The Tripal Plant PopGen Submit (TPPS) Module supports a flexible submission interface for genotype, phenotype, environmental, and metadata for population, association, or landscape genetics studies. Submitted studies can be any combination of Phenotype = Genotype x Environment. The portal walks the user through specific questions and collects georeferenced coordinates on plant accessions. The portal also supports ontology standards, including the Minimal Information About a Plant Phenotyping Experiment (MIAPPE) (http://www.miappe.org/) and standard genotyping file formats, such as VCF.
This module supports sequence similarity search on a Tripal website through a new dual application option. The Tripal module provides access to the speed increase available through Diamond for BLASTP/BLASTX style searches as well as traditional NCBI BLAST for BLASTN. Both applications are integrated into a single interface that provides file upload or copy/paste sequence support for the query and access to formatted databases for NCBI BLAST or Diamond. The target databases can be customized for the categories of whole genome, gene, protein, and transcriptome/unigene.
TripalMap module displays map data stored in Chado. The module provides interfaces to view all linkage groups of a map, choose a linkage group and zoom in to a specific region of a linkage group, compare maps that share the same markers, change colors of markers/QTL, etc. The interface can be integrated in Tripal map page and hyperlinked to/from any Tripal page that are displayed in maps (marker, QTL, heritable morphological marker and/or gene). The admin page will allow site developers some flexibility of the display pattern.
Takes advantage of ontology hierarchy to expand term searches to children, siblings, and parents. The module provide a UI for testing the functionality, but the main use is expected to be the functions that carry out the graph searching. The expectation is that this module can be used by other modules that search data object with associated ontology terms.
This is an implementation of the Breeding API (http://docs.brapi.apiary.io/) for Drupal with Tripal module installed. The Breeding API specifies a standard interface for plant phenotype/genotype databases to serve their data to crop breeding applications. It is a shared, open API, to be used by all data providers and data consumers who wish to participate. Initiated in May 2014, it is currently in an actively developing state, so now is the time for potential participants to help shape the specifications to ensure their needs are addressed.
This module extends Tripal to support association of files with data stored in the Chado database. The module will also provide an API to allow other modules to create "plugins" for specific file types. The module is still in development but it is expected that it will provide plugins for Images, BAM and VCF files. These plugins will provide the functionality for visualization and access to these types of files. This file is of importance to the future Tripal Exchange module will provide web services for data house in Chado and in files.<p>
The Chado Controller is a module for Chado database divided in 3 parts: 1) Annotation History: this sub-module keeps track of any modifications made on Chado database. Each transaction is recorded so it is possible to retrieve which user made which modification and when. 2) Access Restriction: it enables access restriction for users and/or groups at any item (feature, stock,...) level.
A tripal module for Chado phylogeny tables, developed for http://legumeinfo.org/.
Supports management of network data, in particular for gene co-expression data. This module is in use on the GenNetEngine. It is still currently being revamped for general use.
A module for management of QTL data. This module provides pages for QTLs, loaders, and relies on a controlled vocabulary developed by representatives from the Dorrie Main lab (CoolSeasonFoodLegumes, Genome Database for Rosaceae, CottonGen), the LIS group (PeanutBase, and LegumeInfo), and others. Two "placeholder" modules are in use by the two organizations. A unified module will be developed when Tripal 3.0 is released. A data dictionary for defining and describing QTL has been developed, along with a Chado data mapping.