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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
LexGrid
 
Resource Report
Resource Website
1+ mentions
LexGrid (RRID:SCR_006627) LexGrid software resource LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible software library, parse, ontology is listed by: BioPortal
is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: OBO
has parent organization: European Bioinformatics Institute
has parent organization: National Cancer Institute
NIH ;
Cancer Biomedical Informatics Grid ;
NLM LM07319
PMID:19261933 Free for academic use nlx_149194 http://www.lexgrid.org/ SCR_006627 Lexical Grid 2026-07-25 12:06:27 1
Phymm and PhymmBL
 
Resource Report
Resource Website
10+ mentions
Phymm and PhymmBL (RRID:SCR_004751) Phymm, PhymmBL software resource Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read is listed by: OMICtools
has parent organization: University of Maryland; Maryland; USA
NLM R01-LM006845 PMID:19648916
PMID:21527926
Open-source license OMICS_01461 SCR_004751 2026-07-25 12:05:53 12
ROSTLAB
 
Resource Report
Resource Website
1+ mentions
ROSTLAB (RRID:SCR_000792) group A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical has parent organization: Columbia University; New York; USA
is parent organization of: PredictNLS
is parent organization of: SNPdbe
NLM LM007329;
NLM GM50291
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-31417 http://cubic.bioc.columbia.edu/services/disis SCR_000792 Rost Group 2026-07-25 12:04:50 1
MUMmerGPU
 
Resource Report
Resource Website
1+ mentions
MUMmerGPU (RRID:SCR_001200) MUMmerGPU software application, software resource, data processing software Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit is listed by: OMICtools
is related to: MUMmer
has parent organization: SourceForge
has parent organization: University of Maryland; Maryland; USA
NLM R01 LM006845;
NIGMS R01 GM083873
PMID:20161021 Free, Available for download, Freely available OMICS_02151 SCR_001200 High-throughput sequence alignment using Graphics Processing Units 2026-07-26 09:03:00 5
Anne O'Tate
 
Resource Report
Resource Website
1+ mentions
Anne O'Tate (RRID:SCR_023086) web application, software resource 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 2026-07-27 09:36:51 1
RobotReviewer
 
Resource Report
Resource Website
1+ mentions
RobotReviewer (RRID:SCR_021064) software application, text-mining software, 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 2026-07-27 09:36:14 1
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 2026-07-27 09:34:30 1
ComiR
 
Resource Report
Resource Website
10+ mentions
ComiR (RRID:SCR_013023) ComiR analysis service resource, service resource, data analysis service, production 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 2026-07-27 09:34:19 26
Automated Microarray Pipeline
 
Resource Report
Resource Website
Automated Microarray Pipeline (RRID:SCR_001219) AMP analysis service resource, service resource, data analysis service, production 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 2026-07-27 09:31:09 0
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
 
Resource Report
Resource Website
10+ mentions
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins (RRID:SCR_003039) DP-Bind analysis service resource, service resource, data analysis service, production service resource This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated. dna binding has parent organization: University at Albany; New York; USA NLM 1R03LM009034-01 PMID:17237068
PMID:16568445
Free, Freely available nif-0000-30426 SCR_003039 2026-07-27 09:31:39 19
Distant Regulatory Elements
 
Resource Report
Resource Website
10+ mentions
Distant Regulatory Elements (RRID:SCR_003058) DiRE analysis service resource, service resource, data analysis service, production service resource Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: NCBI
NLM ;
Intramural Research Program
PMID:18487623 Free, Freely available nif-0000-30448, biotools:dire https://bio.tools/dire SCR_003058 Distant Regulatory Elements of co-regulated genes 2026-07-27 09:31:39 25
GO-Module
 
Resource Report
Resource Website
1+ mentions
GO-Module (RRID:SCR_005813) GO-Module analysis service resource, service resource, data analysis service, production 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 2026-07-27 09:32:23 3
iPOP
 
Resource Report
Resource Website
10+ mentions
iPOP (RRID:SCR_008991) iPOP data or information resource, data set Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male has parent organization: Stanford University; Stanford; California Healthy Breetwor Family Foundation ;
Korber Foundation ;
Fundacion Marcelino Botin ;
Fundacion Lilly ;
NLM T15-LM007033;
NIGMS R24-GM61374;
NHLBI T32 HL094274;
NHLBI KO8 HL083914;
NIH New Investigator DP2 award OD004613;
Spanish Ministry of Science and Innovation Projects ;
Spanish Ministry of Science and Innovation Projects ;
European Union FP7 Genica ;
European Union FP7 TELOMARKER ;
European Research Council Advanced Grant
PMID:22424236 Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. nlx_152492 SCR_008991 Snyderome, Integrated Personal Omics Profiling 2026-07-27 09:33:13 12
PubMed
 
Resource Report
Resource Website
10000+ mentions
PubMed (RRID:SCR_004846) database, data or information resource, bibliography Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut. biomedical, literature, publication, open, access, bibliography, gold standard is used by: Knowledgebase for Addiction Related Genes
is used by: Drug Related Gene Database
is used by: ChannelPedia
is used by: Molecular Imaging and Contrast Agent Database
is used by: Colwiz
is used by: Nowomics
is used by: PINT
is listed by: OMICtools
is listed by: FORCE11
is listed by: LabWorm
is related to: Chilibot: Gene and Protein relationships from MEDLINE
is related to: ImpactStory
is related to: Automated recognition of brain region mentions in neuroscience literature.
is related to: Information Hyperlinked Over Proteins
is related to: PubMed Central
is related to: PIE the search
is related to: Anne O'Tate
is related to: PubBrain
is related to: Europe PubMed Central
is related to: ResearchGate
is related to: CBioC
is related to: CiteAb
is related to: LitInspector
is related to: RefMED
is related to: Pubmed Commons
is related to: iBIOFind
is related to: Ensembl Variation
is related to: MEDLINE
is related to: XplorMed
is related to: Linked Neuron Data
is related to: NCBI Structure
is related to: MeSH
is related to: MEDLINE
is related to: EBIMed
is related to: Coremine Medical
is related to: NIF Literature
is related to: GoPubMed
is related to: Integrated Auto-Extracted Annotation
is related to: Polbase
is related to: Integrated Manually Extracted Annotation
is related to: DaTo
is related to: NIF Registry Automated Crawl Data
has parent organization: NCBI
works with: Open Regulatory Annotation Database
works with: rentrez
NLM Free, Freely available nlx_82958, OMICS_01195 http://www.force11.org/node/4652, http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed SCR_004846 Pub Med 2026-07-28 09:41:08 98390
Protein Data Bank Markup Language
 
Resource Report
Resource Website
1+ mentions
Protein Data Bank Markup Language (RRID:SCR_005085) PDBML narrative resource, markup language, data or information resource, standard specification, interchange format Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. xml is related to: RCSB PDB Software Tools
has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
NSF ;
NIGMS ;
DOE ;
NLM ;
NCI ;
NCRR ;
NIBIB ;
NINDS
PMID:15509603 nlx_144096 SCR_005085 PDBML: Protein Data Bank Markup Language 2026-07-28 09:41:09 2
NCBI Sequence Read Archive (SRA)
 
Resource Report
Resource Website
5000+ mentions
NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) SRA service resource, data or information resource, data repository, database, storage service resource Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them. sequence, blast, next-generation sequence, alignment, read placement, reference sequence, roche 454 gs system, illumina genome analyzer, applied biosystems solid system, helicos heliscope, complete genomics, pacific biosciences smrt, high-throughput sequencing, data analysis service, gold standard is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is listed by: OMICtools
is related to: European Nucleotide Archive (ENA)
is related to: RecountDB
is related to: SRAdb
is related to: DDBJ Sequence Read Archive
is related to: Bgee: dataBase for Gene Expression Evolution
is related to: NCBI BioSample
is related to: DDBJ Sequence Read Archive
is related to: METAGENOTE
has parent organization: NCBI
works with: SARS-CoV-2-Sequences
works with: Signaling Pathways Project
NLM PMID:22009675
PMID:21062823
Free, Available for download, Freely available OMICS_01031, nlx_86174, r3d100010775 https://doi.org/10.17616/R31S69 SCR_004891 Sequence Read Archive, , SRA, NCBI SRA 2026-07-28 09:41:09 6671
Unified Medical Language System
 
Resource Report
Resource Website
10+ mentions
Unified Medical Language System (RRID:SCR_006363) UMLS narrative resource, data or information resource, database, standard specification, data access protocol, software resource, international standard specification, web service 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) 2026-07-28 09:41:33 44
EVidenceModeler
 
Resource Report
Resource Website
1000+ mentions
EVidenceModeler (RRID:SCR_014659) EVM software application, data analysis software, sequence analysis software, software resource, data processing software 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 2026-07-28 09:43:30 1135
GLIMMPSE
 
Resource Report
Resource Website
1+ mentions
GLIMMPSE (RRID:SCR_016297) software application, software resource, data analysis software, data processing software 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 2026-07-28 09:44:10 8
GeneSigDB
 
Resource Report
Resource Website
10+ mentions
GeneSigDB (RRID:SCR_013275) GeneSigDB service resource, data or information resource, data repository, data analysis service, storage service resource, data access protocol, software resource, database, production service resource, web service, 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 2026-07-28 09:43:12 24

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