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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | data or information resource, database | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene, https://doi.org/10.17616/R3GG7M | SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-09-12 12:55:47 | 863 | ||||
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JASPAR Resource Report Resource Website 5000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Carlsberg Foundation ; EMBRACEa Sixth Framework Network of Excellence ; European Union ; Novo Nordisk Foundation ; Sars Centre |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-09-12 12:55:50 | 5785 | |||
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PlantLoc Resource Report Resource Website 1+ mentions |
PlantLoc (RRID:SCR_003138) | PlantLoc | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif. | subcellular localization, protein |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
PMID:23729470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01632 | SCR_003138 | PlantLoc: Plant Proteins Subcellular Localization Prediction Server | 2026-09-12 12:55:52 | 4 | ||||||
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RIKEN BioResource Center Resource Report Resource Website 1000+ mentions |
RIKEN BioResource Center (RRID:SCR_003250) | BRC, RIKEN BRC | biomaterial supply resource, material resource, organism supplier | RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad. | RIN, Resource Information Network, experimental animal, experimental plant, cultured cell line, dna, animal, plant, cell line, genetic material, virus, gene, cultured cell, embryo, sperm, tissue, organ, seed, cell, recombinant host, bioresource, FASEB list, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: Federation of International Mouse Resources is related to: MGI strains has parent organization: RIKEN Tsukuba Institute; Kansai; Japan is parent organization of: JCM works with: Cellosaurus works with: International Mouse Strain Resource |
PMID:19448331 PMID:34532769 |
Free, Freely available | nif-0000-31407 | SCR_003250 | RIKEN Tsukuba Institute RIKEN BioResource Center | 2026-09-12 12:55:54 | 2268 | ||||||
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miR-PREFeR Resource Report Resource Website 1+ mentions |
miR-PREFeR (RRID:SCR_003353) | software resource | An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24930140 | Free, Available for download, Freely available | biotools:mir-prefer, OMICS_04637 | https://bio.tools/mir-prefer | SCR_003353 | miRNA PREdiction From small RNA-Seq data, miR-PREFeR: microRNA PREdiction From small RNAseq data | 2026-09-12 12:55:56 | 8 | ||||||
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PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; China NSFC ; NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-09-12 12:55:56 | 1441 | |||
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GRBio Resource Report Resource Website 10+ mentions |
GRBio (RRID:SCR_002228) | GRBio | data access protocol, data or information resource, database, people resource, software resource, web service | Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections. | biospecimen repository, biodiversity, biorepository, specimen, institution, registry, biological collection, natural history museum, herbaria, darwin core identifier, taxonomy |
lists: Culture Collection of Algae at the University of Cologne lists: Universidade Federal do Ceara, Centro Ciencias Agrarias lists: Central College of Bangalore lists: Culture Collection of Fungi lists: Carter County Museum is related to: Culture Collection of Algae at the University of Cologne is related to: Universidade Federal do Ceara, Centro Ciencias Agrarias is related to: Culture Collection of Fungi is related to: Carter County Museum |
Public, The community can contribute to this resource | nlx_155523 | SCR_002228 | Global Registry of Biorepositories | 2026-09-12 12:55:38 | 11 | |||||||
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Genevestigator Resource Report Resource Website 100+ mentions |
Genevestigator (RRID:SCR_002358) | Genevestigator | analysis service resource, commercial organization, data analysis service, data or information resource, database, production service resource, service resource | A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. | gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list | is parent organization of: RefGenes | 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation | nif-0000-21172, OMICS_00763 | SCR_002358 | 2026-09-12 12:55:40 | 407 | ||||||||
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TAPIR: target prediction for plant microRNAs Resource Report Resource Website 10+ mentions |
TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) | TAPIR | Web server designed for prediction of plant microRNA targets. | prediction of plant microRNA targets, microrna, target, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:20430753 | biotools:tapir, OMICS_04004 | https://bio.tools/tapir | SCR_000237 | 2026-09-12 12:55:05 | 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 | 2026-09-12 12:57:59 | 4 | ||||||||
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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 | 2026-09-12 01:01:24 | 1384 | ||||||
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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 | 2026-09-12 01:01:29 | 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 | 2026-09-12 01:01:27 | 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 | 2026-09-12 01:01:28 | 8 | |||
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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 | 2026-09-12 01:01:35 | 29 | |||||
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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 | 2026-09-12 01:00:52 | 1 | ||||||
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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 | 2026-09-12 01:02:02 | 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 | 2026-09-12 01:02:05 | 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 | 2026-09-12 01:02:07 | 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 | 2026-09-12 01:02:07 | 46 |
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