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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | service resource, data or information resource, data analysis service, database, production service resource, analysis 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 |
University of Potsdam ; Germany ; German Federal Ministry of Education and Research ; Fond der Chemischen Industrie |
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 | 2026-07-28 09:42:59 | 201 | |||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | service resource, data or information resource, data repository, database, image collection, d spatial image, 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 | 2026-07-28 09:41:54 | 7 | |||||
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mGOASVM Resource Report Resource Website 1+ mentions |
mGOASVM (RRID:SCR_013098) | mGOASVM | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | 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 | 2026-07-28 09:43:10 | 4 | ||||||||
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BOLD Resource Report Resource Website 100+ mentions |
BOLD (RRID:SCR_004278) | BOLD | service resource, data or information resource, data repository, data analysis service, storage service resource, database, production service resource, analysis service resource | DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library. | protists, taxonomy, dna, barcode, dna barcode, gene sequence, primer, publication, barcode index number, unique identifier, annotation, platform, data management, data sharing, dna sequence, bioinformatics, molecular biology, biology, geography, species, sequence cluster, map, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Guelph; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada ; Ontario Innovation Trust ; NSERC ; Gordon and Betty Moore Foundation |
PMID:18784790 | Free, Public | DOI:10.17616/R3PP7J, nlx_29236, DOI:10.25504/FAIRsharing.en9npn, DOI:10.5883, r3d100010129 | http://www.boldsystems.org/, https://doi.org/10.17616/R3PP7J, https://doi.org/10.17616/r3pp7j, https://doi.org/10.5883/, https://dx.doi.org/10.5883/, https://fairsharing.org/10.25504/FAIRsharing.en9npn, https://doi.org/10.17616/R3KG65 | SCR_004278 | BOLD Systems, Barcode of Life Database Systems, Barcode of Life Database, Barcode of Life Data Systems, BOLD : The Barcode of Life Data System | 2026-07-28 09:40:58 | 298 | ||||
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Cell Type Ontology Resource Report Resource Website 1+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | controlled vocabulary, data or information resource, ontology | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-07-28 09:40:56 | 6 | |||
|
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 | 2026-07-28 09:42:24 | 3 | |||||
|
GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | data or information resource, service resource, database | 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 | 2026-07-28 09:41:15 | 28 | |||||
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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 | 2026-07-28 09:41:27 | 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 | 2026-07-28 09:41:34 | 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 | 2026-07-28 09:41:38 | 138 | ||||||
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Global Crop Diversity Trust Resource Report Resource Website |
Global Crop Diversity Trust (RRID:SCR_010658) | tissue bank, biomaterial supply resource, material resource | Not yet vetted by NIF curator | nlx_68877 | SCR_010658 | 2026-07-28 09:42:50 | 0 | ||||||||||||
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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 | 2026-07-28 09:43:29 | 329 | |||||||
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Svalbard Global Seed Vault Resource Report Resource Website |
Svalbard Global Seed Vault (RRID:SCR_010706) | service resource, biobank, material storage repository, storage service resource | Secure seed bank on the Norwegian island of Spitsbergen in remote Arctic Svalbard archipelago to preserve wide variety of plant seeds that are duplicate samples, or "spare" copies, of seeds held in gene banks worldwide. The seed vault is attempt to ensure against loss of seeds in other genebanks during large-scale regional or global crises. | grid.425357.2, nlx_85627 | https://ror.org/03vabvg16 | SCR_010706 | 2026-07-28 09:42:51 | 0 |
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