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http://purl.bioontology.org/ontology/XEO

Ontology to help plant scientists in documenting and sharing metadata describing the abiotic environment.

Proper citation: XEML Environment Ontology (RRID:SCR_010450) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ZEA

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

Proper citation: Maize Gross Anatomy Ontology (RRID:SCR_010353) Copy   

•   Source: SciCrunch Registry

https://www.jic.ac.uk/

An independent, international center of excellence in plant science and microbiology. Their mission is: * To generate knowledge of plants and microbes through innovative research * To apply their knowledge of nature''s diversity to benefit agriculture, the environment, human health and well-being * To train scientists for the future * To engage with policy makers and the public

Proper citation: John Innes Centre; Norwich; United Kingdom (RRID:SCR_011330) 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.arabidopsisreactome.org

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

Proper citation: Arabidopsis Reactome (RRID:SCR_002063) Copy   

•   Source: SciCrunch Registry

http://www.phi-base.org/

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

Proper citation: PHI-base (RRID:SCR_003331) 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://solgenomics.net/

A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions.

Proper citation: SGN (RRID:SCR_004933) Copy   

•   Source: SciCrunch Registry

http://www.ala.org.au/

Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA.

Proper citation: Atlas of Living Australia (RRID:SCR_006467) Copy   

•   Source: SciCrunch Registry

http://genome.unmc.edu/ngLOC/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.

Proper citation: ngLOC (RRID:SCR_003150) Copy   

•   Source: SciCrunch Registry

https://plantcyc.org/content/plantcyc-15.2.0

Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

Proper citation: PlantCyc (RRID:SCR_002110) 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://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.btool.org/WegoLoc

Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.

Proper citation: WegoLoc (RRID:SCR_001402) Copy   

•   Source: SciCrunch Registry

http://www.genscript.com/psort/wolf_psort.html

Data analysis service for protein subcellular localization prediction.

Proper citation: WoLF PSORT (RRID:SCR_002472) Copy   

•   Source: SciCrunch Registry

http://webdocs.cs.ualberta.ca/~bioinfo/PA/Sub/

Web server specialized to predict the subcellular localization of proteins using established machine learning techniques.

Proper citation: Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) 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.psort.org

Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses.

Proper citation: Psort (RRID:SCR_007038) Copy   

•   Source: SciCrunch Registry

http://podb.nibb.ac.jp/Organellome/PODBworld/en/

Images and movies of plant organelle dynamics that were obtained from plant research, based on the Plant Organelles Database. This educational tool is written in layman''''s terms to engage members of the non-scientific community such as students and school teachers. Additional content: ''''What happens, if organelle functions become defective '''' was added in anticipation that readers will be interested in this subject. The Scientific Research of Priority Areas on Organelle Differentiation as the Strategy for Environmental Adaptation in Plants was started on 2004 to promote a comprehensive understanding of plant organelle research, and research with plant scientists all over Japan has been conducted for the past five years. The Plant Organelles Database (PODB), which contains images and movies of various plant organelles that were obtained from this project''''s research was constructed but was designed for scientists. ''''The Plant Organelles World'''' was created for the non-scientific community to understand. Plants have developed mechanisms to adapt to the environment, which is different from the mammalian system of adaption. From recent plant research, the small compartments in cells, ''''organelles'''', have been shown to be involved in various responses to environmental changes. The dramatic development of bio-imaging analysis tools such as green fluorescent protein (GFP), which won a Nobel prize for chemistry in 2008, has contributed to recent plant science, because it has become easier to biotechnologically introduce GFP and its derivatives into cells, leading to convenient methods of observing the inside of cells. As a result, we can analyze organelle dynamics and obtain insights related to understanding the way plants live, as well as forming a deeper understanding of organelles.

Proper citation: Plant Organelles World (RRID:SCR_006313) Copy   

•   Source: SciCrunch Registry