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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
Ensembl Genomes
 
Resource Report
Resource Website
100+ mentions
Ensembl Genomes (RRID:SCR_006773) database, software resource, data access protocol, web service, data or information resource Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site. genome, gold standard, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Ensembl
is related to: Ensembl
is related to: g:Profiler
has parent organization: European Bioinformatics Institute
European Molecular Biology Laboratory ;
European Union FELICS 021902 (RII3);
BBSRC BB/F019793/1
PMID:24163254
PMID:19884133
r3d100011197, OMICS_01648, nlx_65207, biotools:ensembl_genomes https://bio.tools/ensembl_genomes
https://doi.org/10.17616/R3MW6M
SCR_006773 Ensembl Genomes: Extending Ensembl across the taxonomic space, EnsemblGenomes, Ensembl Genome 2026-02-15 09:19:34 276
Psort
 
Resource Report
Resource Website
100+ mentions
Psort (RRID:SCR_007038) PSORT software application, portal, data analysis service, data processing software, software resource, data set, service resource, production service resource, data or information resource, topical portal, analysis service resource, data analysis software Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses. subcellular, localization, prediction, gram, gram-positive, gram-negative, sequence, fasta, protein, protein localization, cell, motif, profile, amino acid, subcellular localization is listed by: OMICtools
is related to: PSORT II
has parent organization: Simon Fraser University; British Columbia; Canada
OMICS_01634, nif-0000-31883 http://psort.hgc.jp/ SCR_007038 Psort.org, PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences 2026-02-15 09:19:26 209
NCBI Genome
 
Resource Report
Resource Website
500+ mentions
NCBI Genome (RRID:SCR_002474) Genome database, service resource, storage service resource, data repository, data or information resource Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available. chromosome, organelle, plasmid, viroid, virus, genome, sequence, map, assembly, annotation, gene mapping, dna, blast, protein cluster, gold standard is listed by: re3data.org
is related to: MapViewer
is related to: UniProt Proteomes
is related to: CaspBase
has parent organization: NCBI
Free, Freely avaialble nif-0000-02802, r3d100010785 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
https://doi.org/10.17616/R3R89S
SCR_002474 Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence 2026-02-15 09:18:19 577
Genomes Online Database
 
Resource Report
Resource Website
100+ mentions
Genomes Online Database (RRID:SCR_002817) GOLD database, service resource, storage service resource, data repository, data or information resource Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data. genome, genetics, metagenome, biosample, phenotype, ecotype, disease, sequencing, FASEB list is listed by: re3data.org
has parent organization: DOE Joint Genome Institute
PMID:22135293
PMID:19914934
PMID:17981842
PMID:16381880
PMID:11125068
PMID:10498782
Free, Freely available, Available for download r3d100010808, nif-0000-02918 https://doi.org/10.17616/R39310 SCR_002817 Genomes On Line Database (GOLD), GOLD:Genomes Online Database 2026-02-15 09:18:23 159
OMPdb
 
Resource Report
Resource Website
OMPdb (RRID:SCR_006221) OMPdb data analysis service, database, service resource, production service resource, data or information resource, analysis service resource A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. beta-barrel, outer membrane protein, gram-negative bacteria, protein, protein sequence, transmembrane, annotation, genome-wide analyses, comparative genomics, sequence, structure, blast, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
PMID:20952406 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01611, biotools:ompdb, nlx_151768 https://bio.tools/ompdb SCR_006221 OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria 2026-02-15 09:19:11 0
NCBI Assembly Archive Viewer
 
Resource Report
Resource Website
100+ mentions
NCBI Assembly Archive Viewer (RRID:SCR_012917) NCBI Assembly Archive Viewer data set, service resource, storage service resource, data repository, data or information resource Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). sequence alignment, sequence chromatogram, assembly, virus is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is related to: GenBank
is related to: Trace Archive
is related to: DNA DataBank of Japan (DDBJ)
is related to: European Nucleotide Archive (ENA)
OMICS_00890, r3d100012688 http://www.ncbi.nlm.nih.gov/assembly
https://doi.org/10.17616/R31NJMA8
http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi SCR_012917 Assembly Archive Viewer, NCBI Assembly, Assembly 2026-02-15 09:20:22 274
xFITOM
 
Resource Report
Resource Website
1+ mentions
xFITOM (RRID:SCR_014445) software application, sequence analysis software, data processing software, software resource, standalone software, data analysis software A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two. transcription factor, binding site, information theory, customizable program, sequence analysis software uses: GenBank
is related to: CollecTF
PMID:21346861 Available for download, Acknowledgement requested http://www.mybiosoftware.com/fitom-1-0-detection-binding-sites-dna-rna-sequences.html compbio.umbc.edu/Software/xFITOM/ http://research.umbc.edu/~erill/ SCR_014445 2026-02-15 09:21:02 7
OrthoVenn2
 
Resource Report
Resource Website
100+ mentions
OrthoVenn2 (RRID:SCR_022504) web service, data access protocol, software resource Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences National Natural Science Foundation of China PMID:31053848 Free, Freely available SCR_022504 2026-02-15 09:22:47 255
AmphoraNet
 
Resource Report
Resource Website
10+ mentions
AmphoraNet (RRID:SCR_005009) AmphoraNet service resource, analysis service resource, data analysis service, production service resource Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Eotvos Lorand University; Budapest; Hungary
PMID:24144838 Acknowledgement requested, Free, Public biotools:amphoranet, OMICS_01450 https://bio.tools/amphoranet SCR_005009 2026-02-15 09:18:53 16
CW-PRED
 
Resource Report
Resource Website
10+ mentions
CW-PRED (RRID:SCR_006188) CW-PRED service resource, analysis service resource, data analysis service, production service resource A web tool for the prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., http://www.ncbi.nlm.nih.gov/pubmed/18464329, was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif. hidden markov model, gram-positive bacteria, protein, classification, cell-wall protein has parent organization: University of Athens Biophysics and Bioinformatics Laboratory Free for academic use, Acknowledgement requested nlx_151733 SCR_006188 CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria 2026-02-15 09:19:10 16
cpnDB: A Chaperonin Database
 
Resource Report
Resource Website
1+ mentions
cpnDB: A Chaperonin Database (RRID:SCR_002263) cpnDB data analysis service, database, service resource, production service resource, data or information resource, analysis service resource A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
Canadian Biotechnology Strategy ;
National Research Council Genomics and Health Initiative
PMID:15289485 Free, Freely available biotools:cpndb, OMICS_01511, nif-0000-02694 https://bio.tools/cpndb http://www.cpndb.ca/cpnDB/home.php SCR_002263 2026-02-15 09:18:16 3
Pathosystems Resource Integration Center
 
Resource Report
Resource Website
1000+ mentions
Pathosystems Resource Integration Center (RRID:SCR_004154) PATRIC data analysis service, bioinformatics resource center, database, service resource, production service resource, data or information resource, analysis service resource 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 2026-02-15 09:18:38 1083
Vector Database
 
Resource Report
Resource Website
1+ mentions
Vector Database (RRID:SCR_005907) Vector Database material resource, biomaterial supply resource Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. This is a free resource for the scientific community that is compiled by Addgene. Only the plasmids deposited at Addgene are available for purchase through this website. vector, vector backbone, plasmid, mammalian expression, bacterial expression, retroviral, lentiviral, worm expression, insect expression, yeast expression, rnai, luciferase, mouse targeting, mammalian, bacterial, yeast, worm, insect, mouse, adenoviral, rnai, cre/lox, marker, neomycin, puromycin, hygromycin, zeocin, blasticidin, gentamicin, bacterial resistance, ampicillin, kanamycin, chloramphenicol, hygromycin, bleocin, zeocin is listed by: One Mind Biospecimen Bank Listing
is related to: ATCC
has parent organization: Addgene
Free nlx_149479 SCR_005907 Addgene Vector Database 2026-02-15 09:19:05 6
Cystic Fibrosis Center - University of Washington Microbiology Core
 
Resource Report
Resource Website
Cystic Fibrosis Center - University of Washington Microbiology Core (RRID:SCR_015403) access service resource, core facility, service resource, resource Core facility which provides tools, reagents, and training for microbiological researchers investigating cystic fibrosis. They specifically provide resources for research in anti-bacterial therapies, anti-bacterial therapy, cystic fibrosis research, cystic fibrosis bacterial strain, cystic fibrosis bacteria provider is listed by: NIDDK Information Network (dkNET)
has parent organization: University of Washington; Seattle; USA
has parent organization: Cystic Fibrosis Center - University of Washington
is organization facet of: Cystic Fibrosis Center - University of Washington
Cystic Fibrosis NIDDK P30DK089507 Available to the research community SCR_015403 2026-02-15 09:21:28 0
PRED-TMBB
 
Resource Report
Resource Website
50+ mentions
PRED-TMBB (RRID:SCR_006190) PRED-TMBB service resource, analysis service resource, data analysis service, production service resource A web tool, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from water-soluble ones when screening large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of the correct prediction rather than the likelihood of the sequences. The training is performed on a non-redundant database consisting of 16 outer membrane proteins (OMP''s) with their structures known at atomic resolution. We show that we can achieve predictions at least as good comparing with other existing methods, using as input only the amino-acid sequence, without the need of evolutionary information included in multiple alignments. The method is also powerful when used for discrimination purposes, as it can discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets, making it a quite reliable solution for screening entire genomes. This web-server can help you run a discriminating process on any amino-acid sequence and thereafter localize the transmembrane strands and find the topology of the loops. protein, hidden markov model, prediction, membrane protein, beta-barrel outer membrane protein, gram-negative bacteria, topology, outer membrane protein, beta-barrel protein, probability, transmembrane strand, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
Greek Ministry of National Education and Religious Affairs PMID:15215419
PMID:15070403
Acknowledgement requested biotools:pred-tmbb, nlx_151734 https://bio.tools/pred-tmbb SCR_006190 PRED-TMBB: A Hidden Markov Model method capable of predicting and discriminating beta-barrel outer membrane proteins 2026-02-15 09:19:11 54
LPSN Database
 
Resource Report
Resource Website
100+ mentions
LPSN Database (RRID:SCR_018151) data or information resource, database, service resource Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections. Collection, published Prokaryote name, International Journal of Systematic and Evolutionary Microbiology, prokaryotes classification, prokaryotes nomenclature, culture collection, data, FASEB list DOI:10.1093/nar/gkt1111 Free, Freely available SCR_018151 List of Prokaryotic names with Standing in Nomenclature Database 2026-02-15 09:22:11 111
Genometa
 
Resource Report
Resource Website
Genometa (RRID:SCR_001181) Genometa software resource A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of. metagenomic, classify, windows, linux, java, bio.tools, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Hannover Medical School; Lower Saxony; Germany
PMID:22927906 Free, Available for download, Freely available biotools:genometa, OMICS_02175 https://bio.tools/genometa SCR_001181 Genometa - Rapid analysis of metagenomic short reads 2026-02-14 01:59:55 0
LMAT
 
Resource Report
Resource Website
10+ mentions
LMAT (RRID:SCR_004646) LMAT software resource Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome is listed by: OMICtools
has parent organization: Lawrence Livermore National Laboratory
has parent organization: SourceForge
PMID:23828782 Open unspecified license OMICS_02285 SCR_004646 Livermore Metagenomics Analysis Toolkit 2026-02-14 02:00:58 15
TSSer
 
Resource Report
Resource Website
TSSer (RRID:SCR_006419) TSSer software resource A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide. differential rna sequencing, transcription start site, rna-seq, genome, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Basel; Basel; Switzerland
PMID:24371151 GNU General Public License biotools:tsser, OMICS_02191 https://bio.tools/tsser SCR_006419 TSSer: a computational pipeline to identify transcription start sites in bacterial genomes 2026-02-14 02:01:09 0
PathSeq
 
Resource Report
Resource Website
50+ mentions
PathSeq (RRID:SCR_005203) PathSeq software resource A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences. virus, microbe, pathogen, dna, rna, next-generation sequencing is listed by: OMICtools
is related to: Amazon Web Services
has parent organization: Broad Institute
PMID:21552235 Acknowledgement requested, Account required, (for Amazon Web Services and you will need to pay for the AWS resource time) OMICS_00221 SCR_005203 PathSeq: Pathogen Discovery 2026-02-14 02:01:03 62

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