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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | production service resource, analysis service resource, source code, service resource, software resource, data analysis service | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-02-17 10:00:49 | 82 | |||||
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UM-BBD Resource Report Resource Website 1+ mentions |
UM-BBD (RRID:SCR_005787) | UM-BBD, UM-BBD enzymeID, UM-BBD pathwayID, UM-BBD reactionID, UM-BBD ruleID | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service, data set | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2014. Database containing information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Its goal is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students. In addition to reactions and pathways, this database also contains Biochemical Periodic Tables and a Pathway Prediction System. * Search the UM-BBD for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. * Go to Pathways and Metapathways in the UM-BBD * Lists of 203 pathways; 1400 reactions; 1296 compounds; 916 enzymes; 510 microorganism entries; 245 biotransformation rules; 50 organic functional groups; 76 reactions of naphthalene 1,2-dioxygenase; 109 reactions of toluene dioxygenase; Graphical UM-BBD Overview; and Other Graphics (Metapathway and Pathway Maps and Reaction Mechanisms). | enzyme, biocatalysis, biodegredation, chemical, pathway, reaction, microorganism, image, chemical compound, gene, enzymology | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Minnesota Supercomputing Institute ; Lhasa Limited ; University of Minnesota; Minnesota; USA ; European Union FP6 ALARM project ; NIH ; NSF 0543416; DOE DE-FG02-01ER63268; NIGMS R01GM56529; NSF 9630427 |
PMID:19767608 PMID:16381924 PMID:12519997 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03607, r3d100011317 | https://doi.org/10.17616/R33D0V | SCR_005787 | UM-BBD pathwayID, University of Minnesota Biocatalysis and Biodegradation Database, UM-BBD reactionID, Biocatalysis/Biodegradation Database, University of Minnesota Biocatalysis/Biodegradation Database, UM-BBD ruleID, Univeristy of Minnesota Biocatalysis/Biodegradation Database, UM-BBD enzymeID | 2026-02-17 10:00:57 | 9 | ||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | data or information resource, project portal, database, service resource, portal | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu https://doi.org/10.17616/R3RK5C |
SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-02-17 10:00:39 | 10026 | ||||||
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Stanford Center for Narcolepsy Resource Report Resource Website |
Stanford Center for Narcolepsy (RRID:SCR_007021) | Stanford Center for Narcolepsy | biomaterial supply resource, tissue bank, brain bank, material resource | The Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy. | brain tissue, brain, tissue, hypocretin, orexin, narcolepsy, sleep disorder, cataplexy, idiopathic hypersomnia, normal control, kleine-levin syndrome, dog, zebrafish, research, therapy |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Stanford University School of Medicine; California; USA |
Narcolepsy, Sleep disorder, Cataplexy, Idiopathic hypersomnia, Normal control, Kleine-Levin Syndrome | Individual gifts ; NIH |
Private: not stated but looks that way | nlx_144254 | http://med.stanford.edu/school/Psychiatry/narcolepsy/ | SCR_007021 | Stanford University Center for Narcolepsy | 2026-02-17 10:01:09 | 0 | ||||
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Minnesota Center for Twin and Family Research Resource Report Resource Website 1+ mentions |
Minnesota Center for Twin and Family Research (RRID:SCR_006948) | MCTFR | data or information resource, topical portal, disease-related portal, research forum portal, portal | Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits. | longitudinal study, clinical study, twin, sibling, parent, longitudinal, gene, environment, adolescent, development, behavior, dna | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Identical twin, Fraternal twin, Sibling, Parent, Twin | NIH | nlx_151990 | SCR_006948 | SIBS, Minnesota Twin Study, MTFS, Sibbling Interaction and Behavior Study, Minnesota Twin Family Study | 2026-02-17 10:01:09 | 3 | ||||||
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MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | software application, data or information resource, topical portal, software resource, portal, simulation software | Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. | comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster |
is listed by: SoftCite has parent organization: University of California at San Francisco; California; USA |
Sandler Family Supporting Foundation ; NIGMS R01 GM54762; NIGMS P01 GM71790; NIH P01 A135707; NIGMS U54 GM62529; IBM ; Intel |
Restricted | nif-0000-30054 | SCR_008395 | 2026-02-17 10:01:21 | 5736 | ||||||||
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MashMap Resource Report Resource Website 10+ mentions |
MashMap (RRID:SCR_022194) | software application, data processing software, software resource, image analysis software, alignment software | Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences. | mapping genome assembly, long DNA sequences, long reads, reference genome, long DNA sequences aligner | NSF CCF1816027; National Human Genome Research Institute ; NIH |
PMID:30423094 DOI:10.1007/978-3-319-56970-3_5 |
Free, Available for download, Freely available | SCR_022194 | 2026-02-17 10:04:15 | 27 | |||||||||
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Biomedical Resource Ontology Resource Report Resource Website 1+ mentions |
Biomedical Resource Ontology (RRID:SCR_004443) | BRO | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO). | sitemap, resource type, owl, resource |
is listed by: BioPortal is listed by: Biositemaps is related to: Biositemaps is related to: iBIOFind is related to: bioDBcore has parent organization: National Centers for Biomedical Computing |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143813 | http://bioportal.bioontology.org/ontologies/1104 https://bioportal.bioontology.org/ontologies/BRO |
SCR_004443 | 2026-02-17 10:00:43 | 3 | ||||||
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | ontology, data access protocol, storage service resource, data or information resource, controlled vocabulary, image collection, database, service resource, software resource, web service, data repository, image repository | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-02-17 10:01:04 | 11 | |||
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Coriell Cell Repositories Resource Report Resource Website 50+ mentions |
Coriell Cell Repositories (RRID:SCR_003244) | CCR | biomaterial supply resource, cell repository, material resource | A biorepository and biomaterial supply resource which establishes, verifies, maintains, and distributes cells, cultures and DNA derived from cell cultures to the scientific community around the world. Scientists can browse the sample catalog and request specific cell lines for their research studies. An inventory of the remaining stock of each cell line and DNA preparation is presented in real time. Coriell's significant cell biobank collections include: NIGMS Human Genetic Cell Repository, NINDS Human Genetics DNA and Cell Line Repository, NIA Aging Cell Repository, NHGRI Sample Repository for Human Genetic Research, NEI Age-Related Eye Disease Study (AREDS) Genetic Repository, HD Community BioRepository, American Diabetes Association, GENNID Study, and Autism Research Resource. The repositories are ISO 9000-2001 compliant. | cellular, molecular, genetics, cell line, culture, cell, dna, reagent, disease, family, gene, pharmacogenetics, population, single nucleotide polymorphism |
is listed by: One Mind Biospecimen Bank Listing is listed by: Multiple Sclerosis Discovery Forum is related to: Integrated Cell Lines is related to: NCBI BioSample is related to: Integrated Manually Extracted Annotation is related to: One Mind Biospecimen Bank Listing is related to: Multiple Sclerosis Discovery Forum has parent organization: Coriell Institute for Medical Research is parent organization of: ADA GENNID Study is parent organization of: NIGMS Human Genetic Cell Repository is parent organization of: NINDS Repository is parent organization of: NHGRI Sample Repository for Human Genetic Research is parent organization of: NEI-AREDS Genetic Repository is parent organization of: COHORT Repository is parent organization of: IPBIR - Integrated Primate Biomaterials and Information Resource is parent organization of: HD Community BioRepository is parent organization of: Autism Research Resource is parent organization of: Yerkes Collection Non-Human Primate Resource is parent organization of: Wistar Institute Collection at Coriell is parent organization of: USIDNET DNA and Cell Repository is parent organization of: CDC Cell and DNA Repository is parent organization of: Leiomyosarcoma Cell and DNA Repository is parent organization of: Human Reference Genetic Material Repository is parent organization of: Aging Cell Repository works with: Cellosaurus |
NIH | Free, Freely available | nif-0000-00182 | http://ccr.coriell.org/ccr/ http://ccr.coriell.org/ |
SCR_003244 | 2026-02-17 09:59:57 | 74 | ||||||
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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 | 2026-02-17 10:00:29 | 52 | ||||
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Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core Resource Report Resource Website 1+ mentions |
Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core (RRID:SCR_007342) | Tulane Tissue Culture Core | biomaterial supply resource, cell repository, material resource | The Stem Cell Research and Regenerative Medicine''s Tissue Culture Core provides cells for research use within the department, as well as for distribution to other facilities. The core obtains hMSCs from bone marrow donor samples and expands these cells for research use. The hMSC''s are also characterized for bone, fat and cartilage differentiation, and are stored on site for use. The Tissue Culture Core also handles the expansion and characterization of mouse and rat MSC''s. The animal cells are cultured in a separate area, and never interact with human derived cells. We also have a supply of hMSC''s marked with GFP+, Mito Red and Mito Blue available. | stem cell, mesenchymal stem cell, marrow stromal cell, frozen, adult, bone marrow, adipose tissue, bone, fat, cartilage |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Tulane University School of Medicine; Louisiana; USA |
United States Department of DefenseBlueprint for Neuroscience Research ; NSF ; NIH |
Public: The Tissue Culture Core provides cells for research use within the department, As well as for distribution to other facilities. | nif-0000-00246 | http://www.som.tulane.edu/gene_therapy/distribute.shtml | SCR_007342 | Tulane Stem Cell Research Regenerative Medicine Tissue Culture Core | 2026-02-17 10:01:14 | 1 | |||||
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National Centers for Biomedical Computing Resource Report Resource Website 1+ mentions |
National Centers for Biomedical Computing (RRID:SCR_010635) | NCBC | data or information resource, portal, organization portal | The NCBCs are a set of networked computation core facilities for biomedical infrastructure funded under the NIH Common Fund, the National Program of Excellence in Biomedical Computing (NPEBC). There are seven funded Centers that cover systems biology, image processing, biophysical modeling, biomedical ontologies, information integration, and tools for gene-phenotype and disease analysis. The centers will create innovative software programs and other tools that enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. Each Center has Cores that are focused on (1) computational science, (2) biomedical computational science and (3) driving biological projects whose intent is to drive the interaction between computational and biomedical computational science. In addition to the Centers, the NIH has a number of active program announcements to develop collaborations with the biomedical research community��this includes announcements from the Biomedical Information Science and Technology Initiative (BISTI) and the Program for Collaborations with National Centers for Biomedical Computing. There are numerous efforts in education and training that emanate from the Centers and there is an annual all hands meeting. | nih (common fund) |
is related to: iDASH is related to: iTools is related to: Center for Computational Biology at UCLA is related to: i2b2 Research Data Warehouse is related to: Informatics for Integrating Biology and the Bedside is related to: National Alliance for Medical Image Computing is related to: Simbios is related to: National Center for Biomedical Ontology is related to: National Center for Integrative Biomedical Informatics is related to: MAGNet - Multiscale Analysis of Genomic and Cellular Networks is related to: iDASH has parent organization: National Institutes of Health is parent organization of: Biositemaps is parent organization of: National Center for Biomedical Ontology is parent organization of: Biomedical Resource Ontology is parent organization of: National Alliance for Medical Image Computing is parent organization of: NCBO Annotator |
NIH | nlx_62048 | SCR_010635 | NIH Roadmap National Centers for Biomedical Computing | 2026-02-17 10:01:49 | 1 | |||||||
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Inxight Resource Report Resource Website 10+ mentions |
Inxight (RRID:SCR_016490) | data or information resource, portal, database, organization portal | Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use. | drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, use | NIH | Free, Freely available | SCR_016490 | 2026-02-17 10:03:25 | 11 | ||||||||||
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OCICB Resource Report Resource Website |
OCICB (RRID:SCR_016597) | OCICB | data or information resource, portal, organization portal | Office of Cyber Infrastructure and Computational Biology of NIAID. | office, cyber, infrastructure, computational, biology, NIAID |
has parent organization: NIAID is parent organization of: Nephele |
NIH | SCR_016597 | Office of Cyber Infrastructure and Computational Biology | 2026-02-17 10:03:26 | 0 | ||||||||
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Complex Portal Resource Report Resource Website 1+ mentions |
Complex Portal (RRID:SCR_015038) | data or information resource, portal, database | Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download. | database, molecular complex, model organism | European Molecular Biology Laboratories Core Funding ; NIH 268201000035C; BBSRC BB/L024179/1 |
PMID:25313161 DOI:10.1093/nar/gku975 |
Open source, Available for download | r3d100013295 | https://doi.org/10.17616/R31NJMR3 | SCR_015038 | EBI Complex Portal | 2026-02-17 10:02:46 | 1 | ||||||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | web application, data or information resource, project portal, database, software resource, portal | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-02-17 10:03:18 | 20 | |||||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | organization portal, storage service resource, data or information resource, topical portal, disease-related portal, database, service resource, portal, data repository | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1 https://commonfund.nih.gov/kidsfirst |
SCR_016493 | Data Resource Portal | 2026-02-17 10:03:02 | 3 | ||||
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BeWith Resource Report Resource Website |
BeWith (RRID:SCR_016573) | BeWith | data analysis software, software application, data processing software, software resource | Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. | clustering, framework, identify, module, mutation, interaction, pattern, gene, cancer | Naomi Kadar award ; NIH |
DOI:10.1371/journal.pcbi.1005695 | Free, Available for download, Freely available | SCR_016573 | BEtweenWITHin, Between-Within, BeWith | 2026-02-17 10:02:43 | 0 | |||||||
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WikiPathways Resource Report Resource Website 1000+ mentions |
WikiPathways (RRID:SCR_002134) | data or information resource, database, service resource | Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community. | database, knowledge environment resource, image, web service, biological pathway, diagram description, reference, pathway, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is related to: PharmGKB is related to: Reactome is related to: NetPath is related to: ConsensusPathDB is related to: NCBI BioSystems Database is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of California at San Francisco; California; USA has parent organization: Maastricht University; Maastricht; Netherlands |
NIH ; Netherlands Bioinformatics Centre ; Google Summer of Code program ; NWO - Netherlands Organization for Scientific Research ; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:22096230 PMID:18651794 |
Free, Freely available | nif-0000-20925 | SCR_002134 | Wiki Pathways | 2026-02-17 09:59:44 | 1696 |
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If you are logged into nidm-terms you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
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