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 CV. In other cases, records such as features, stocks, libraries, etc., can also be present in remote databases and these associations can be made through dbxref linker tables. The API functions provided here provide tools to easily work with external databases.

Parent topics

File

tripal_chado/api/modules/tripal_chado.db.api.inc, line 8

Provides API functions specificially for managing external database reference records in Chado.

Functions

Name	Location	Description
chado_associate_dbxref	tripal_chado/api/modules/tripal_chado.db.api.inc	Add a record to a database reference linking table (ie: feature_dbxref).
chado_autocomplete_dbxref	tripal_chado/api/modules/tripal_chado.db.api.inc	This function is intended to be used in autocomplete forms for searching for accession that begin with the provided string.
chado_get_db	tripal_chado/api/modules/tripal_chado.db.api.inc	Retrieves a chado db variable.
chado_get_dbxref	tripal_chado/api/modules/tripal_chado.db.api.inc	Retrieves a chado database reference variable.
chado_get_dbxref_url	tripal_chado/api/modules/tripal_chado.db.api.inc	Generates a URL for the controlled vocabulary term.
chado_get_db_select_options	tripal_chado/api/modules/tripal_chado.db.api.inc	Create an options array to be used in a form element which provides a list of all chado dbs.
chado_insert_db	tripal_chado/api/modules/tripal_chado.db.api.inc	Adds a new database to the Chado DB table and returns the DB object.
chado_insert_dbxref	tripal_chado/api/modules/tripal_chado.db.api.inc	Add a database reference.