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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Unified Medical Language System Resource Report Resource Website 10+ mentions |
Unified Medical Language System (RRID:SCR_006363) | UMLS | international standard specification, web service, data or information resource, data access protocol, software resource, narrative resource, database, standard specification | Database of key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records. This set of files and software brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems. Users can use the UMLS to enhance or develop applications, such as electronic health records, classification tools, dictionaries and language translators. The UMLS has three tools, which we call the Knowledge Sources: * Metathesaurus: Terms and codes from many vocabularies, including CPT, ICD-10-CM, LOINC, MeSH, RxNorm, and SNOMED CT * Semantic Network: Broad categories (semantic types) and their relationships (semantic relations) * SPECIALIST Lexicon and Lexical Tools: Natural language processing tools We use the Semantic Network and Lexical Tools to produce the Metathesaurus. Metathesaurus production involves: * Processing the terms and codes using the Lexical Tools * Grouping synonymous terms into concepts * Categorizing concepts by semantic types from the Semantic Network * Incorporating relationships and attributes provided by vocabularies * Releasing the data in a common format Although we integrate these tools for Metathesaurus production, you can access them separately or in any combination according to your needs. The UMLS Terminology Services (UTS) provides three ways to access the UMLS: Web Browsers, Local Installation, and Web Services APIs. | interoperability, electronic health record, classification tool, dictionary, language translator, classification, terminology, semantic, metathesaurus, vocabulary, thesaurus, natural language processing |
is used by: DisGeNET is related to: MeSH is related to: ConceptWiki has parent organization: National Library of Medicine |
NLM | License required and only issued to individuals, Not to groups or organizations - no charge for licensing the UMLS from NLM. | nlx_152104 | SCR_006363 | Unified Medical Language System (UMLS) | 2026-02-14 02:04:29 | 44 | ||||||
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EVidenceModeler Resource Report Resource Website 1000+ mentions |
EVidenceModeler (RRID:SCR_014659) | EVM | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format). | sequence analysis software, framework, ab intio gene, gene prediction, protein alignment, transcript alignment, consensus gene structure | NIAID N01 AI30071; NLM R01 LM006845 |
PMID:18190707 | Free, Available for download, Freely available | SCR_017649 | SCR_014659 | 2026-02-14 02:04:36 | 1135 | |||||||
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Gene functional conservation across cell types and species Resource Report Resource Website |
Gene functional conservation across cell types and species (RRID:SCR_023292) | data or information resource, portal, project portal | We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain. | Brain Initiative Cell Census Network, single-nucleus atlases, middle temporal gyrus, human, chimp, gorilla, macaque, marmoset, 57 consensus cell types common to all species, 57 consensus cell types identification, | is related to: BICCN | NLM R01LM012736; NLM R01MH113005; NLM U19MH114821; NLM F32MH114501; NARSAD Young Investigator Award ; NHGRI R01HG009318; NLM U01MH114812 |
DOI:10.1101/2022.09.20.508736 | Free, Freely available | SCR_023292 | 2026-02-14 02:05:47 | 0 | ||||||||
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LINCS Data Portal 2.0 Resource Report Resource Website 1+ mentions |
LINCS Data Portal 2.0 (RRID:SCR_022566) | LDP v2 | data or information resource, portal | Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures. | LINCS Data Portal, Cell, molecules, drug | is related to: LINCS Data Portal | NHLBI U54HL127624; BD2K-LINCS Data Coordination and Integration Center ; NCATS U24TR002278; NLM U01LM012630 |
PMID:31701147 | Free, Freely available | SCR_022566 | Library of Integrated Network Based Cellular Signatures 2.0 | 2026-02-14 02:05:49 | 2 | ||||||
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SimpleITK Resource Report Resource Website 10+ mentions |
SimpleITK (RRID:SCR_024693) | software resource, software library, software toolkit | Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms. | multi dimensional image analysis, Insight Segmentation and Registration Toolkit, | is related to: Insight Segmentation and Registration Toolkit | NLM | PMID:24416015 | Free, Available for download, Freely available | https://github.com/SimpleITK/SimpleITK | SCR_024693 | Simple Insight Segmentation and Registration Toolkit | 2026-02-14 02:05:59 | 37 | ||||||
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MedGen Resource Report Resource Website 1+ mentions |
MedGen (RRID:SCR_000111) | MedGen | data or information resource, database | A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution. | medical genetics, medical, genetics, disease, clinical |
is listed by: OMICtools is listed by: Genetic Testing Registry has parent organization: NCBI |
NLM 1ZIHLM200888-05 | PMID:32329672 | nlx_156941, OMICS_01549 | SCR_000111 | 2026-02-14 02:05:42 | 6 | |||||||
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Automated Microarray Pipeline Resource Report Resource Website |
Automated Microarray Pipeline (RRID:SCR_001219) | AMP | data analysis service, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis. | microarray, normalization |
is listed by: OMICtools is related to: Gene Ontology has parent organization: TM4 |
NLM R01-LM008795 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02125 | http://www.tm4.org/amp.html | SCR_001219 | TM4 AMP, AMP: Automated Microarray Pipeline, AMP (TM4 Microarray Software Suite), TM4 Microarray Software Suite: Automated Microarray Pipeline, TM4 Microarray Software Suite: AMP | 2026-02-14 02:06:01 | 0 | |||||
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NCBI BioSample Resource Report Resource Website 100+ mentions |
NCBI BioSample (RRID:SCR_004854) | BioSample | data or information resource, database | Database containing descriptions of biological source materials used in experimental assays. Sources include: GenBank, Sequence Read Archive (SRA), Coriell, ATCC. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their samples. As the capacity and complexity of biological data sets expands, databases face new challenges in ensuring that the information is adequately organized and described. The NCBI BioSample database is being developed to help address the challenges by providing the means by which data generators can organize and describe a broad range of sample types, and link to corresponding sets of experimental data in archival databases. | RIN, Resource Information Network, dna, rna, cell, cell line, stem cell, biomaterial, gold standard, RRID Community Authority |
is listed by: OMICtools is listed by: Resource Information Network is related to: GenBank is related to: BioSample Database at EBI is related to: ATCC is related to: NCBI Sequence Read Archive (SRA) is related to: Coriell Cell Repositories is related to: CannSeek Database of Cannabis sativa SNPs has parent organization: NCBI |
NLM | PMID:22139929 | The community can contribute to this resource | nlx_143929, r3d100012828, OMICS_01024 | https://doi.org/10.17616/R31NJME4 | SCR_004854 | BioSample Database, NCBI BioSample Database | 2026-02-14 02:06:20 | 410 | ||||
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NRG-CING Resource Report Resource Website 1+ mentions |
NRG-CING (RRID:SCR_006079) | NRG-CING | data or information resource, database | NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. | macromolecular structure, nmr, macromolecule, restraint, chemical shift, validation report, validation, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Worldwide Protein Data Bank (wwPDB) is related to: NMR Restraints Grid is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Radboud University; Nijmegen; The Netherlands |
Netherlands Organization for Scientific Research (NWO) 700.55.443; Netherlands Bioinformatics Centre (NBIC) ; EU FP6 LSHG-CT-2005-018988; EU FP6 LHSG-CT-2004-512092; EU FP7 261572; Brussels Institute for Research and Innovation BB2B 2010-1-12; NLM LM05799 |
PMID:22139937 | Free | nlx_151486, biotools:nrg-cing | https://bio.tools/nrg-cing | SCR_006079 | 2026-02-14 02:05:59 | 1 | |||||
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GO-Module Resource Report Resource Website 1+ mentions |
GO-Module (RRID:SCR_005813) | GO-Module | data analysis service, production service resource, service resource, analysis service resource | GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool | functional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: AmiGO has parent organization: University of Illinois at Chicago; Illinois; USA |
NIH ; Cancer Research Foundation ; NLM K22 LM008308; NCI 1U54CA121852; NCRR UL1 RR024999 |
PMID:21421553 | Free for academic use | nlx_149322 | SCR_005813 | Hierarchical optimization of enriched GO terms | 2026-02-14 02:05:53 | 3 | |||||
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | data or information resource, database | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NINDS ; NIDDK ; European Molecular Biology Laboratory ; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; NBDC - National Bioscience Database Center ; Japan Science and Technology Agency |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-02-14 02:06:26 | 1215 | ||||
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pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-02-14 02:06:31 | 70 | ||||||
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SNPs3D Resource Report Resource Website 100+ mentions |
SNPs3D (RRID:SCR_010787) | SNPs3D | data or information resource, database | A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. | single nucleotide polymorphism, single nucleotide variation, gene, FASEB list |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM | The community can contribute to this resource | OMICS_00163 | SCR_010787 | 2026-02-14 02:06:14 | 116 | |||||||
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ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | data analysis service, production service resource, service resource, analysis service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-02-14 02:06:41 | 26 | ||||
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Robot Reviewer Resource Report Resource Website 1+ mentions |
Robot Reviewer (RRID:SCR_018961) | software resource, text extraction software, software application | Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments. | Automated review, data mining, manuscript screening, artificial intelligence, automatic evidence synthesis, evidence synthesis, trial conduct information, data trial, bias, bias assessement | NLM R01 LM012086; NCI UH2 CA203711; UK Medical Research Council |
PMID:26104742 | Free, Freely available | SCR_018961 | 2026-02-14 02:06:25 | 5 | |||||||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data analysis software, software resource, data processing software, software application | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016297 | , GLIMMPSE Version 3 | 2026-02-14 02:04:57 | 8 | ||||||||
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Anne O'Tate Resource Report Resource Website 1+ mentions |
Anne O'Tate (RRID:SCR_023086) | software resource, web application | Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining. | Value added PubMed search engine, analysis and text mining | has parent organization: University of Illinois at Chicago; Illinois; USA | NLM LM 007292; NLM LM 08364 |
PMID:18279519 PMID:33684153 |
Free, Freely available | SCR_023086 | 2026-02-14 02:05:06 | 1 | ||||||||
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RobotReviewer Resource Report Resource Website 1+ mentions |
RobotReviewer (RRID:SCR_021064) | software resource, text-mining software, software application, web application | 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 | 2026-02-14 02:04:36 | 1 | ||||||
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CCPN Data Model Resource Report Resource Website |
CCPN Data Model (RRID:SCR_016982) | data repository, storage service resource, data processing software, data storage software, data or information resource, service resource, software application, software resource, database | 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 | 2026-02-14 02:03:07 | 0 | |||||||
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SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | sequence analysis software, data processing software, data analysis software, software application, software resource | 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 | 2026-02-14 02:09:03 | 1 |
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