Index for bioseqdb

Dumped on 2005-04-07

# Index of database - bioseqdb

- public

- biodatabase
- bioentry
- bioentry_dbxref
- bioentry_path
- bioentry_qualifier_value
- bioentry_reference
- bioentry_relationship
- biosequence
- comment
- dbxref
- dbxref_qualifier_value
- location
- location_qualifier_value
- ontology
- reference
- seqfeature
- seqfeature_dbxref
- seqfeature_path
- seqfeature_qualifier_value
- seqfeature_relationship
- taxon
- taxon_name
- term
- term_dbxref
- term_path
- term_relationship
- term_relationship_term
- term_synonym
- constrain_taxon( )
- unconstrain_taxon( )

## Table: biodatabase

biodatabase Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| biodatabase_id | integer | PRIMARY KEY DEFAULT nextval('biodatabase_pk_seq'::text)
| name | character varying(128) | UNIQUE NOT NULL
| authority | character varying(128) |
| description | text |

Tables referencing this one via Foreign Key Constraints:

- bioentry

Index - Schema public

## Table: bioentry

bioentry Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| bioentry_id | integer | PRIMARY KEY DEFAULT nextval('bioentry_pk_seq'::text)
biodatabase.biodatabase_id | biodatabase_id | integer | UNIQUE#1 UNIQUE#2 NOT NULL
taxon.taxon_id | taxon_id | integer |
| name | character varying(40) | NOT NULL
| accession | character varying(40) | UNIQUE#1 NOT NULL
| identifier | character varying(40) | UNIQUE#2
| division | character varying(6) |
| description | text |
| version | integer | UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:

- bioentry_dbxref

- bioentry_path

- bioentry_qualifier_value

- bioentry_reference

- bioentry_relationship

- biosequence

- comment

- seqfeature

Index - Schema public

## Table: bioentry_dbxref

bioentry_dbxref Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
bioentry.bioentry_id | bioentry_id | integer | PRIMARY KEY
dbxref.dbxref_id | dbxref_id | integer | PRIMARY KEY
| rank | integer |

Index - Schema public

## Table: bioentry_path

bioentry_path Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
bioentry.bioentry_id | object_bioentry_id | integer | UNIQUE#1 NOT NULL
bioentry.bioentry_id | subject_bioentry_id | integer | UNIQUE#1 NOT NULL
term.term_id | term_id | integer | UNIQUE#1 NOT NULL
| distance | integer | UNIQUE#1

Index - Schema public

## Table: bioentry_qualifier_value

bioentry_qualifier_value Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
bioentry.bioentry_id | bioentry_id | integer | UNIQUE#1 NOT NULL
term.term_id | term_id | integer | UNIQUE#1 NOT NULL
| value | text |
| rank | integer | UNIQUE#1 NOT NULL

Index - Schema public

## Table: bioentry_reference

bioentry_reference Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
bioentry.bioentry_id | bioentry_id | integer | PRIMARY KEY
reference.reference_id | reference_id | integer | PRIMARY KEY
| start_pos | integer |
| end_pos | integer |
| rank | integer | PRIMARY KEY

Index - Schema public

## Table: bioentry_relationship

bioentry_relationship Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| bioentry_relationship_id | integer | PRIMARY KEY DEFAULT nextval('bioentry_relationship_pk_seq'::text)
bioentry.bioentry_id | object_bioentry_id | integer | UNIQUE#1 NOT NULL
bioentry.bioentry_id | subject_bioentry_id | integer | UNIQUE#1 NOT NULL
term.term_id | term_id | integer | UNIQUE#1 NOT NULL
| rank | integer |

Index - Schema public

## Table: biosequence

biosequence Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
bioentry.bioentry_id | bioentry_id | integer | PRIMARY KEY
| version | integer |
| length | integer |
| alphabet | character varying(10) |
| seq | text |

Index - Schema public

## Table: comment

comment Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| comment_id | integer | PRIMARY KEY DEFAULT nextval('comment_pk_seq'::text)
bioentry.bioentry_id | bioentry_id | integer | UNIQUE#1 NOT NULL
| comment_text | text | NOT NULL
| rank | integer | UNIQUE#1 NOT NULL

Index - Schema public

## Table: dbxref

dbxref Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| dbxref_id | integer | PRIMARY KEY DEFAULT nextval('dbxref_pk_seq'::text)
| dbname | character varying(40) | UNIQUE#1 NOT NULL
| accession | character varying(40) | UNIQUE#1 NOT NULL
| version | integer | UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:

- bioentry_dbxref

- dbxref_qualifier_value

- location

- reference

- seqfeature_dbxref

- term_dbxref

Index - Schema public

## Table: dbxref_qualifier_value

dbxref_qualifier_value Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
dbxref.dbxref_id | dbxref_id | integer | PRIMARY KEY
term.term_id | term_id | integer | PRIMARY KEY
| rank | integer | PRIMARY KEY
| value | text |

Index - Schema public

## Table: location

location Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| location_id | integer | PRIMARY KEY DEFAULT nextval('location_pk_seq'::text)
seqfeature.seqfeature_id | seqfeature_id | integer | UNIQUE#1 NOT NULL
dbxref.dbxref_id | dbxref_id | integer |
term.term_id | term_id | integer |
| start_pos | integer |
| end_pos | integer |
| strand | integer | NOT NULL
| rank | integer | UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:

- location_qualifier_value

Index - Schema public

## Table: location_qualifier_value

location_qualifier_value Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
location.location_id | location_id | integer | PRIMARY KEY
term.term_id | term_id | integer | PRIMARY KEY
| value | character varying(255) | NOT NULL
| int_value | integer |

Index - Schema public

## Table: ontology

ontology Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| ontology_id | integer | PRIMARY KEY DEFAULT nextval('ontology_pk_seq'::text)
| name | character varying(32) | UNIQUE NOT NULL
| definition | text |

Tables referencing this one via Foreign Key Constraints:

- term

- term_path

- term_relationship

Index - Schema public

## Table: reference

reference Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| reference_id | integer | PRIMARY KEY DEFAULT nextval('reference_pk_seq'::text)
dbxref.dbxref_id | dbxref_id | integer | UNIQUE
| location | text | NOT NULL
| title | text |
| authors | text |
| crc | character varying(32) | UNIQUE

Tables referencing this one via Foreign Key Constraints:

- bioentry_reference

Index - Schema public

## Table: seqfeature

seqfeature Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| seqfeature_id | integer | PRIMARY KEY DEFAULT nextval('seqfeature_pk_seq'::text)
bioentry.bioentry_id | bioentry_id | integer | UNIQUE#1 NOT NULL
term.term_id | type_term_id | integer | UNIQUE#1 NOT NULL
term.term_id | source_term_id | integer | UNIQUE#1 NOT NULL
| display_name | character varying(64) |
| rank | integer | UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:

- location

- seqfeature_dbxref

- seqfeature_path

- seqfeature_qualifier_value

- seqfeature_relationship

Index - Schema public

## Table: seqfeature_dbxref

seqfeature_dbxref Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
seqfeature.seqfeature_id | seqfeature_id | integer | PRIMARY KEY
dbxref.dbxref_id | dbxref_id | integer | PRIMARY KEY
| rank | integer |

Index - Schema public

## Table: seqfeature_path

seqfeature_path Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
seqfeature.seqfeature_id | object_seqfeature_id | integer | UNIQUE#1 NOT NULL
seqfeature.seqfeature_id | subject_seqfeature_id | integer | UNIQUE#1 NOT NULL
term.term_id | term_id | integer | UNIQUE#1 NOT NULL
| distance | integer | UNIQUE#1

Index - Schema public

## Table: seqfeature_qualifier_value

seqfeature_qualifier_value Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
seqfeature.seqfeature_id | seqfeature_id | integer | PRIMARY KEY
term.term_id | term_id | integer | PRIMARY KEY
| rank | integer | PRIMARY KEY
| value | text | NOT NULL

Index - Schema public

## Table: seqfeature_relationship

seqfeature_relationship Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| seqfeature_relationship_id | integer | PRIMARY KEY DEFAULT nextval('seqfeature_relationship_pk_seq'::text)
seqfeature.seqfeature_id | object_seqfeature_id | integer | UNIQUE#1 NOT NULL
seqfeature.seqfeature_id | subject_seqfeature_id | integer | UNIQUE#1 NOT NULL
term.term_id | term_id | integer | UNIQUE#1 NOT NULL
| rank | integer |

Index - Schema public

## Table: taxon

taxon Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| taxon_id | integer | PRIMARY KEY DEFAULT nextval('taxon_pk_seq'::text)
| ncbi_taxon_id | integer | UNIQUE
| parent_taxon_id | integer |
| node_rank | character varying(32) |
| genetic_code | smallint |
| mito_genetic_code | smallint |
| left_value | integer | UNIQUE
| right_value | integer | UNIQUE

Tables referencing this one via Foreign Key Constraints:

- bioentry

- taxon_name

Index - Schema public

## Table: taxon_name

taxon_name Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
taxon.taxon_id | taxon_id | integer | UNIQUE#1 NOT NULL
| name | character varying(255) | UNIQUE#1 NOT NULL
| name_class | character varying(32) | UNIQUE#1 NOT NULL

Index - Schema public

## Table: term

term Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| term_id | integer | PRIMARY KEY DEFAULT nextval('term_pk_seq'::text)
| name | character varying(255) | UNIQUE#1 NOT NULL
| definition | text |
| identifier | character varying(40) | UNIQUE
| is_obsolete | character(1) | UNIQUE#1
ontology.ontology_id | ontology_id | integer | UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:

- bioentry_path

- bioentry_qualifier_value

- bioentry_relationship

- dbxref_qualifier_value

- location

- location_qualifier_value

- seqfeature

- seqfeature_path

- seqfeature_qualifier_value

- seqfeature_relationship

- term_dbxref

- term_path

- term_relationship

- term_relationship_term

- term_synonym

Index - Schema public

## Table: term_dbxref

term_dbxref Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
term.term_id | term_id | integer | PRIMARY KEY
dbxref.dbxref_id | dbxref_id | integer | PRIMARY KEY
| rank | integer |

Index - Schema public

## Table: term_path

term_path Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| term_path_id | integer | PRIMARY KEY DEFAULT nextval('term_path_pk_seq'::text)
term.term_id | subject_term_id | integer | UNIQUE#1 NOT NULL
term.term_id | predicate_term_id | integer | UNIQUE#1 NOT NULL
term.term_id | object_term_id | integer | UNIQUE#1 NOT NULL
ontology.ontology_id | ontology_id | integer | UNIQUE#1 NOT NULL
| distance | integer | UNIQUE#1

Index - Schema public

## Table: term_relationship

term_relationship Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| term_relationship_id | integer | PRIMARY KEY DEFAULT nextval('term_relationship_pk_seq'::text)
term.term_id | subject_term_id | integer | UNIQUE#1 NOT NULL
term.term_id | predicate_term_id | integer | UNIQUE#1 NOT NULL
term.term_id | object_term_id | integer | UNIQUE#1 NOT NULL
ontology.ontology_id | ontology_id | integer | UNIQUE#1 NOT NULL

Tables referencing this one via Foreign Key Constraints:

- term_relationship_term

Index - Schema public

## Table: term_relationship_term

term_relationship_term Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
term_relationship.term_relationship_id | term_relationship_id | integer | PRIMARY KEY
term.term_id | term_id | integer | UNIQUE NOT NULL

Index - Schema public

## Table: term_synonym

term_synonym Structure
F-Key | Name | Type | Description
--- | --- | --- | ---
| synonym | character varying(255) | PRIMARY KEY
term.term_id | term_id | integer | PRIMARY KEY

Index - Schema public

## Function: constrain_taxon( )

### Returns: integer

### Language: SQL

    CREATE RULE rule_taxon_i
           AS ON INSERT TO taxon
           WHERE (SELECT oid FROM taxon WHERE ncbi_taxon_id = new.ncbi_taxon_id)
           	     IS NOT NULL
           DO INSTEAD NOTHING
    ;
    SELECT 1;

## Function: unconstrain_taxon( )

### Returns: integer

### Language: SQL

    DROP RULE rule_taxon_i ON taxon;
    SELECT 1;

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