Description of Schema


Tables

db
dbxref

db

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Comments:

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TABLE: db
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A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.
Field Name Data Type Size Default Value Other Foreign Key
db_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL contact_id bigint, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED,
urlprefix varchar 255 NULL
url varchar 255 NULL

Constraints

Type Fields
NOT NULLdb_id
NOT NULLname
UNIQUEname

dbxref

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Comments:

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TABLE: dbxref
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A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table _dbxref). A dbxref is generally written as : or as ::.
Field Name Data Type Size Default Value Other Foreign Key
dbxref_id integer 20 PRIMARY KEY, NOT NULL
db_id integer 20 UNIQUE, NOT NULL db.db_id
accession varchar 1024 UNIQUE, NOT NULL, The local part of the identifier. Guaranteed by the db authority to be unique for that db.
version varchar 255 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
dbxref_idx1db_id
dbxref_idx2accession
dbxref_idx3version

Constraints

Type Fields
NOT NULLdbxref_id
NOT NULLdb_id
FOREIGN KEYdb_id
NOT NULLaccession
NOT NULLversion
UNIQUEdb_id, accession, version

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SQL::Translator 0.11020