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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | software application, data visualization software, data processing software, software resource | The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways. | protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, plugin |
is listed by: Biositemaps is related to: Cytoscape is related to: Michigan Molecular Interactions has parent organization: University of Michigan; Ann Arbor; USA has parent organization: National Center for Integrative Biomedical Informatics |
NIH ; NIDA U54 DA021519; NLM R01 LM008106; NCRR P41 RR018627 |
PMID:18812364 | nif-0000-33090 | http://mimiplugin.ncibi.org/index.html | SCR_003424 | Cytoscape Plugin for MiMI, MiMI Plugin - Cytoscape Plugin for MiMI | 2026-02-15 09:18:30 | 1 | |||||
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Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | software application, software resource, authoring tool | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-02-15 09:18:29 | 147 | |||||
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sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | software application, data processing software, software resource, alignment software, image analysis software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-02-15 09:18:04 | 0 | ||||||
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International Mouse Strain Resource Resource Report Resource Website 10+ mentions |
International Mouse Strain Resource (RRID:SCR_001526) | IMSR | organism supplier, material resource, biomaterial supply resource | Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known. | RIN, Resource Information Network, mouse, strain, stock, inbred, mutant, genetically engineered, embryo, embryonic stem cell line, database, knockout mouse, mutant mouse strain, transgenic mouse, embryonic mouse, live mouse, gamete, ovary, sperm, germplasm, model organism, RRID Community Authority |
uses: Vanderbilt Cryopreserved Mouse Repository uses: Janvier Labs uses: Korea Mouse Phenotyping Center uses: CLEA Japan, Inc. uses: genOway uses: Inotiv uses: Cyagen Biosciences uses: Cam-Su Genomic Resource Center is used by: BioSample Database at EBI is used by: Integrated Animals lists: Oak Ridge Collection at JAX lists: National Resource Center for Mutant Mice lists: JAX Mice and Services lists: National Applied Research Laboratories lists: Oriental BioService Inc. is listed by: Resource Information Network is related to: NIF Data Federation is related to: Recombinase (cre) Activity is related to: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines is related to: Mouse Genome Informatics (MGI) has parent organization: MRC Mammalian Genetics Unit works with: Shanghai Model Organisms Center works with: European Mouse Mutant Archive works with: Texas A and M Institute for Genomic Medicine works with: JAX Mice and Services works with: CMMR - Canadian Mouse Mutant Repository works with: RIKEN BioResource Center works with: Center for Animal Resources and Development works with: National Institute of Genetics; Shizuoka; Japan works with: NHMRC Australian PhenomeBank works with: Taconic Biosciences works with: Charles River Laboratories works with: Medical Research Council Harwell: An International Centre for Mouse Genetics |
NLM LM009693 | PMID:10098412 PMID:26373861 |
Restricted | nif-0000-09876 | http://www.findmice.org/ | SCR_001526 | IMSR, International Mouse Strain Resource | 2026-02-15 09:18:07 | 13 | ||||
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Globin Gene Server Resource Report Resource Website 10+ mentions |
Globin Gene Server (RRID:SCR_001480) | Globin Gene Server | source code, data analysis service, database, software resource, training material, service resource, production service resource, data or information resource, narrative resource, analysis service resource, resource | Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles. | dna sequence, hemoglobin, mutation, globin gene cluster, sequence comparison, functional genomics, gene, alignment, genetic analysis, variant, gene expression, protein, thalassemia, globin gene, genome, pairwise alignment, multiple alignment, annotation, sequence analysis, dna |
is listed by: NIDDK Information Network (dkNET) has parent organization: Pennsylvania State University |
NLM R01LM05773; NLM R01LM05110; NIDDK DK27635 |
PMID:11857738 PMID:11480780 PMID:9799599 PMID:9576329 PMID:8088828 |
Free, Freely available | nlx_152723 | SCR_001480 | 2026-02-15 09:18:06 | 27 | ||||||
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Biological Magnetic Resonance Data Bank (BMRB) Resource Report Resource Website 500+ mentions |
Biological Magnetic Resonance Data Bank (BMRB) (RRID:SCR_002296) | BioMagResBank, BMRB | database, service resource, storage service resource, data repository, data or information resource | Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. | magnetic resonance, data bank, depository, database, data repository, spectral data, quantitative data, nmr, spectroscopy, macromolecule, metabolite, metabolomics, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: 3DVC is listed by: re3data.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Nucleic Acid Database is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: NRG-CING is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: CCPN Data Model has parent organization: University of Wisconsin-Madison; Wisconsin; USA is parent organization of: NMR Restraints Grid |
NLM LM05799 | PMID:18288446 PMID:17984079 PMID:12766409 PMID:36478084 |
Free, Freely available | nif-0000-21058 | SCR_002296 | BMRB, BioMagResBank, Biological Magnetic Resonance DataBank, BioMag Res Bank | 2026-02-15 09:18:16 | 752 | |||||
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NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | database, service resource, storage service resource, data repository, data or information resource | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) 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: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap https://bio.tools/dbgap https://doi.org/10.17616/R3GS4K |
SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-02-15 09:18:23 | 683 | ||||
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Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) Resource Report Resource Website 10+ mentions |
Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) | PDBP | biospecimen repository, material storage repository, service resource, storage service resource | Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders. | parkinson's, clinical neuroinformatics, magnetic resonance, diagnostic, progression, biomarker, clinical |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NINDS Repository is related to: MIPAV: Medical Image Processing and Visualization has parent organization: National Institute of Neurological Disorders and Stroke |
Parkinson's disease | nlm ; NINDS |
PMID:25976927 | Restricted | nlx_155919 | http://www.nitrc.org/projects/pdbp | http://pdbp.ninds.nih.gov/index.jsp | SCR_002517 | Parkinson's Disease Biomarkers Program, PDBP: Parkinsons Disease Biomarkers Program, Parkinson’s Disease Biomarkers Program Data Management Resource, PDBP DMR | 2026-02-15 09:18:19 | 24 | ||
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Michigan Molecular Interactions Resource Report Resource Website 1+ mentions |
Michigan Molecular Interactions (RRID:SCR_003521) | MiMI | data analysis service, database, software resource, data access protocol, web service, service resource, production service resource, data or information resource, analysis 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 | 2026-02-15 09:18:32 | 5 | |||||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | database, software resource, data access protocol, web service, service resource, storage service resource, data repository, data or information resource, software repository | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools http://www.loni.usc.edu/research/software |
http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-02-15 09:20:13 | 45 | |||
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GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | data analysis service, software resource, database, data access protocol, web service, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-02-15 09:20:42 | 24 | ||||
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Informatics for Integrating Biology and the Bedside Resource Report Resource Website 10+ mentions |
Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) | i2b2 | organization portal, portal, data set, software resource, training resource, data or information resource | i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license. | genetic, biology, biomedical, computing, genomic, health, healthcare, informatic, origin, patient, therapy, predoctoral, postdoctoral |
is related to: National Centers for Biomedical Computing is parent organization of: i2b2 Cross-Institutional Clinical Translational Research project is parent organization of: Smoking NLP Challenge Data |
NLM U54LM008748 | Free, Public, Acknowledgement requested | nif-0000-33133 | SCR_013629 | 2026-02-15 09:20:44 | 27 | |||||||
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PubReader Resource Report Resource Website 1+ mentions |
PubReader (RRID:SCR_013814) | web application, software resource | A web application which serves as an alternate way to read scientific literature in PubMed Central and Bookshelf. PubReader features an easy-to-read multi-column display, a figure strip for access to figures, and a search function. It is designed especially to support reading on tablets and other smaller devices but is available for reading on laptops and desktops. | web application, literature, tablet, mobile device |
is used by: PubMed Central is used by: Bookshelf is listed by: Connected Researchers is related to: NCBI is related to: PubMed Central is related to: Bookshelf is related to: Connected Researchers has parent organization: NCBI |
NIH ; NLM ; United States Department of Health and Human Services ; U.S. Government |
Free, Public | SCR_013814 | 2026-02-15 09:20:52 | 1 | |||||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | software application, data processing software, software resource, image analysis software, software toolkit | A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. | image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University; Indiana; USA |
NLM R01 LM011360; NSF IIS-1117335 |
http://www.iu.edu/~hdbig/ | SCR_014120 | High Dimensional Brain Imaging Genomics Toolkit | 2026-02-15 09:20:55 | 0 | ||||||||
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RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | text-mining software, software application, web application, software resource | Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials. | Data automatic extraction, clinical trial reports, automatically extract key data, Evidence Based Medicine, text journal articles processing, randomized controlled trials |
is related to: Northeastern University; Massachusetts; USA is related to: University of Texas at Austin; Texas; USA |
NLM R01 LM012086; Medical Research Council UK ; NCI UH2 CA203711 |
PMID:29093610 DOI:10.1093/jamia/ocv044 |
Free, Available for download, Freely available | https://github.com/ijmarshall/robotreviewer https://robotreviewer.vortext.systems/ |
SCR_021064 | Automating Biomedical Evidence Synthesis | 2026-02-15 09:22:28 | 1 | ||||||
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CCPN Data Model Resource Report Resource Website |
CCPN Data Model (RRID:SCR_016982) | software application, database, data processing software, software resource, service resource, storage service resource, data repository, data storage software, data or information resource | Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature. | data, macromolecular, NMR, spectroscopy, deposition, mining, interoperability, conversion |
is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Collaborative Computing Project for NMR works with: CCPN Analysis works with: CCPN Analysis |
EU ; BBSRC ; NLM P41 LM005799; NIGMS GM67965 |
PMID:15815974 PMID:15613391 PMID:21953355 |
Free, Public | SCR_016982 | The CCPN Data Model | 2026-02-15 09:21:53 | 0 | |||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | software application, data visualization software, data processing software, software resource, image analysis software | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NLM R01 LM011360; NIA U01 AG024904; NIA RC2 AG036535; NIA R01 AG19771; NIA P30 AG10133; NSF IIS-1117335; NIBIB R01 EB022574 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-02-15 09:21:25 | 5 | ||||||
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HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | software application, sequence analysis software, source code, data processing software, software resource, data analysis software | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2 https://bio.tools/hisat2 https://sources.debian.org/src/hisat2/ |
SCR_015530 | HISAT | 2026-02-15 09:21:18 | 17595 | |||||
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ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software toolkit, software resource | Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . | compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic | has parent organization: University of Pennsylvania; Philadelphia; USA | NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NEI EY022300; NHLBI HL134015; NLM LM009012; NLM LM010098; NLM LM011360; NCATS TR001263; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | Relief Based Algorithm Training Environment | 2026-02-15 09:21:57 | 0 | ||||||
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SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins. | identifying phage tailspike proteins, phage tailspike protein, deplolymerase, right-handed beta-helix, | NLM ; NSF |
PMID:37503040 | Free, Available for download, Freely available | SCR_024831 | 2026-02-15 09:23:40 | 1 |
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Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF 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.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
