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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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miRNEST Resource Report Resource Website 1+ mentions |
miRNEST (RRID:SCR_008907) | miRNEST | data or information resource, database | A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species. | microrna, expressed sequence tag, rna-seq read, sequence, polymorphism, mirna sequence, small rna sequence, single nucleotide polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland |
European Social Fund ; Adam Mickiewicz University PBWB-08/2011; Polish Ministry of Science and Higher Education N N301 160935; Polish Ministry of Science and Higher Education N N516 441938 |
PMID:22135287 | nlx_151465, biotools:mirnest | http://mirnest.amu.edu.pl, https://bio.tools/mirnest | SCR_008907 | miRNEST - a database of animal and plant microRNAs | 2026-09-05 06:31:55 | 4 | |||||
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Global Crop Diversity Trust Resource Report Resource Website |
Global Crop Diversity Trust (RRID:SCR_010658) | biomaterial supply resource, material resource, tissue bank | Not yet vetted by NIF curator | nlx_68877 | SCR_010658 | 2026-09-05 06:31:59 | 0 | ||||||||||||
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Plantagora Resource Report Resource Website 1+ mentions |
Plantagora (RRID:SCR_001227) | Plantagora | data or information resource, data set, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies. | next-generation sequencing, genome assembly, sequencing, genome, 454, illumina, simulate |
is listed by: OMICtools has parent organization: University of Arizona; Arizona; USA |
PMID:22174807 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02116 | SCR_001227 | Plantagora - a resource for plant genome assembly | 2026-09-05 06:30:36 | 1 | ||||||
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EOL - Encyclopedia of Life Resource Report Resource Website 100+ mentions |
EOL - Encyclopedia of Life (RRID:SCR_005905) | EOL | data or information resource, database, portal | Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise. | life, encyclopedia, environmental sciences, ecology, ecological survey, life sciences, specie, species diversity, diversity, taxon, image, video, audio, FASEB list |
is listed by: re3data.org is related to: Pensoft is related to: Biodiversity Heritage Library |
John D. and Catherine T. MacArthur Foundation ; Alfred P. Sloan Foundation |
PMID:24891832 | Creative Commons License, Acknowledgement requested, Note that a single page may be made up of many different data elements, Each covered by a different license, Http://eol.org/info/copyright_and_linking#using_content | r3d100010229, nlx_149476 | https://doi.org/10.17616/R35S3D | SCR_005905 | Encyclopedia of Life | 2026-09-05 06:30:41 | 151 | ||||
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Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-09-05 06:31:21 | 4 | ||||
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MapViewer Resource Report Resource Website 100+ mentions |
MapViewer (RRID:SCR_003092) | Map Viewer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. | genome, mapping, sequencing, chromosome |
is listed by: OMICtools is related to: NCBI Genome is related to: Consensus CDS has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00921, nif-0000-03103 | SCR_003092 | Entrez Map Viewer, NCBI Map Viewer | 2026-09-05 06:31:19 | 244 | |||||||
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PlantProm DB Resource Report Resource Website 1+ mentions |
PlantProm DB (RRID:SCR_003359) | PlantProm | data or information resource, database | Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools. | proximal promoter sequence, rna polymerase ii, transcription start site, promoter, monocot, dicot, dna sequence, taxonomy, promoter type, nucleotide frequency matrix, nucleotide composition, motif, transcription, regulatory element |
is listed by: OMICtools has parent organization: University of London; London; United Kingdom |
Pakistan European Union | PMID:12519961 | Free, Available for download, Freely available | nif-0000-03308, OMICS_01875 | http://www.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom | http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom | SCR_003359 | Plant Promoter Database, PlantProm DB | 2026-09-05 06:31:20 | 8 | |||
|
GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | data or information resource, database, service resource | An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes. | functional annotation, function, annotation, gene, visualization, ortholog, ontology, microarray, gene annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Set Enrichment Analysis is related to: MapMan is related to: Biomine is related to: SEGS has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
Slovenian Research Agency J4-2228; Slovenian Research Agency P2-0103 |
PMID:24194592 | Creative Commons Attribution-NonCommercial-ShareAlike License | biotools:gomapman, OMICS_02280 | https://bio.tools/gomapman | SCR_005060 | 2026-09-05 06:31:28 | 29 | |||||
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iLoc-Plant Resource Report Resource Website 1+ mentions |
iLoc-Plant (RRID:SCR_011973) | iLoc-Plant | analysis service resource, data analysis service, production service resource, service resource | Data analysis service for predicting subcellular localization of plant proteins with single and multiple sites. | subcellular localization, protein, classifier | is listed by: OMICtools | PMID:21984117 | Acknowledgement requested | OMICS_01624 | SCR_011973 | iLoc-Plant: Predicting subcellular localization of plant proteins with single and multiple sites | 2026-09-05 06:32:01 | 1 | ||||||
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BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | analysis service resource, data analysis service, production service resource, service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-09-05 06:32:01 | 46 | ||||||||
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Cell-PLoc Resource Report Resource Website 100+ mentions |
Cell-PLoc (RRID:SCR_011966) | Cell-PLoc | analysis service resource, data analysis service, production service resource, service resource | A package of web-servers for predicting subcellular localization of proteins in different organisms. | subcellular localization, protein, gram-negative protein, gram-positive protein, virus |
is listed by: OMICtools has parent organization: Shanghai Jiao Tong University; Shanghai; China is parent organization of: Euk-mPLoc |
PMID:18274516 | OMICS_01617 | SCR_011966 | Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in different organisms | 2026-09-05 06:32:01 | 254 | |||||||
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PLACE- A Database of Plant Cis-acting Regulatory DNA Elements Resource Report Resource Website 100+ mentions |
PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) | PLACE | data or information resource, database | A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained. | motif, cis-acting regulatory dna element, FASEB list |
is listed by: OMICtools has parent organization: National Institute of Agrobiological Sciences; Ibaraki; Japan |
PMID:9847208 | Free, Acknowledgement requested | nif-0000-03296, OMICS_00557 | SCR_013428 | 2026-09-05 06:32:07 | 351 | |||||||
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ProRepeat Resource Report Resource Website 1+ mentions |
ProRepeat (RRID:SCR_006113) | ProRepeat | data or information resource, database | ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons. | amino acid, tandem, repeat, protein, sequence, nucleotide sequence, repeat fragment, protein repeat, proteome, sequence length, gene, taxon, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB is related to: RefSeq has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
PMID:22102581 | nlx_151587, biotools:prorepeat | https://bio.tools/prorepeat | SCR_006113 | 2026-09-05 06:31:33 | 1 | |||||||
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OBO Tracker: Plant Ontology (PO) TERM requests Resource Report Resource Website 1+ mentions |
OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) | OBO SF PO | data or information resource, database | Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users. | plant, ontology, term |
is related to: OBO has parent organization: SourceForge |
The community can contribute to this resource, Account required | nlx_99576 | SCR_006497 | Tracker: PO TERM requests, Tracker: Plant Ontology TERM requests, SourceForge.net: Open Biomedical Ontologies: Plant Ontology (PO) TERM requests, Source Forge OBO Plant Ontology (PO) term request tracker, Tracker: Plant Ontology (PO) TERM requests | 2026-09-05 06:31:35 | 2 | |||||||
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Catalogue of Life Resource Report Resource Website 100+ mentions |
Catalogue of Life (RRID:SCR_006701) | CoL | data or information resource, database | Comprehensive and authoritative global index of species of animals, plants, fungi and micro-organisms. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.3 million species. This figure continues to rise as information is compiled from diverse sources around the world. There are two distinct versions of the Catalogue of Life: the Dynamic Checklist and the Annual Checklist. Choose the version most suited to your needs. If you have a taxonomic database and would like to join the Species 2000 federation of databases in the Catalogue of Life please contact the Species 2000 Secretariat: all candidate databases go through a peer review process. The Annual Checklist Exchange Format defines the format for exchanging data. | taxon, name, relationship, distribution, taxonomy, region, synonymy, taxonomic tree, specie, FASEB list |
is related to: Phenoscape Knowledgebase has parent organization: University of Reading; Reading; United Kingdom |
The community can contribute to this resource, Commercial use requires written permission, Acknowledgement required | nlx_153875, r3d100011241 | https://doi.org/10.17616/R31050 | SCR_006701 | Catalog of Life | 2026-09-05 06:31:36 | 174 | ||||||
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RESNET Resource Report Resource Website 1000+ mentions |
RESNET (RRID:SCR_002121) | ResNet | data or information resource, database | Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | biological relationship, biomedical, literature, interaction, FASEB list |
is listed by: Biositemaps has parent organization: Indiana University School of Medicine; Indiana; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20909 | http://www.ariadnegenomics.com/products/databases/ariadne-resnet/ | SCR_002121 | Ariadne ResNet Databases, ResNet Databases | 2026-09-05 06:31:16 | 1384 | ||||||
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MapMan Resource Report Resource Website 1000+ mentions |
MapMan (RRID:SCR_003543) | MapMan | software application, software resource | Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes. | metabolic pathway, biological process, genomics, pathway, array, visualization, gene, transcript, protein, enzyme, metabolite |
is related to: GoMapMan has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany |
PMID:19389052 PMID:14996223 PMID:16009995 PMID:16649112 |
nlx_157682 | SCR_003543 | MapMan Application Software | 2026-09-05 06:32:29 | 1251 | |||||||
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BAR Resource Report Resource Website 10+ mentions |
BAR (RRID:SCR_006748) | BAR | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available. | gene expression, protein, molecular marker, mapping, tool, genomic, genomics, functional genomics, interaction, molecular interaction, protein-protein interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada |
nlx_152191, biotools:bioanalres_bar | https://bio.tools/bioanalres_bar | SCR_006748 | Bio-Analytic Resource for Plant Biology, Bio-Analytic Resource, Bio-Analytic Resource - the BAR | 2026-09-05 06:26:00 | 48 | ||||||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-09-05 06:26:05 | 6 | |||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | d spatial image, data or information resource, data repository, database, image collection, service resource, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-09-05 06:26:15 | 7 |
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