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http://lemur.amu.edu.pl/share/php/mirnest/home.php

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.

Proper citation: miRNEST (RRID:SCR_008907) Copy   

•   Source: SciCrunch Registry

http://genebank.nibio.go.jp/

Not yet vetted by NIF curator

Proper citation: Global Crop Diversity Trust (RRID:SCR_010658) 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://jci-bioinfo.cn/iLoc-Plant

Data analysis service for predicting subcellular localization of plant proteins with single and multiple sites.

Proper citation: iLoc-Plant (RRID:SCR_011973) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

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.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

A package of web-servers for predicting subcellular localization of proteins in different organisms.

Proper citation: Cell-PLoc (RRID:SCR_011966) Copy   

•   Source: SciCrunch Registry

http://www.dna.affrc.go.jp/PLACE/

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.

Proper citation: PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) 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://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

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

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

Proper citation: Protein Clusters (RRID:SCR_003459) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: MapViewer (RRID:SCR_003092) Copy   

•   Source: SciCrunch Registry

http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

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.

Proper citation: PlantProm DB (RRID:SCR_003359) Copy   

•   Source: SciCrunch Registry

http://www.regjeringen.no/en/dep/lmd/campain/svalbard-global-seed-vault.html?id=462220

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.

Proper citation: Svalbard Global Seed Vault (RRID:SCR_010706) Copy   

•   Source: SciCrunch Registry