Tripal Extensions

The following is a list of extensions that have been provided by Tripal site developers and which can be imported into another Tripal site. If you have custom extensions you would like to share, please let us know by joining the Tripal mailing list and sending a request. Consider adding your extensions even if only in development state as this encourages collaboration and reduces duplication of effort. Use the fields below to filter.
Bulk Loader Template
This template provides a means of loading marker by germplasm genotype matricies (See GenotypeSampleData.txt for an example) into Chado by creating Natural Diversity Experiments for each Genotype (ie: each element in the matrix) and linking it to the corresponding stock and marker.  This module requires the sequence and relationship ontologies.
Extension Module
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. The listserve for discussions and announcements is at Cornell University[1]. Additional documentation is in the Github wiki[2]. [1]: http://mail2.sgn.cornell.edu/cgi-bin/mailman/listinfo/plant-breeding-api [2]: https://github.com/plantbreeding/documentation
Extension Module
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. The administration interface manages users and groups access restrictions and other management interfaces can me customized through Drupal view module. 3) Chado Inspector: this sub-module can automatically fill some data fields (for instance the "owner" featureprop) according to a given context and check data integrity to report warnings and errors to administrators or to users (data curators). This module is in design/alpha stage and is not working yet.
Extension Module
This module can be used to display and browse a hierarchical tree representation of any controlled vocabulary (CV) stored into Chado (cvterm table). The vocabulary to browse must have relationships stored into the cvterm_relationship table where the children term is the subject (subject_id) and the parent term is the object (object_id). Circular relationships and network relationships are not an issue since the tree is not generated nor loaded when the CV browser page is accessed; Only root elements are displayed and each first level of a subtree is loaded (ajax) when the used click on the parent node. A generic CV browser page can be used to browse any CV from CV root term(s) or from user-selected terms. The URL of the page can be constructed this way: 'tripal/cvbrowser/' + <either 'cv' or 'cvterm', depending on the type of identifiers provided after> + <CV or CV term identifier(s) or name(s) (separated by "+" signs if more than on value is provided)>. Examples: - tripal/cvbrowser/cv/biological_process+molecular_function+cellular_component - tripal/cvbrowser/cvterm/1234
Materialized View
The materialized view chado_feature_synonyms_list</span> described in this page is part of the tutorial on how to Expand Feature Search to Include Synonyms (http://tripal.info/node/136/). The materialized view focuses on feature synonyms, but the code can however be easily adapted to support other types of synonymes (cvterm synonyms, library synonyms and so forth). The included sql code uses the Postgres functions, array_agg, supported from Postgres version 8.4 If you are using an older version the following code would not work. Also, that would mean that you are using a really old database installation, please consider upgrading.
Extension Module
MCL (Mainlab Chado Loader) is a module that enables users to upload their biological data to chado database schema. Users are required to transfer their biological data into various types of data template files. MCL, then, uploads these data template files into a chado schema. MCL requires each type of data template to have a corresponding class file. MCL predefines the class files for major data template types such as marker, QTL, germplasm, map, project. The flexibility of Chado schema often allows, however, the same type of biological data to be stored in various ways.. When their data are modeled and stored differently in Chado, users can modify these predefined class files. Otherwise users can inherit the existing template class. MCL also allow for users to define a new class file for a new data template. Two related modules are also available: Mainlab Tripal Data Display (https://github.com/tripal/mainlab_tripal) that organizes and extends the default display of the biological data hosted on a Tripal-enabled site and Mainlab Chado Search (https://github.com/tripal/chado_search) that enables advanced search function for biological data stored in a Tripal/Chado database.
Extension Module
Mainlab Chado Search is a module that enables advanced search function for biological data stored in a Tripal/Chado database. By default, a set of search interfaces are provided, such as 'Gene Search' for searching genes and/or transcripts, 'Marker Search' for searching genetic markers, and 'Sequence Search' for searching any sequences stored in the Chado feature table. Searches for other data types, such as QTL, Map, Trait, Stock, Organism are also provided but may require modification to the materialized view to adjust for site-specific data storage. The Mainlab Chado Search module depends on the Tripal materialized views system for gathering data the site administrator wishes to make searchable. Using a materialized view not only improves the search performance, but also allows the administrator to restrict data by modifying the materialized view definition. This design also allows site developers to adopt this module when data in Chado is not stored in the exact same way. Two related modules are also available: Mainlab Tripal Data Display (https://github.com/tripal/mainlab_chado_loader) that organizes and extends the default display of the biological data hosted on a Tripal-enabled site and Mainlab Chado Loader and data collection templates (https://github.com/tripal/mainlab_tripal)
Extension Module
Mainlab Tripal Data Display contains a set of Drupal/PHP templates that organize and extend the default display of the biological data hosted on a Tripal-enabled site (i.e. http://tripal.info). Supported data type includes orgainsm, marker, QTL, germplasm (stock), map (featuremap), project, heritable phenotypic marker (MTL), environment (ND geolocation), haplotype block, polymorphism, eimage, generic gene (genes created by parsing Genbank files using the Mainlab 'tripal_genbank_parser' module), feature, and pub. Each of the templates can be turned on/off as desired. The module supports overriding built-in templates so site-specific customization is also supported (see Overriding templates under the Administration section). Two related modules are also available: Mainlab Chado Loader and data collection templates (https://github.com/tripal/mainlab_chado_loader) and Mainlab Chado Search (https://github.com/tripal/chado_search) that enables advanced search function for biological data stored in a Tripal/Chado database.
Extension Module
This module provides a more specialized interface to genotypic information stored in the Chado Natural Diversity module tables including adding summaries of this information to feature pages and providing a powerful marker by germplasm matrix. The module adds specialized panes to marker and variant features to better display/summarize genotypic data. These include "Genotypes" pane with genotype distribution pie chart (HighCharts module needed), and "Sequences" pane which displays a region of the parent sequence for a marker with any known variants highlighted by their IUPAC wobble code to aid new marker design. The module also provides a search view displaying all the genotypes for a given stock in a marker (rows) by stock (columns) table. The user can indicate which stocks/germplasm they want to see and there is no set number of germplasm they can add.
Extension Module
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.

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