|
Database consists of the following four tables: - coordinate_systems - stores a list of DAS coordinate systems.
- feature - contains a list of submitted features.
- history - stores history of modifications
- group - shows which features are grouped together
COORDINATE_SYSTEMThis table contains a list of DAS coordinate systems. The list is periodically synchronized with DAS registry. | Name | Type | Description | | id | int(11) | PRIMARY KEY, which is assigned as a key to the following relations: FEATURES(ID), HISTORY(ID),GROUPS(ID). | | name | varchar(64) | Name of the coordinate system. | | label | varchar(64) | Additional information. | | uri | varchar(64) | URI identificator. |
FEATURES_IDThis table contains collection of the features, belonging to a particular coordinate system. | Name | Type | Description | | id | int(11) | PRIMARY KEY | | featureid | varchar(64) | UNIQUE, NOT NULL. The featureid field provides an unique identificator of the feature. | | featuretype | varchar(32) | Type of the feature. For example, exon or intron. | | method | varchar(32) | This field indicates method that was used to identify the feature. | | segmentid | varchar(64) | The segmentid provides id of the segment in the reference sequence, to which the feature belongs. | | start | int(11) | The start position of the feature in the reference segment. | | end | int(11) | The end position of the feature in the reference segment. | | strand | char(1) | The strand specifies orientation of the transcription. Here the valid values are: '+' if the feature is on the sense strand, '-' if it is on the antisense strand, or 0 for the features unrelated to transcription, for example literature. | | phase | char(1) | This field has value '.' if the position of the feature is relative to an open reading frame, or 0 if not. | | score | float | The score is a floating point number. It shows the score of the method, that was used to find the feature. | | attributes | text | A human readable note, that additionally can contain a link to a web-site with more information about the feature, and id of a group to which the feature belongs. The group description can be found in the respective GROUPS table. |
HISTORY_IDThis table is an archive of modifications that were made with the features. It stores copy of the record before modification, time when the modification was made, id of user that made the changes and a description about made changes. The data can be used for restoring the feature or viewing the history of feature modifications. | Name | Type | Description | | id | int(11) | PRIMARY KEY | | featureid | varchar(64) | UNIQUE, NOT NULL. The featureid field provides an unique identificator of the feature. | | featuretype | varchar(32) | Type of the feature. For example, exon or intron. | | method | varchar(32) | Method that was used to identify the feature. | | segmentid | varchar(64) | The segmentid provides id of the segment in the reference sequence, to which the feature belongs. | | start | int(11) | The start position of the feature in the reference segment. | | end | int(11) | The end position of the feature in the reference segment. | | strand | char(1) | The strand specifies orientation of the transcription. Here the valid values are: '+' if the feature is on the sense strand, '-' if it is on the antisense strand, 0 for the features unrelated to transcription, for example literature. | | phase | char(1) | This field has value '.' if the position of the feature is relative to an open reading frame, or 0 if not. | | score | float | The score is a floating point number. It shows the score of the method, that was used to find the feature. | | attributes | text | A human readable note, that can also contain a link to a web-site with more information about the feature, and id of a group to which the feature belongs. The group description can be found in the respective GROUPS table. | | action | char(1) | The action specifies the type of changes performed with the feature : 'M' - modify, 'D' - delete. | | user | varchar(200) | The user OpenID identifier as it was provided on the login page. | | date | timestamp | This field sets the date of modification. | | commit_msg | text | Free text message with description about made changes. |
GROUPS_IDThis table reflects the fact that some features are grouped together. The classical example is when exons and introns belong to one gene, and they can be logically grouped together. | Name | Type | Description | | id | int(11) | PRIMARY KEY | | groupid | varchar(64) | UNIQUE id of the group. NOT NULL | | attributes | text | Description of the group. |
|
Sign in to add a comment
