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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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John Innes Centre; Norwich; United Kingdom Resource Report Resource Website 1+ mentions |
John Innes Centre; Norwich; United Kingdom (RRID:SCR_011330) | JIC | institution | An independent, international center of excellence in plant science and microbiology. Their mission is: * To generate knowledge of plants and microbes through innovative research * To apply their knowledge of nature''s diversity to benefit agriculture, the environment, human health and well-being * To train scientists for the future * To engage with policy makers and the public |
is related to: European Gram Negative AntiBacterial Engine is related to: Pharma-Planta Consortium is parent organization of: Arabidopsis Reactome is parent organization of: modelcrop.org |
ISNI: 0000 0001 2175 7246, nlx_158284, Wikidata: Q365105, grid.14830.3e | https://ror.org/055zmrh94 | SCR_011330 | John Innes Centre, John Innes Center | 2026-02-07 02:08:14 | 5 | ||||||||
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Laboratory for Fluorescence Dynamics Resource Report Resource Website 10+ mentions |
Laboratory for Fluorescence Dynamics (RRID:SCR_001437) | LFD | service resource, access service resource, biomedical technology research center, 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) | 2026-02-10 09:54:30 | 46 | ||||||
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Gabi Primary Database Resource Report Resource Website 10+ mentions |
Gabi Primary Database (RRID:SCR_002755) | GABI | production service resource, data repository, data or information resource, database, analysis service resource, data analysis service, service resource, storage service resource |
Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload. |
molecular plant physiology, plant genome, genome, blast, sequence, snp, mapping, proteomics, image collection | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | German Resource Center for Genome Research RZPD GmbH ; Max Planck Society ; BMBF 0312272; BMBF 0313112; BMBF 0315046 |
PMID:18812395 | Free, Freely available | nif-0000-02866, r3d100012432 | http://gabi.rzpd.de/ https://doi.org/10.17616/R3QB61 |
SCR_002755 | GabiPD | 2026-02-11 10:56:39 | 13 | ||||
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Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | controlled vocabulary, data or information resource | A structured controlled vocabulary for the representation of plant environmental conditions. | obo, environment, gene expression, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157554 | http://purl.bioontology.org/ontology/PECO http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo http://www.gramene.org/plant_ontology/index.html#eo |
SCR_003460 | 2026-02-11 10:56:43 | 0 | ||||||||
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ngLOC Resource Report Resource Website 10+ mentions |
ngLOC (RRID:SCR_003150) | ngLOC | production service resource, software resource, data analysis service, service resource, analysis service 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 | 2026-02-11 10:56:42 | 22 | |||||
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Proteome Analyst Specialized Subcellular Localization Server Resource Report Resource Website 1+ mentions |
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) | PA-SUB | data analysis service, service resource, production service resource, analysis 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 | 2026-02-11 10:56:36 | 1 | ||||||
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WoLF PSORT Resource Report Resource Website 100+ mentions |
WoLF PSORT (RRID:SCR_002472) | WoLF PSORT | data analysis service, service resource, production service resource, analysis 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 | 2026-02-11 10:56:33 | 129 | |||||||
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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 | 2026-02-11 10:56:41 | 198 | |||
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SGN Resource Report Resource Website 500+ 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 | 2026-02-11 10:57:00 | 993 | |||
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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 | 2026-02-11 10:56:24 | 3 | |||||||
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WegoLoc Resource Report Resource Website 1+ mentions |
WegoLoc (RRID:SCR_001402) | WegoLoc | data analysis service, service resource, production service resource, analysis 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 | 2026-02-11 10:56:13 | 4 | |||||||
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Atlas of Living Australia Resource Report Resource Website 100+ mentions |
Atlas of Living Australia (RRID:SCR_006467) | ALA | data or information resource, database | Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA. | data sharing, biodiversity, image, photograph, dna, conservation, natural resource, literature, nomenclature, australia, morphology, life stage, stage, behavior, reproduction, habitat, genetic, region, species, portal, data set, data analysis service, metadata standard, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: CSIRO has parent organization: GBIF - Global Biodiversity Information Facility |
Creative Commons Attribution License, v3 Australia License, Provider content may be covered by other Terms of Use, Http://www.ala.org.au/about-the-atlas/terms-of-use/ | nlx_152016, DOI:10.26197, DOI:10.25504/FAIRsharing.2f66da, r3d100010918, DOI:10.17616/R3VG9S | https://doi.org/10.26197 https://dx.doi.org/10.26197 http://doi.org/10.17616/R3VG9S https://fairsharing.org/10.25504/FAIRsharing.2f66da https://doi.org/10.17616/R3VG9S |
SCR_006467 | 2026-02-11 10:57:25 | 147 | |||||||
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GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse https://bio.tools/gbrowse https://sources.debian.org/src/gbrowse/ |
SCR_006829 | Generic Genome Browser | 2026-02-11 10:57:25 | 43 | ||||
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PlantCyc Resource Report Resource Website 1000+ mentions |
PlantCyc (RRID:SCR_002110) | PMN | project portal, portal, data or information resource, database | Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. | enzyme, gene, biochemical pathway, compound, metabolism, plant metabolic, reaction, database |
is listed by: Plant Metabolic Network has parent organization: Carnegie Institution for Science |
NSF 1026003; NSF 0640769 |
PMID:20522724 | Free, Available for download, Freely available | , nif-0000-20890, nlx_15806 plant | http://www.plantcyc.org/ | SCR_002110 | 2026-02-11 10:56:23 | 3633 | |||||
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PGN Resource Report Resource Website |
PGN (RRID:SCR_004559) | PGN | production service resource, data repository, data or information resource, database, data set, storage service resource, data analysis service, service resource, analysis service resource | Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future. | expressed sequence tag, genomics, functional annotation, blast, sequencing, chromatogram | has parent organization: Cornell University; New York; USA | NSF DBI-9872617; NSF DBI-0115684 |
nlx_55223 | SCR_004559 | PGN - Plant Genome Network, Plant Genome Network | 2026-02-11 10:56:55 | 0 | |||||||
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PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | production service resource, data or information resource, database, data analysis service, service resource, analysis service resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2026-02-11 10:58:43 | 9 | ||||
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Leaf Senescence Database Resource Report Resource Website 1+ mentions |
Leaf Senescence Database (RRID:SCR_010227) | LSD | data repository, data or information resource, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019. Database of leaf senescence to collect SAGs, mutants, phenotypes and literature references. Leaf senescence has been recognized as the last phase of plant development, a highly ordered process regulated by genes called SAGs. By integrating the data from mutant studies and transgenic analysis, they collected many SAGs related to regulation of the leaf senescence in various species. Additionally, they have categorized SAGs according to their functions in regulation of leaf senescence and used standard criteria to describe senescence associated phenotypes for mutants. Users are welcome to submit the new SAGs. | gene, mutant, leaf, phenotype, blast, plant development, sag | has parent organization: Peking University; Beijing; China | Senescence, Aging | Postdoctoral Fellowship at Peking-Tsinghua Center for Life Sciences ; Ministry of Science and Technology of China 2009CB119101; Ministry of Agriculture of China 2010ZX08010-002; Natural Science Foundation of China 31071160; China Postdoctoral Science Foundation 2012M520108; China Postdoctoral Science Foundation 2013T60031 |
PMID:24185698 PMID:21097471 |
THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_156775 | SCR_010227 | 2026-02-11 10:58:14 | 7 | |||||
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XEML Environment Ontology Resource Report Resource Website |
XEML Environment Ontology (RRID:SCR_010450) | XEO | ontology, controlled vocabulary, data or information resource | Ontology to help plant scientists in documenting and sharing metadata describing the abiotic environment. | obo | is listed by: BioPortal | nlx_157631 | SCR_010450 | 2026-02-11 10:58:19 | 0 | |||||||||
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Maize Gross Anatomy Ontology Resource Report Resource Website |
Maize Gross Anatomy Ontology (RRID:SCR_010353) | ZEA | ontology, controlled vocabulary, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157462 | http://www.maizemap.org/ | SCR_010353 | 2026-02-11 10:58:17 | 0 | |||||||
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Ensembl Genomes Resource Report Resource Website 100+ mentions |
Ensembl Genomes (RRID:SCR_006773) | data or information resource, database, software resource, web service, data access protocol | 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 | 2026-02-11 10:57:26 | 276 |
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