Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Tuberculosis Database Resource Report Resource Website 50+ mentions |
Tuberculosis Database (RRID:SCR_006619) | TBDB | data or information resource, database | Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. | genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list |
is listed by: re3data.org is related to: SMD is related to: BioCyc has parent organization: Broad Institute has parent organization: Stanford University School of Medicine; California; USA |
Tuberculosis | Bill and Melinda Gates Foundation | PMID:20488753 PMID:18835847 |
Acknowledgement requested, Public, (Published data) | nif-0000-03537, r3d100010930 | https://doi.org/10.17616/R39G8F | SCR_006619 | TB Database, TBDatabase | 2026-08-03 09:33:07 | 64 | |||
|
SILVA Resource Report Resource Website 10000+ mentions |
SILVA (RRID:SCR_006423) | data or information resource, database | High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online. | ribosomal rna, gene sequence, gene, sequence, alignment, taxonomy, 16s, 18s, 23s, 28s, phylogeny, probe, primer, alignment service, fish, arb, ribocon, geoblast, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: RNAcentral is related to: ARB project is related to: SINA is related to: European ribosomal RNA database has parent organization: German Collection of Microorganisms and Cell Cultures |
German Collection of Microorganisms and Cell Cultures | PMID:23193283 PMID:24293649 PMID:17947321 |
biotools:silva, OMICS_01514, nif-0000-03464, r3d100011323, rid_000103 | https://bio.tools/silva, https://doi.org/10.17616/R3FP60 | SCR_006423 | SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-08-03 09:33:01 | 13429 | ||||||
|
BacMap: Bacterial Genome Atlas Resource Report Resource Website 1+ mentions |
BacMap: Bacterial Genome Atlas (RRID:SCR_006988) | BacMap | data or information resource, atlas, database | An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. It uses a visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom ''gene card'' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. A complete listing of the species and strains in the BacMap database is available on the BacMap homepage. Below each species/strain name is a list of the sequenced chromosomes and plasmids that are available. Some features of BacMap include: * Maps are available for 2023 bacterial chromosomes. * Each map supports zooming and rotation. * Map gene labels are hyperlinked to detailed textual annotations. * Maps can be explored manually, or with the help of BacMap''s built in text search and BLAST search. * A written synopsis of each bacterial species is provided. * Several charts illustrating the proteomic and genomic characteristics of each chromosome are available. * Flat file versions of the BacMap gene annotations, gene sequences and protein sequences can be downloaded. BacMap can be used to: * Obtain basic genome statistics. * Visualize the genomic context of genes. * Search for orthologues and paralogues in a genome of interest. * Search for conserved operon structure. * Look for gene content differences between bacterial species. * Obtain pre-calculated annotations for bacterial genes of interest. | gene, gene annotation, gene sequence, genome, bacteria, chromosome, protein sequence | has parent organization: University of Alberta; Alberta; Canada | Alberta Science Research Authority ; Western Economic Diversification ; Genome Canada ; Genome Prairie ; Western Economic Diversification Canada |
PMID:15608206 | Free, Acknowledgement requested | nif-0000-02591, r3d100012724 | https://doi.org/10.17616/R35502 | SCR_006988 | BacMap: An Interactive Atlas for Exploring Bacterial Genomes, BacMap genome atlas | 2026-08-03 09:33:13 | 4 | ||||
|
ProLysED - Prokaryotic Lysis Enzymes Database Resource Report Resource Website |
ProLysED - Prokaryotic Lysis Enzymes Database (RRID:SCR_007183) | ProLysED | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 14, 2014. Database on the subject of bacterial (prokaryotic) proteases. ProLysED is a freely browsable using the Demo account. Certain services will require user registration. | protease | has parent organization: National University of Malaysia; Selangor; Malaysia | PMID:16128617 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03344 | http://genome.ukm.my/prolyses/ | SCR_007183 | Prokaryotic Lysis Enzymes Database | 2026-08-03 09:33:21 | 0 | |||||
|
Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core Resource Report Resource Website |
Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core (RRID:SCR_015262) | resource, service resource, access service resource, core facility | Core composed of the Viral Unit, which provides labeled andn unlabeled viral components, and Bacterial Unit, which provides bacteria and bacterial proteins for research. The retroviral unit focues on the viral components of the retrovirus HIV-1. | microbe core, virology, retrovirus, hiv, aids, bacterial |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Alabama at Birmingham School of Medicine; Alabama; USA has parent organization: Mucosal HIV and Immunobiology Center is organization facet of: Mucosal HIV and Immunobiology Center |
Mucosal HIV | NIDDK DK064400 | Available to the DDRCC community | SCR_015262 | 2026-08-03 09:35:51 | 0 | ||||||||
|
Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-08-03 09:32:15 | 4 | ||||
|
Type-III-Secretion-System related database Resource Report Resource Website |
Type-III-Secretion-System related database (RRID:SCR_002941) | T3DB | data or information resource, database | Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes. | type iii secretion system, gene, protein, ortholog |
is listed by: OMICtools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:22545727 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05160 | SCR_002941 | T3SS-related Database | 2026-08-03 09:31:54 | 0 | ||||||
|
NBC Resource Report Resource Website 1+ mentions |
NBC (RRID:SCR_004772) | NBC | data analysis service, service resource, analysis service resource, production service resource | Webserver for taxonomic classification of metagenomic reads. | metagenome, genome, virus, taxonomy, next-generation sequencing, taxonomic classification, classification |
is listed by: OMICtools has parent organization: Drexel University; Pennsylvania; USA |
NSF DBI-0845827; DOE DE-SC0004335 |
PMID:1062764 PMID:19956701 |
OMICS_01458 | SCR_004772 | Naive Bayes Classification tool, Na����ve Bayesian Classification tool, Naive Bayesian Classification Tool | 2026-08-03 09:32:43 | 3 | ||||||
|
HOMD Resource Report Resource Website 100+ mentions |
HOMD (RRID:SCR_012770) | HOMD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on April 14,2022. Database of comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to use tools for viewing all publicly available oral bacterial genomes. Data is also downloadable. | taxon, genome, 16s rna, sequence, actinobacteria, bacteroidetes, chlamydiae, chloroflexi, euryarchaeota, firmicutes, fusobacteria, proteobacteria, spirochaetes, sr1, synergistetes, tenericutes, tm7, nomenclature, naming scheme, human, FASEB list | has parent organization: Forsyth Institute | NIDCR ; ARRA ; DOE contract U01 DE016937; DOE DE016937; DOE DE015847; DOE DE017106 |
PMID:20624719 PMID:20656903 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22198, r3d100012898 | SCR_012770 | Human Oral Microbiome Database | 2026-08-03 09:35:14 | 137 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
