Difference between revisions of "Chado Organism Module"
From GMOD
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| − | | '' UNIQUE#1 NOT NULL ''<br /><br />A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern | + | | '' UNIQUE#1 NOT NULL ''<br /><br />A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern. |
|- class="tr0" | |- class="tr0" | ||
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Revision as of 03:56, 1 March 2007
Contents
Introduction
Tables
Table: organism
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.
| F-Key | Name | Type | Description |
|---|---|---|---|
| organism_id | serial | PRIMARY KEY | |
| abbreviation | character varying(255) | ||
| genus | character varying(255) | UNIQUE#1 NOT NULL | |
| species | character varying(255) | UNIQUE#1 NOT NULL A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern. | |
| common_name | character varying(255) | ||
| comment | text |
Tables referencing this one via Foreign Key Constraints:
Table: organism_dbxref
| F-Key | Name | Type | Description |
|---|---|---|---|
| organism_dbxref_id | serial | PRIMARY KEY | |
| organism_id | integer | UNIQUE#1 NOT NULL | |
| dbxref_id | integer | UNIQUE#1 NOT NULL |
Table: organism_relationship
| F-Key | Name | Type | Description |
|---|---|---|---|
| organism_relationship_id | serial | PRIMARY KEY | |
| subject_id | integer | UNIQUE#1 NOT NULL | |
| object_id | integer | UNIQUE#1 NOT NULL | |
| type_id | integer | UNIQUE#1 NOT NULL |
Table: organismpath
| F-Key | Name | Type | Description |
|---|---|---|---|
| organismpath_id | serial | PRIMARY KEY | |
| subject_id | integer | UNIQUE#1 NOT NULL | |
| object_id | integer | UNIQUE#1 NOT NULL | |
| type_id | integer | UNIQUE#1 NOT NULL | |
| pathdistance | integer | UNIQUE#1 |
Table: organismprop
Tag-value properties - follows standard chado model.
| F-Key | Name | Type | Description |
|---|---|---|---|
| organismprop_id | serial | PRIMARY KEY | |
| organism_id | integer | UNIQUE#1 NOT NULL | |
| type_id | integer | UNIQUE#1 NOT NULL | |
| value | text | ||
| rank | integer | UNIQUE#1 NOT NULL |
