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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
HCV Databases
 
Resource Report
Resource Website
50+ mentions
HCV Databases (RRID:SCR_002863) HCV Databases data or information resource, topical portal, portal, disease-related portal The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools. hcv, hepatitis c virus, hepatitis c, database, data analysis service, sequence, immunology, annotation, FASEB list has parent organization: HIV Databases
is parent organization of: HCV Sequence Database
is parent organization of: HCV Immunology Database
Hepatitis C NIAID Free, Freely available nif-0000-02944 SCR_002863 Hepatitis C Virus Database, Hepatitis C Virus Database Project, HCV Database, Hepatitis C Virus Databases, Hepatitis C Virus (HCV) Database Project 2026-02-17 10:00:00 66
Pathosystems Resource Integration Center
 
Resource Report
Resource Website
1000+ mentions
Pathosystems Resource Integration Center (RRID:SCR_004154) PATRIC bioinformatics resource center, data or information resource, production service resource, analysis service resource, database, service resource, data analysis service A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list is listed by: OMICtools
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
NIAID PMID:24225323
PMID:17142235
Free, Public, Acknowledgement requested r3d100010142, OMICS_01658, nlx_17476 http://patricbrc.vbi.vt.edu/portal/portal/patric/Home
https://doi.org/10.17616/R3WS3X
http://patric.vbi.vt.edu/ SCR_004154 PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center 2026-02-17 10:00:32 1083
JCVI CMR
 
Resource Report
Resource Website
10+ mentions
JCVI CMR (RRID:SCR_005398) JCVI_CMR, JCVI CMR, TIGR_CMR, TIGR CMR data or information resource, production service resource, analysis service resource, database, service resource, data analysis service Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis. microbial, prokaryotic, genome, annotation, dna sequence, protein, rna gene, blast, FASEB list is used by: NIF Data Federation
is related to: AmiGO
has parent organization: J. Craig Venter Institute
is parent organization of: JCVI GenProp
NSF ;
NIAID ;
DOE
Free nif-0000-03555 SCR_005398 JCVI Comprehensive Microbial Resource, J. Craig Venter Institute Comprehensive Microbial Resource, CMR, Comprehensive Microbial Resource 2026-02-17 10:00:54 37
EVidenceModeler
 
Resource Report
Resource Website
1000+ mentions
EVidenceModeler (RRID:SCR_014659) EVM software application, data processing software, data analysis software, software resource, sequence analysis 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 2026-02-17 10:02:52 1135
NIAID Overview of Coronaviruses
 
Resource Report
Resource Website
1+ mentions
NIAID Overview of Coronaviruses (RRID:SCR_018290) data or information resource, topical portal, portal, funding resource Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses. Coronavirus, COVID-19, data, infectious disease, NIAID is listed by: Data and Computational Resources to Address COVID-19
is related to: NIAID
COVID-19 NIAID Free, Freely available SCR_018290 2026-02-17 10:03:44 3
Pathema
 
Resource Report
Resource Website
1+ mentions
Pathema (RRID:SCR_010585) Pathema data or information resource, production service resource, analysis service resource, database, service resource, data analysis service Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. bacillus anthracis, clostridium botulinum, burkholderia mallei, burkholderia pseudomallei, clostridium perfringens, entamoeba histolytica, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: J. Craig Venter Institute
NIAID contract HHSN266200400038C PMID:19843611 biotools:pathema, nlx_45829 https://bio.tools/pathema SCR_010585 Pathema Genome Resource, Pathema Bioinformatics Resource Center 2026-02-17 10:01:31 6
CytoMAP
 
Resource Report
Resource Website
10+ mentions
CytoMAP (RRID:SCR_021227) software application, data processing software, data analytics software, data analysis software, software resource, software toolkit Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA NIAID R01 AI134713;
NIAID R21 AI142667;
NIAID R01 AI134246;
NIAID R01 AI076327;
NIAID U19 AI135976;
NIAID T32 AI10667;
NIGMS T32 GM007270;
NICHD T32 HD007233;
NSF DGE 1762114
PMID:32320656 Free, Available for download, Freely available SCR_021227 Histo-Cytometric Multidimensional Analysis Pipeline 2026-02-17 10:04:02 22
SpiecEasi
 
Resource Report
Resource Website
10+ mentions
SpiecEasi (RRID:SCR_022712) SpiecEasi data analysis software, software application, data processing software, software resource Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference NIAID AI007180;
NIDDK DK103358;
NIGMS GM63270;
Simons Foundation
PMID:25950956 Free, Available for download, Freely available SCR_022712 SParse InversE Covariance Estimation for Ecological Association Inference 2026-02-17 10:04:17 15
PlasmoDB
 
Resource Report
Resource Website
1000+ mentions
PlasmoDB (RRID:SCR_013331) data access protocol, storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, software resource, web service, data analysis service, data repository Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list uses: SynView
is related to: GeneDB Pfalciparum
has parent organization: Eukaryotic Pathogen Database Resources
has parent organization: Pennsylvania State University
has parent organization: University of Georgia; Georgia; USA
malaria NIAID PMID:18957442 nif-0000-03314, SCR_017665 SCR_013331 PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource 2026-02-17 10:02:22 1239
Virus Pathogen Resource (ViPR)
 
Resource Report
Resource Website
100+ mentions
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) ViPR software application, storage service resource, data or information resource, data processing software, database, service resource, software resource, data visualization software, data repository Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list is recommended by: National Library of Medicine
is listed by: Data and Computational Resources to Address COVID-19
is listed by: DataCite
is listed by: re3data.org
is listed by: FAIRsharing
has parent organization: University of Texas Southwestern Medical Center; Texas; USA
COVID-19 NIAID Restricted nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 http://www.viprbrc.org/
https://doi.org/10.17616/r30p93
https://doi.org/10.35083/
https://doi.org/10.35084/
https://dx.doi.org/10.35083/
https://dx.doi.org/10.35084/
https://fairsharing.org/10.25504/FAIRsharing.2qx8n8
SCR_012983 Virus Pathogen Resource, ViPR 2026-02-17 10:01:56 140
Collaboratory of AIDS Researchers for Eradciation (CARE)
 
Resource Report
Resource Website
Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) CARE data or information resource, portal, organization portal, consortium The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV. AIDS, HIV, drug development, data-sharing enabler, is related to: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA
is related to: Gladstone Institute of Neurological Disease
is related to: UCSF School of Medicine; California; USA
is related to: Case Western Reserve University; Ohio; USA
is related to: Merck
is related to: UC Davis School of Medicine; California; USA
is related to: University of California at San Diego; California; USA
is related to: University of Utah School of Medicine; Utah; USA
is related to: University of Minnesota Twin Cities; Minnesota; USA
NIAID ;
NIMH
SCR_013681 2026-02-17 10:02:36 0
Immune Tolerance Network TrialShare
 
Resource Report
Resource Website
10+ mentions
Immune Tolerance Network TrialShare (RRID:SCR_013699) ITN TrialShare, TrialShare clinical trial, storage service resource, data or information resource, service resource, data repository Immune tolerance data management and visualization portal for studies sponsored by Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published Figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter. clinical trial, clinical data, biological specimens, is recommended by: National Library of Medicine
is related to: Immune Tolerance Network (ITN)
Type 1 diabetes, Diabetes, Allergy, Asthma, Autoimmune disease, Transplantation, Immunological disorder NIAID Restricted https://www.itntrialshare.org/login/home/login.view?returnUrl=%2Fproject%2Fhome%2Fstart.view%3F SCR_013699 , ITN, TrialShare, Trial Share, Immune Tolerance Network 2026-02-17 10:02:26 27
Clinical Islet Transplantation Consortium (CITC)
 
Resource Report
Resource Website
1+ mentions
Clinical Islet Transplantation Consortium (CITC) (RRID:SCR_014385) CITC, CIT access service resource, service resource Network of clinical centers and a data coordinating center established to conduct studies of islet transplantation in patients with type 1 diabetes. type 1 diabetes, consortium, network, islet transplantation, clinical is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Research Resources
is listed by: Diabetes Research Centers
Type 1 diabetes, Diabetes NIDDK U01 DK070431;
NIAID
SCR_014385 Clinical Islet Transplantation Consortium 2026-02-17 10:02:47 1
VDJ Server
 
Resource Report
Resource Website
10+ mentions
VDJ Server (RRID:SCR_014356) software application, web application, collaboration tool, data processing software, data analysis software, software resource A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires. omics data, web application, scalable resource, immune repertoire has parent organization: University of Texas Southwestern Medical Center; Texas; USA
has parent organization: J. Craig Venter Institute
has parent organization: Yale University; Connecticut; USA
NIAID 1R01A1097403 Free, Open source analysis software is available for local use http://wiki.vdjserver.org/vdjserver/index.php/VDJServer_Wiki SCR_014356 VDJServer 2026-02-17 10:02:38 16
Clinical Trials in Organ Transplantation (CTOT)
 
Resource Report
Resource Website
1+ mentions
Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) CTOT organization portal, data or information resource, consortium, project portal, portal Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients. graft, graft patient, patient survival, clinical study, transplant, transplant recipient, mechanistic study is listed by: NIDDK Information Network (dkNET)
is listed by: Diabetes Research Centers
is related to: Clinical Trials in Organ Transplantation in Children (CTOT-C)
NIAID UM2 AI117870 Public, Available to the scientific community SCR_015859 Clinical Trials in Organ Transplantation 2026-02-17 10:03:11 1
Clinical Trials in Organ Transplantation in Children (CTOT-C)
 
Resource Report
Resource Website
1+ mentions
Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) CTOT-C organization portal, data or information resource, consortium, project portal, portal Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients. heart, kidney, lung, pediatric, cooperative research program, niaid, clinical study, mechanistic study, transplant is listed by: NIDDK Information Network (dkNET)
is related to: Clinical Trials in Organ Transplantation (CTOT)
NIAID UM2 AI117870 Public, Available to the scientific community SCR_015860 NIAID Clinical Trials in Organ Transplantation in Children, Clinical Trials in Organ Transplantation in Children, NIAID CTOT-C 2026-02-17 10:02:55 1
Database of Immune Cell Epigenomes
 
Resource Report
Resource Website
50+ mentions
Database of Immune Cell Epigenomes (RRID:SCR_018259) DICE data access protocol, data or information resource, database, software resource, web service Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis has parent organization: La Jolla Institute for Immunology William K. Bowes Jr Foundation ;
NIAID R24 AI108564;
NCRR S10 RR027366;
NIH Office of the Director S10 OD016262
PMID:30449622 Free, Freely available SCR_018259 Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics 2026-02-17 10:03:44 59
TimeZone
 
Resource Report
Resource Website
1+ mentions
TimeZone (RRID:SCR_018564) data analysis software, software application, data processing software, software resource Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome NIGMS R01 GM084318;
NIAID RC4 AI092828
PMID:23471110 Free, Available for download, Freely available SCR_018564 2026-02-17 10:03:06 1
EpiModel
 
Resource Report
Resource Website
1+ mentions
EpiModel (RRID:SCR_018539) software application, data processing software, data analysis software, software resource, software toolkit Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools is listed by: Debian
is listed by: bio.tools
NICHD R01 HD068395;
NIMH R21 MH112449;
NICHD R21 HD075662;
NIDA P30 DA027828;
NIAID P30 AI050409;
NIAID P30 AI027757;
NICHD T32 HD007543
PMID:29731699 Free, Available for download, Freely available biotools:epimodel https://bio.tools/epimodel SCR_018539 2026-02-17 10:03:29 7
GOnet
 
Resource Report
Resource Website
1+ mentions
GOnet (RRID:SCR_018977) data access protocol, production service resource, analysis service resource, service resource, software resource, web service Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
works with: Gene Ontology
NIH Common Fund ;
NIGMS ;
NHGRI R24 HG010032;
NIAID U19 AI118610;
NIAID U19 AI118626
PMID:30526489 biotools:GOnet https://github.com/mikpom/gonet
https://bio.tools/GOnet
SCR_018977 2026-02-17 10:03:10 3

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