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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-07-25 12:05:39 | 0 | ||||||||
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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 | 2026-07-25 12:07:14 | 5 | ||||||||
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WegoLoc Resource Report Resource Website 1+ mentions |
WegoLoc (RRID:SCR_001402) | WegoLoc | analysis service resource, service resource, data analysis service, production 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 | 2026-07-27 09:31:11 | 4 | |||||||
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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 | analysis service resource, service resource, data analysis service, production 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 | 2026-07-27 09:31:40 | 1 | ||||||
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WoLF PSORT Resource Report Resource Website 100+ mentions |
WoLF PSORT (RRID:SCR_002472) | WoLF PSORT | analysis service resource, service resource, data analysis service, production 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 | 2026-07-27 09:31:33 | 129 | |||||||
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GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr, http://www.greenphyl.org/v3/, https://bio.tools/greenphyldb | SCR_002834 | 2026-07-28 09:40:41 | 19 | ||||||
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Gabi Primary Database Resource Report Resource Website 10+ mentions |
Gabi Primary Database (RRID:SCR_002755) | GABI | analysis service resource, service resource, data or information resource, data repository, data analysis service, database, production 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 | 2026-07-28 09:40:40 | 13 | ||||
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PGN Resource Report Resource Website |
PGN (RRID:SCR_004559) | PGN | service resource, data set, data or information resource, data repository, data analysis service, storage service resource, database, production 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 | 2026-07-28 09:41:01 | 0 | |||||||
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Plant Organelles World Resource Report Resource Website |
Plant Organelles World (RRID:SCR_006313) | Plant Organelles World | image collection, data or information resource, video resource | Images and movies of plant organelle dynamics that were obtained from plant research, based on the Plant Organelles Database. This educational tool is written in layman''''s terms to engage members of the non-scientific community such as students and school teachers. Additional content: ''''What happens, if organelle functions become defective '''' was added in anticipation that readers will be interested in this subject. The Scientific Research of Priority Areas on Organelle Differentiation as the Strategy for Environmental Adaptation in Plants was started on 2004 to promote a comprehensive understanding of plant organelle research, and research with plant scientists all over Japan has been conducted for the past five years. The Plant Organelles Database (PODB), which contains images and movies of various plant organelles that were obtained from this project''''s research was constructed but was designed for scientists. ''''The Plant Organelles World'''' was created for the non-scientific community to understand. Plants have developed mechanisms to adapt to the environment, which is different from the mammalian system of adaption. From recent plant research, the small compartments in cells, ''''organelles'''', have been shown to be involved in various responses to environmental changes. The dramatic development of bio-imaging analysis tools such as green fluorescent protein (GFP), which won a Nobel prize for chemistry in 2008, has contributed to recent plant science, because it has become easier to biotechnologically introduce GFP and its derivatives into cells, leading to convenient methods of observing the inside of cells. As a result, we can analyze organelle dynamics and obtain insights related to understanding the way plants live, as well as forming a deeper understanding of organelles. | organelle, electron microscopy, environment |
is related to: Plant Organelles Database has parent organization: National Institute for Basic Biology; Okazaki; Japan |
PMID:21115470 | nlx_151997 | SCR_006313 | 2026-07-28 09:41:34 | 0 | ||||||||
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Plant Organelles Database Resource Report Resource Website 1+ mentions |
Plant Organelles Database (RRID:SCR_006520) | PODB, PODB2 | service resource, narrative resource, data or information resource, data repository, database, experimental protocol, image collection, video resource, storage service resource | Database of images, movies, and protocols to promote a comprehensive understanding of plant organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles. It consists of 5 individual parts, ''Perceptive Organelles Database'', ''The Organelles Movie Database'', ''The Organellome Database'', ''The Functional Analysis Database'', and ''External Links to other databases and Web pages''. All the data and protocols in ''The Organelle Movie Database'', ''The Organellome Database'' and ''The Functional Analysis Database'' are populated by direct submission of experimentally determined data from plant researchers. Your active contributions by submission of data and protocols to our database would also be appreciated. * Perceptive Organelles Database: This database contains images and movies of organelles in various tissues during different developmental stages in response to environmental stimuli. * Organelles Movie Database: This database contains time-lapse images, Z slices and projection images of organelles in various tissues during different developmental stages, visualized using fluorescent and non-fluorescent probes. * Organellome Database: This database contains images for cellular structures that are composed of organelle images in various tissues during different developmental stages, visualized with fluorescent and non-fluorescent probes. * Functional Analysis Database: This database is a collection of protocols for plant organelle research. * External Links: Access to biological databases. | organelle, developmental stage, environmental stimuli, development, environment, stimulus, biochemical assay, nucleic acid, protein, gene expression, genome mapping, histology, tissue isolation, organelle isolation, plant growth, maintenance, visualization, observation, plant organelle, movement, division, subcellular positioning, behavior, external stimuli, green fluorescent protein, biogenesis, differentiation, interaction |
is related to: Plant Organelles World has parent organization: National Institute for Basic Biology; Okazaki; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT 16085101; Japan Society for the Promotion of Science 228052 |
PMID:21115470 PMID:19755394 PMID:17932059 |
Free for scientific and educational use provided the contributor and the Organellome Database and the Organelles Movie Database are properly credited. If you wish to use commercially, Please contact the contributors of the corresponding images and movies for permission. | nlx_151998, r3d100011300 | https://doi.org/10.17616/R3933R | SCR_006520 | Plant Organelles Database 2 | 2026-07-28 09:41:35 | 7 | ||||
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Ensembl Genomes Resource Report Resource Website 100+ mentions |
Ensembl Genomes (RRID:SCR_006773) | data or information resource, database, data access protocol, software resource, web service | 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 | 2026-07-28 09:41:39 | 276 | ||||||
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Psort Resource Report Resource Website 100+ mentions |
Psort (RRID:SCR_007038) | PSORT | software application, service resource, data set, data analysis software, data or information resource, data analysis service, data processing software, software resource, production service resource, analysis service resource, topical portal, portal | 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 | 2026-07-28 09:41:42 | 209 | |||||||
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Protein Lounge Resource Report Resource Website 10+ mentions |
Protein Lounge (RRID:SCR_002117) | ProteinLounge | service resource, narrative resource, data or information resource, data analysis service, database, production service resource, analysis service resource, training material | Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal. | gene, antigen, bioinformatics, kinase, life science, peptide, phosphatase, signal transduction pathway, sirna, systems biology, protein, biology, cellular network, protein interaction, cell signaling, cell survival, apoptosis, peptide-antigen, kinase-phosphatase, image, pathway | Restricted | nif-0000-20903 | SCR_002117 | Protein Lounge - Redefining Biology | 2026-07-28 09:40:21 | 29 | ||||||||
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NCBI Genome Resource Report Resource Website 500+ mentions |
NCBI Genome (RRID:SCR_002474) | Genome | service resource, data or information resource, data repository, database, storage service 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 | 2026-07-28 09:40:26 | 577 | ||||||
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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 | 2026-07-28 09:41:43 | 43 | ||||
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Leaf Senescence Database Resource Report Resource Website 1+ mentions |
Leaf Senescence Database (RRID:SCR_010227) | LSD | service resource, data or information resource, data repository, database, 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 | 2026-07-28 09:42:43 | 7 | |||||
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XEML Environment Ontology Resource Report Resource Website |
XEML Environment Ontology (RRID:SCR_010450) | XEO | controlled vocabulary, data or information resource, ontology | Ontology to help plant scientists in documenting and sharing metadata describing the abiotic environment. | obo | is listed by: BioPortal | nlx_157631 | SCR_010450 | 2026-07-28 09:42:46 | 0 | |||||||||
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Maize Gross Anatomy Ontology Resource Report Resource Website |
Maize Gross Anatomy Ontology (RRID:SCR_010353) | ZEA | controlled vocabulary, data or information resource, ontology | 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 | 2026-07-28 09:42:44 | 0 | |||||||
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Israel Plant Gene Bank Resource Report Resource Website |
Israel Plant Gene Bank (RRID:SCR_008718) | tissue bank, biomaterial supply resource, material resource | Not yet vetted by NIF curator | nlx_13472 | SCR_008718 | 2026-07-28 09:42:22 | 0 | ||||||||||||
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Nordic Genetic Resource Centre (Plants) Resource Report Resource Website |
Nordic Genetic Resource Centre (Plants) (RRID:SCR_010529) | tissue bank, biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22485 | SCR_010529 | 2026-07-28 09:42:53 | 0 |
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