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| GeneX-2.0 DB: Feature Table | ||
|---|---|---|
| Table Type | Inherits | Comment |
| DATA | none | The Feature table gives detail information concerning each individual element (spot) of a given ArrayDesign. In particular, it indicates the location of the spot on the Array and characterizes the genetic material that will be bound to an instance of the ArrayDesign at the given location. |
| Column Information | ||||
|---|---|---|---|---|
| Column Name | Full Name | Data Type | Not NULL | Comment |
| ad_fk | Array Design | int | true | the ArrayDesign to which the spot belongs |
| feature_concentration | Feature Concentration | float | false | used to indicate the concentration of the probe on the array (may differ from the default value in the referenced ArrayDesign, but will be measured in the same units) |
| feature_description | Feature Description | char128 | false | a meaningful description of the genetic material that will be placed on an instance at this position; in some cases, e.g. foreign DNA used as a control, the rep_fk will be left null, and this field will provide the only description of what material has been used, and hence the significance of expression levels observed at these positions in an instance of the ArrayDesign |
| feature_identifier | Feature Identifier | char128 | false | the GOD file identifier for the position on the ArrayDesign |
| feature_pk | Accession Number | serial | false | |
| feature_type | Feature Type | char128 | true | distinguishes various kinds of control spot from those linked to Reporters iff type = seqfeat then rep_fk must be supplied |
| grid_col_image_location | Grid Column Number | char128 | false | This field supports designs that track the grids in a row,column format |
| grid_image_location | Grid Image Location | char128 | false | these fields specify the position of the spot with respect to the entire Array; their purpose is to allow our software to generate a virtual image that can be compared to the actual image for an PhysicalBioAssay instance. The x and y are specified relative to the origin of distinct blocks of spots; the location of the block is given by the grid_image_location. They may be left null for data without images. the current specification seems problematic, in that unless we know how to translate a grid location into an x-y coordinate for the block, we don't know how to lay out the blocks. Further, it would seem to make more sense to translate at insert time into a simple x-y spec for each spot, since this makes the virtual image easier to calculate, and the latter will be done many times, while the insert will only occur once... JES: Mon Oct 9 15:59:26 MST 2000 Changed to type varchar to support 'Field1', 'A15', etc |
| grid_row_image_location | Grid Row Number | char128 | false | This field supports designs that track the grids in a row,column format |
| pin_identifier | Pin | char128 | false | Indicates which pin of the spotter is used to print this spot. |
| print_sequence | Print Sequence | int | false | Indicates the order of printing of spots on a single visit of a pin to a source well. Used in replicate resolution coupled with rep_fk and source_visit, and tracking systematic variation in spot data. A value of 0 represents a virtual spot that represents the result of resolving replicates across print_sequence. |
| rep_fk | Sequence Feature | int | false | indicates what genetic element will be placed on an instance at this location; may be null, in the case of controls which are not characterized to the level of detail required by Reporter |
| source_visit | Source Visit | int | false | Distinguishes the visits to a source well that is represented by the rep_fk relationship to the sequence feature. If used, assumes that a sequence feature entry represents a unique source well. Used coupled with print_sequence and rep_fk to resolve replicates. A value of 0 represents a virtual spot that represents the value resulting from resolving replicates across source visits. |
| sub_sequence_end | Sub-sequence End | int | false | these fields indicate the subsequence of the Reporter actually used on the Array. When these are left null, the entire Reporter is implied. These may be useful when a PCR product or oligonucleotide is used on the array. |
| sub_sequence_start | Sub-sequence Start | int | false | |
| x_image_location | X Image Location | char128 | false | |
| y_image_location | Y Image Location | char128 | false | |
| Primary Key Information |
|---|
| Column Name |
| feature_pk |
| Foreign Key Information | |||
|---|---|---|---|
| Column Name | Foreign Table | Primary Key in Foreign Table | Foreign Key Type |
| ad_fk | ArrayDesign | ad_pk | MANY_TO_ONE |
| rep_fk | Reporter | rep_pk | MANY_TO_ONE |
| Unique Column Information |
|---|
| Column Names |
| feature_identifier ad_fk |
| x_image_location y_image_location grid_row_image_location grid_col_image_location grid_image_location ad_fk |
| Index Information | |
|---|---|
| Name | Column Name |
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