Chado Library Module
Contents
Introduction
Tables
library
Field Name Data Type Size Default Value Other Foreign Key library_id integer 11 PRIMARY KEY, NOT NULL organism_id integer 10 UNIQUE, NOT NULL organism.organism_id name varchar 255 uniquename text 64000 UNIQUE, NOT NULL type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id
library_synonym
The type_id foreign key links to a controlled vocabulary of library types. examples of this would be: 'cDNA_library' or 'genomic_library'
Field Name Data Type Size Default Value Other Foreign Key library_synonym_id integer 11 PRIMARY KEY, NOT NULL synonym_id integer 10 UNIQUE, NOT NULL synonym.synonym_id library_id integer 10 UNIQUE, NOT NULL library.library_id pub_id integer 10 UNIQUE, NOT NULL pub.pub_id is_current boolean 0 true NOT NULL is_internal boolean 0 false NOT NULL
library_pub
pub_id: the pub_id link is for relating the usage of a given synonym to the publication in which it was used is_current: the is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library is_internal: typically a synonym exists so that somebody querying the db with an obsolete name can find the object they're looking for (under its current name. If the synonym has been used publicly & deliberately (eg in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (eg, there was a typo which went public), then the is_internal bit may be set to 'true' so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.
Field Name Data Type Size Default Value Other Foreign Key library_pub_id integer 11 PRIMARY KEY, NOT NULL library_id integer 10 UNIQUE, NOT NULL library.library_id pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
libraryprop
Field Name Data Type Size Default Value Other Foreign Key libraryprop_id integer 11 PRIMARY KEY, NOT NULL library_id integer 10 UNIQUE, NOT NULL library.library_id type_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id value text 64000 NULL rank integer 10 0 UNIQUE, NOT NULL
library_cvterm
Field Name Data Type Size Default Value Other Foreign Key library_cvterm_id integer 11 PRIMARY KEY, NOT NULL library_id integer 10 UNIQUE, NOT NULL library.library_id cvterm_id integer 10 UNIQUE, NOT NULL cvterm.cvterm_id pub_id integer 10 UNIQUE, NOT NULL pub.pub_id
library_feature
The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.
Field Name Data Type Size Default Value Other Foreign Key library_feature_id integer 11 PRIMARY KEY, NOT NULL library_id integer 10 UNIQUE, NOT NULL library.library_id feature_id integer 10 UNIQUE, NOT NULL feature.feature_id
