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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-29 11:22:58 | 6 | |||||
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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 | 2026-08-29 11:20:27 | 10 | ||||||||
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mGOASVM Resource Report Resource Website 1+ mentions |
mGOASVM (RRID:SCR_013098) | mGOASVM | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available. | subcellular localization, gram-negative protein, virus, protein |
is listed by: OMICtools has parent organization: Hong Kong Polytechnic University; Hong Kong; China |
PMID:23130999 | OMICS_01627 | SCR_013098 | 2026-08-29 11:24:29 | 4 | ||||||||
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Crop Ontology Resource Report Resource Website 10+ mentions |
Crop Ontology (RRID:SCR_010299) | CO | controlled vocabulary, data or information resource, ontology | Ontology that includes crop-specific trait ontologies for several economically important plants like rice, wheat, maize, potato, musa, chickpea and sorghum along with other important domains for crop research such as germplasm, passport, trait measurement scales, experimental design factors etc. | obo | is listed by: BioPortal | nlx_157378 | http://cropontology.org/ | SCR_010299 | 2026-08-29 11:23:26 | 12 | ||||||||
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Plant Anatomy Resource Report Resource Website |
Plant Anatomy (RRID:SCR_010408) | PAE | controlled vocabulary, data or information resource, ontology | THIS RESOURCES IS NO LONGER IN SERVICE, documented on April 23, 2014. REPLACED BY: Plant Ontology (PO). A controlled vocabulary of plant morphological and anatomical structures representing organs, tissues, cell types, and their biological relationships based on spatial and developmental organization. Note that this has been subsumed into the PO. This file is created by filtering plant_ontology_assert.obo to contain only terms from the plant anatomical entity branch of the PO. For more information, please see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/ | obo |
is listed by: BioPortal has parent organization: Plant Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157553 | SCR_010408 | 2026-08-29 11:23:30 | 0 | ||||||||
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Bayer CropScience Resource Report Resource Website 1+ mentions |
Bayer CropScience (RRID:SCR_010498) | commercial organization | Crop science company with products in crop protection and nonagricultural pest control. It also has activities in seeds and plant traits. (Adapted from Wikipedia) | crop, crop protection, pest control, seed, plant trait | nlx_158080 | SCR_010498 | 2026-08-29 11:23:43 | 6 | |||||||||||
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C-mii Resource Report Resource Website 1+ mentions |
C-mii (RRID:SCR_010839) | C-mii | software resource | A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed. | ubuntu linux, windows | is listed by: OMICtools | PMID:23281648 | GNU General Public License | OMICS_00394 | SCR_010839 | C-mii: A software for Computational miRNA identificaion, C-mii (A software for Computational miRNA identificaion) | 2026-08-29 11:23:39 | 4 | ||||||
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PMTED Resource Report Resource Website 1+ mentions |
PMTED (RRID:SCR_010854) | PMTED | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A Plant MicroRNA Target Expression Database to study the microRNA (miRNA) functions by inferring their target gene expression profiles among the large amount of existing microarray data. You may also predict your miRNA targets and retrieve their microarray expression data. | gene expression, target, bioprocess, microrna, condition | is listed by: OMICtools | National High-tech Development Plan 863 Program | OMICS_00413 | SCR_010854 | Plant MicroRNA Target Expression Database | 2026-08-29 11:23:39 | 6 | |||||||
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PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family. | protein model, protein sequence, gene family, protein, transcriptional control, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Fond der Chemischen Industrie ; German Federal Ministry of Education and Research ; University of Potsdam ; Germany |
PMID:19858103 PMID:17286856 |
Free, Freely available | biotools:plntfdb, OMICS_00561 | http://plntfdb.bio.uni-potsdam.de/v3.0/, https://bio.tools/plntfdb | SCR_010899 | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-08-29 11:23:58 | 218 | |||||
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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 | 2026-08-29 11:23:03 | 7 | |||||
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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 | 2026-08-29 11:28:39 | 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 | 2026-08-29 11:28:42 | 151 | ||||
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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 | 2026-08-29 11:30:20 | 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 | 2026-08-29 11:30:37 | 0 | ||||||||||||
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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 | 2026-08-29 11:30:08 | 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 | 2026-08-29 11:30:38 | 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 | 2026-08-29 11:30:08 | 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 | 2026-08-29 11:30:42 | 351 | |||||||
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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 | 2026-08-29 11:30:42 | 1251 | |||||||
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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 | 2026-08-29 11:29:44 | 1 |
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