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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ngLOC Resource Report Resource Website 10+ mentions |
ngLOC (RRID:SCR_003150) | ngLOC | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License. | subcellular localization, protein, eukaryote, prokaryote, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22780965 PMID:17472741 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01629, biotools:ngloc | https://bio.tools/ngloc | SCR_003150 | ngLOC - A Bayesian method for predicting protein subcellular localization | 2026-09-05 06:29:56 | 22 | |||||
|
Proteome Analyst Specialized Subcellular Localization Server Resource Report Resource Website 1+ mentions |
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) | PA-SUB | analysis service resource, data analysis service, production service resource, service resource | Web server specialized to predict the subcellular localization of proteins using established machine learning techniques. | subcellular localization, protein, machine learning, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Alberta; Alberta; Canada |
PMID:14990451 | Free, Available for download, Freely available | biotools:pa-sub, OMICS_01631 | https://psort.org/#:~:text=Proteome%20Analyst's%20Subcellular%20Localization%20Server, proteins%20to%20many%20localization%20sites. | SCR_003143 | 2026-09-05 06:31:20 | 1 | ||||||
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PHI-base Resource Report Resource Website 100+ mentions |
PHI-base (RRID:SCR_003331) | PHI-base | data or information resource, database | Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC). | gene expression, pathogenic bacteria, virulence, infection, target site, gene, pathogen-host interaction, interaction, phenotype, pathogen, disease, host, anti-infective, nucleotide sequence, amino acid sequence, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian |
BBSRC BB/1000488/1 | PMID:17942425 PMID:17153929 PMID:16381911 |
Free, Freely available | nif-0000-03276, r3d100011301, biotools:phi-base | https://bio.tools/phi-base, https://doi.org/10.17616/R35D1V | http://www4.rothamsted.bbsrc.ac.uk/phibase/ | SCR_003331 | Pathogen Host Interaction base, Pathogen Host Interaction, Pathogen Host Interaction-Base | 2026-09-05 06:31:20 | 239 | |||
|
SGN Resource Report Resource Website 1000+ mentions |
SGN (RRID:SCR_004933) | SGN, SGN ref | data or information resource, database | A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. | database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Sol Genomics Network - Bulk download is related to: AmiGO has parent organization: Boyce Thompson Institute for Plant Research |
USDA ; ATC Inc. Advanced Technologies Cambridge ; NSF 0116076; NSF 9872617; NSF 975866; NSF 0421634 |
PMID:20935049 PMID:16010005 |
Public, The community can contribute to this resource | r3d100012078, nlx_89764, biotools:sol_genomics_network | https://bio.tools/sol_genomics_network, https://doi.org/10.17616/R3FS95 | http://www.sgn.cornell.edu/ | SCR_004933 | SGN ref, Sol Genomics Network | 2026-09-05 06:31:27 | 1261 | |||
|
WegoLoc Resource Report Resource Website 1+ mentions |
WegoLoc (RRID:SCR_001402) | WegoLoc | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information. | subcellular localization, protein |
is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01636 | SCR_001402 | weighted gene ontology term based subcellular locallization prediction | 2026-09-05 06:31:13 | 4 | |||||||
|
Arabidopsis Reactome Resource Report Resource Website 1+ mentions |
Arabidopsis Reactome (RRID:SCR_002063) | data or information resource, database | Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context. | pathway, reaction, biological process |
uses: AraCyc uses: KEGG is listed by: 3DVC has parent organization: John Innes Centre; Norwich; United Kingdom |
European Union LSHG-CT-2006-037704 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20812 | SCR_002063 | Arabidopsis Reactome - a curated knowledgebase of plant biological pathways | 2026-09-05 06:31:15 | 3 | |||||||
|
WoLF PSORT Resource Report Resource Website 100+ mentions |
WoLF PSORT (RRID:SCR_002472) | WoLF PSORT | analysis service resource, data analysis service, production service resource, service resource | Data analysis service for protein subcellular localization prediction. | subcellular localization, protein | is listed by: OMICtools | Restricted | OMICS_01637 | SCR_002472 | WoLF PSORT - Protein Subcellular Localization prediction | 2026-09-05 06:31:18 | 166 | |||||||
|
Laboratory for Fluorescence Dynamics Resource Report Resource Website 50+ mentions |
Laboratory for Fluorescence Dynamics (RRID:SCR_001437) | LFD | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community. | fluorescence, measurement, microscopy, spectroscopy, biochemistry, cell culture, data analysis, biomolecule, membrane, in-vitro, optical spectroscopy, biological process, tissue culture, fluorescence microscopy, optical and laser technology center | has parent organization: University of California at Irvine; California; USA | NIGMS 8P41GM103540; NCRR 5P41RR003155 |
Restricted | nlx_152663 | SCR_001437 | Laboratory for Fluorescence Dynamics (LFD) | 2026-09-05 06:33:21 | 51 | ||||||
|
GRBio Resource Report Resource Website 10+ mentions |
GRBio (RRID:SCR_002228) | GRBio | data access protocol, data or information resource, database, people resource, software resource, web service | Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections. | biospecimen repository, biodiversity, biorepository, specimen, institution, registry, biological collection, natural history museum, herbaria, darwin core identifier, taxonomy |
lists: Culture Collection of Algae at the University of Cologne lists: Universidade Federal do Ceara, Centro Ciencias Agrarias lists: Central College of Bangalore lists: Culture Collection of Fungi lists: Carter County Museum is related to: Culture Collection of Algae at the University of Cologne is related to: Universidade Federal do Ceara, Centro Ciencias Agrarias is related to: Culture Collection of Fungi is related to: Carter County Museum |
Public, The community can contribute to this resource | nlx_155523 | SCR_002228 | Global Registry of Biorepositories | 2026-09-05 06:24:45 | 11 | |||||||
|
Genevestigator Resource Report Resource Website 100+ mentions |
Genevestigator (RRID:SCR_002358) | Genevestigator | analysis service resource, commercial organization, data analysis service, data or information resource, database, production service resource, service resource | A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. | gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list | is parent organization of: RefGenes | 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation | nif-0000-21172, OMICS_00763 | SCR_002358 | 2026-09-05 06:24:47 | 407 | ||||||||
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Arabidopsis Hormone Database Resource Report Resource Website 10+ mentions |
Arabidopsis Hormone Database (RRID:SCR_001792) | AHD, AHD2.0 | controlled vocabulary, data or information resource, data repository, database, ontology, service resource, storage service resource | Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions. | arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis service |
is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 30625003; National Natural Science Foundation of China 30730011; Ministry of Science and Technology of China 2009CB119101; Ministry of Education of China ED20060047 |
PMID:21045062 PMID:19015126 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02559 | SCR_001792 | Arabidopsis Hormone Database 2.0 | 2026-09-05 06:24:39 | 28 | |||||
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | data or information resource, database | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene, https://doi.org/10.17616/R3GG7M | SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-09-05 06:24:54 | 863 | ||||
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JASPAR Resource Report Resource Website 5000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Carlsberg Foundation ; EMBRACEa Sixth Framework Network of Excellence ; European Union ; Novo Nordisk Foundation ; Sars Centre |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-09-05 06:24:56 | 5785 | |||
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PlantLoc Resource Report Resource Website 1+ mentions |
PlantLoc (RRID:SCR_003138) | PlantLoc | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif. | subcellular localization, protein |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
PMID:23729470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01632 | SCR_003138 | PlantLoc: Plant Proteins Subcellular Localization Prediction Server | 2026-09-05 06:24:58 | 4 | ||||||
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RIKEN BioResource Center Resource Report Resource Website 1000+ mentions |
RIKEN BioResource Center (RRID:SCR_003250) | BRC, RIKEN BRC | biomaterial supply resource, material resource, organism supplier | 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 | 2026-09-05 06:25:00 | 2268 | ||||||
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miR-PREFeR Resource Report Resource Website 1+ mentions |
miR-PREFeR (RRID:SCR_003353) | software resource | An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24930140 | Free, Available for download, Freely available | biotools:mir-prefer, OMICS_04637 | https://bio.tools/mir-prefer | SCR_003353 | miRNA PREdiction From small RNA-Seq data, miR-PREFeR: microRNA PREdiction From small RNAseq data | 2026-09-05 06:25:02 | 8 | ||||||
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PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; China NSFC ; NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-09-05 06:25:02 | 1441 | |||
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TAPIR: target prediction for plant microRNAs Resource Report Resource Website 10+ mentions |
TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) | TAPIR | Web server designed for prediction of plant microRNA targets. | prediction of plant microRNA targets, microrna, target, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:20430753 | biotools:tapir, OMICS_04004 | https://bio.tools/tapir | SCR_000237 | 2026-09-05 06:24:15 | 10 | ||||||||
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BOLD Resource Report Resource Website 100+ mentions |
BOLD (RRID:SCR_004278) | BOLD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library. | protists, taxonomy, dna, barcode, dna barcode, gene sequence, primer, publication, barcode index number, unique identifier, annotation, platform, data management, data sharing, dna sequence, bioinformatics, molecular biology, biology, geography, species, sequence cluster, map, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Guelph; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada ; Ontario Innovation Trust ; NSERC ; Gordon and Betty Moore Foundation |
PMID:18784790 | Free, Public | DOI:10.17616/R3PP7J, nlx_29236, DOI:10.25504/FAIRsharing.en9npn, DOI:10.5883, r3d100010129 | http://www.boldsystems.org/, https://doi.org/10.17616/R3PP7J, https://doi.org/10.17616/r3pp7j, https://doi.org/10.5883/, https://dx.doi.org/10.5883/, https://fairsharing.org/10.25504/FAIRsharing.en9npn, https://doi.org/10.17616/R3KG65 | SCR_004278 | BOLD Systems, Barcode of Life Database Systems, Barcode of Life Database, Barcode of Life Data Systems, BOLD : The Barcode of Life Data System | 2026-09-05 06:29:57 | 499 | ||||
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Cell Type Ontology Resource Report Resource Website 10+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | controlled vocabulary, data or information resource, ontology | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-09-05 06:29:57 | 10 |
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