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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | database, service resource, storage service resource, data repository, data or information resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-02-15 09:18:11 | 53 | ||||
|
APD Resource Report Resource Website 100+ mentions |
APD (RRID:SCR_006606) | APD, APD2 | database, service resource, storage service resource, data repository, data or information resource | Database and data analysis system dedicated to glossary, nomenclature, classification, information search, prediction, design, and statistics of Antimicrobial peptides and beyond. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in the past several years. Peptides will be registered into this database if: # they are from natural sources (bacteria, protozoa, fungi, plants, and animals); # their antimicrobial activities are demonstrated (MIC | amino acid, amphibian, antimicrobial peptide, antimicrobial, bacteria, cd, insect, nmr spectroscopy, plant, residue, x-ray diffraction, x-ray crystallography, circular dichroism, protein structure, protein sequence, protein motif, resistant microbe, anticancer, antiviral, antifungal, antibacterial, peptide, peptide family, post-translationally modified peptide, peptide binding target, membrane, protein, dna, rna, lps, sugar, prediction, peptide design, statistics, data analysis service, FASEB list | has parent organization: University of Nebraska College of Medicine; Nebraska; USA | University of Nebraska College of Medicine; Nebraska; USA ; Eppley Institute |
PMID:18957441 PMID:14681488 |
Acknowledgement requested, The community can contribute to this resource | nif-0000-02553, r3d100012901 | https://doi.org/10.17616/R3023M | SCR_006606 | Antimicrobial Peptide Database, The Antimicrobial Peptide Database | 2026-02-15 09:19:19 | 207 | ||||
|
Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | software application, sequence analysis software, data processing software, software resource, data analysis software | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NHGRI R01 HG003647; Sloan Foundation ; NCRR P41 RR024851 |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-02-15 09:18:42 | 5 | |||||
|
MetaPhlAn Resource Report Resource Website 500+ mentions |
MetaPhlAn (RRID:SCR_004915) | software application, sequence analysis software, data processing software, software resource, data analysis resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes. | microbial community, microbial composition, microbial genome, microbial sequence |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: Bitbucket has parent organization: Harvard T.H. Chan School of Public Health |
PMID:22688413 DOI:10.1038/nmeth.3589 |
OMICS_02286 | http://huttenhower.sph.harvard.edu/metaphlan https://bitbucket.org/nsegata/metaphlan/ https://sources.debian.org/src/metaphlan2/ |
SCR_004915 | MetaPhlAn, Metagenomic Phylogenetic Analysis, MetaPhlAn version 2, MetaPhlAn - Metagenomic Phylogenetic Analysis, MetaPhlAn v2 | 2026-02-15 09:18:51 | 637 | |||||||
|
PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | data analysis service, data set, service resource, production service resource, data or information resource, analysis service resource | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-02-15 09:18:55 | 225 | |||||
|
ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-02-15 09:19:07 | 77 | |||||
|
MetaLocGramN Resource Report Resource Website 1+ mentions |
MetaLocGramN (RRID:SCR_003154) | MetaLocGramN | data analysis service, software resource, data access protocol, web service, service resource, production service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice. | subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteria |
is listed by: OMICtools is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland |
PMID:22705560 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01626 | SCR_003154 | 2026-02-15 09:18:27 | 3 | |||||||
|
RIKEN BioResource Center Resource Report Resource Website 1000+ mentions |
RIKEN BioResource Center (RRID:SCR_003250) | BRC, RIKEN BRC | organism supplier, material resource, biomaterial supply resource | RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad. | RIN, Resource Information Network, experimental animal, experimental plant, cultured cell line, dna, animal, plant, cell line, genetic material, virus, gene, cultured cell, embryo, sperm, tissue, organ, seed, cell, recombinant host, bioresource, FASEB list, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: Federation of International Mouse Resources is related to: MGI strains has parent organization: RIKEN Tsukuba Institute; Kansai; Japan is parent organization of: JCM works with: Cellosaurus works with: International Mouse Strain Resource |
PMID:19448331 PMID:34532769 |
Free, Freely available | nif-0000-31407 | SCR_003250 | RIKEN Tsukuba Institute RIKEN BioResource Center | 2026-02-15 09:18:29 | 2208 | ||||||
|
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) | access service resource, core facility, service resource, resource | 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 | 2026-02-15 09:21:13 | 0 |
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 SPARC SAWG Resources search. From here you can search through a compilation of resources used by SPARC SAWG and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that SPARC SAWG 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 SPARC SAWG then you can log in from here to get additional features in SPARC SAWG 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 SPARC SAWG 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.
