | 2026-08-09 09:03:47 | 2 |
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