Chado API
- 2.x tripal_core/api/tripal_core.chado_general.api.inc tripal_chado_api
- 3.x tripal_chado/tripal_chado.module tripal_chado_api
- 1.x tripal_core/api/tripal_core_chado.api.inc tripal_chado_api
The Tripal Chado (tripal_chado) module provides an application programming interface (API) to support customizations and creation of new extensions using the Chado database schem as a data store.
File
- tripal_chado/
tripal_chado.module, line 15 - The Tripal Chado module.
Functions
Name |
Location | Description |
|---|---|---|
| chado_get_tokens |
tripal_chado/ |
Returns an array of tokens based on Tripal Entity Fields. |
| chado_publish_records |
tripal_chado/ |
Publishes content in Chado as a new TripalEntity entity. |
| chado_replace_tokens |
tripal_chado/ |
Replace all Chado Tokens in a given string. |
Sub-Topics
|
Name |
Location | Description |
|---|---|---|
| Chado Analysis |
tripal_chado/ |
Provides API functions for working with analysis records in Chado that go beyond the generic Chado API functions. |
| Chado Contact |
tripal_chado/ |
Provides API functions for working with chado records in Chado that go beyond the generic Chado API functions. |
| Chado Custom Tables |
tripal_chado/ |
Provides an API to manage custom tables in Chado. |
| Chado CV |
tripal_chado/ |
Provides API functions specificially for managing controlled vocabulary records in Chado. Please note that Tripal v3 provides a generic set of API functions for working with controlled vocabularies (CVs). This allows for CVs to be stored using any… |
| Chado DB |
tripal_chado/ |
External databases can be used to indicate the source for a variety of data. The most common use is with controlled vocabularies (CV). Chado expects that every CV have an external database record, where the database name must be the short name of the… |
| Chado Entity |
tripal_chado/ |
Provides an application programming interface (API) to migrate content. |
| Chado Entity |
tripal_chado/ |
Provides an application programming interface (API) to manage entities that use Chado as their base data. |
| Chado Feature |
tripal_chado/ |
Provides API functions specificially for managing feature records in Chado especially retrieving relationships and sequences derived from relationships and feature alignments. |
| Chado Materalized Views |
tripal_chado/ |
Provides an application programming interface (API) to manage materialized views in Chado The Perl-based chado comes with an interface for managing materialzed views. This API provides an alternative Drupal-based method. |
| Chado Organism |
tripal_chado/ |
Provides API functions specificially for managing organism records in Chado. |
| Chado Phylotree |
tripal_chado/ |
Provides API functions specificially for managing phylogenetic and taxonomic tree records in Chado. The API consists of functions for creation, retrieval, update and deltion (CRUD) for phylogenetic tree records as well as importing of trees in the… |
| Chado Publication |
tripal_chado/ |
Provides API functions specificially for managing publication records in Chado. |
| Chado Query |
tripal_chado/ |
Provides an API for querying of chado including inserting, updating, deleting and selecting from specific chado tables. There is also a generic function, chado_query(), to execute and SQL statement on chado. It is ideal to use these functions to… |
| Chado Schema |
tripal_chado/ |
Provides an application programming interface (API) for describing Chado tables. This API consists of a set of functions, one for each table in Chado. Each function simply returns a Drupal style array that defines the table. |
| Chado Stock |
tripal_chado/ |
Provides API functions specificially for managing stock records in Chado. The stock table of Chado is used for storing a variety of data types besides just stocks from a stock collection. Examples of other records commonly stored in the stock… |
| Chado Views Integration |
tripal_chado_views/ |
Provides API functions that support direct integration of Chado tables with Drupal Views. This is different from the entity and field integration that Tripal v3 provides. Here Chado tables are directly integrated. Tripal provides a web interface… |
| Semantic Web |
tripal_chado/ |
Provides an application programming interface (API) for semantic web support. |
| Semantic Web |
tripal_chado/ |
This API generates objects containing the full details of a record(s) in chado. |