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http://www.ncbi.nlm.nih.gov/genome

Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

Proper citation: NCBI Genome (RRID:SCR_002474) Copy   

•   Source: SciCrunch Registry

http://www.greenphyl.org/

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

Proper citation: GreenPhylDB (RRID:SCR_002834) Copy   

•   Source: SciCrunch Registry

http://www.gabipd.org/

Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research.
GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated.
* GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload.

Proper citation: Gabi Primary Database (RRID:SCR_002755) Copy   

•   Source: SciCrunch Registry

http://www.lfd.uci.edu/

Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.

Proper citation: Laboratory for Fluorescence Dynamics (RRID:SCR_001437) Copy   

•   Source: SciCrunch Registry

http://archive.gramene.org/plant_ontology/ontology_browse.html#eo

A structured controlled vocabulary for the representation of plant environmental conditions.

Proper citation: Plant Environmental Conditions (RRID:SCR_003460) Copy   

•   Source: SciCrunch Registry

http://www.croptrust.org/main/

Not yet vetted by NIF curator

Proper citation: Israel Plant Gene Bank (RRID:SCR_008718) Copy   

•   Source: SciCrunch Registry

http://www.nordgen.org/index.php/en/content/view/full/467

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023.

Proper citation: Nordic Genetic Resource Centre (Plants) (RRID:SCR_010529) Copy   

•   Source: SciCrunch Registry

http://gbrowse.org/

A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.

Proper citation: GBrowse (RRID:SCR_006829) Copy   

•   Source: SciCrunch Registry

http://www.cropscience.bayer.com/

Crop science company with products in crop protection and nonagricultural pest control. It also has activities in seeds and plant traits. (Adapted from Wikipedia)

Proper citation: Bayer CropScience (RRID:SCR_010498) Copy   

•   Source: SciCrunch Registry

http://www3a.biotec.or.th/c-mii/

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.

Proper citation: C-mii (RRID:SCR_010839) Copy   

•   Source: SciCrunch Registry

https://github.com/hangelwen/miR-PREFeR

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.

Proper citation: miR-PREFeR (RRID:SCR_003353) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/webtools/tapir/

Web server designed for prediction of plant microRNA targets.

Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy   

•   Source: SciCrunch Registry

http://mapman.gabipd.org/web/guest/mapman

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.

Proper citation: MapMan (RRID:SCR_003543) Copy   

•   Source: SciCrunch Registry

http://www.i3crb.fr/

Project to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R��seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC''''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy.

Proper citation: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France (RRID:SCR_006991) Copy   

•   Source: SciCrunch Registry

http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

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.

Proper citation: GOblet (RRID:SCR_006998) Copy   

•   Source: SciCrunch Registry

http://organelledb.lsi.umich.edu/

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.

Proper citation: Organelle DB (RRID:SCR_007837) Copy   

•   Source: SciCrunch Registry

http://www.plantagora.org/

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.

Proper citation: Plantagora (RRID:SCR_001227) Copy   

•   Source: SciCrunch Registry

http://eol.org/

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.

Proper citation: EOL - Encyclopedia of Life (RRID:SCR_005905) Copy   

•   Source: SciCrunch Registry

http://www.ariadnegenomics.com/products/databases/resnet/

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.

Proper citation: RESNET (RRID:SCR_002121) Copy   

•   Source: SciCrunch Registry

https://obofoundry.org/ontology/cl.html

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.

Proper citation: Cell Type Ontology (RRID:SCR_004251) Copy   

•   Source: SciCrunch Registry