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| GeneX-2.0 DB: PhysicalBioAssay Table | ||
|---|---|---|
| Table Type | Inherits | Comment |
| DATA | Identifiable | The PhysicalBioAssay table is used in two related, but distinct fashions: to represent the primary data for gene expression experiments and to represent processed data such as averaged values across replicates or ratio values for treatment vs. controls. In representing the primary data, it describes an instance of an ArrayDesign that has been used to assay gene expression levels in a preparation of the mRNA from a sample that has been subjected to a specific treatment in the context of an experiment. It contains detailed information as to the treatment and protocols used on this ArrayDesign instance. The actual expression levels for each spot are stored in the PhysicalBioAssaySpots table. In general, the PhysicalBioAssay table has the same relationship to the PhysicalBioAssaySpots table as the ArrayDesign table has to the ArrayDesignSpots table. However, there several cases in which the relationship breaks down to some extent. First, there may be PhysicalBioAssays for which no ArrayDesign is given. Second, for spots that represent controls on a given ArrayDesign, we may choose not to store expression levels for the control spots. Finally, in cases of ArrayDesigns with replicate spots (i.e. the same Reporter is used in different locations on the ArrayDesign), replicates will be broken out into separate PhysicalBioAssay rows. For example, an ArrayDesign with 1000 distinct Reporters, each of which has been replicated 2 times on the ArrayDesign will have 3000 corresponding ArrayDesignSpot rows, while a given instance of the ArrayDesign will be represented by three distinct PhysicalBioAssay rows, each of which has 1000 corresponding PhysicalBioAssaySpots rows. A related example is when mutiple channels are used to detect the signal of the expression level for each spot. In this case, an ArrayDesign that has 1000 distinct Reporters may be represented by two or more PhysicalBioAssay rows, each with 1000 PhysicalBioAssaySpot rows representing the expression level reported by one channel. PhysicalBioAssays that represent primary data will be grouped into sets around the ReplicateDef table. This set of primary data may then be used to define derived PhysicalBioAssays representing the averaged values across members of the replicate set. Further, these ReplicateDefs can be used to describe TreatmentDefs which define the levels of the treatment and associated control ReplicateDefs. The TreatmentDef may reference a third type of PhysicalBioAssay that is derived from the ratio between the averaged values for the treatment replicates and the averaged values of the control replicates. |
| Column Information | ||||
|---|---|---|---|---|
| Column Name | Full Name | Data Type | Not NULL | Comment |
| archive_data_uri | Archive Data URI | char128 | false | The URI to the file-system directory in which data associated with this Physical BioAssay is archived |
| array_fk | Array | int | true | The chip or array used with this assay |
| pba_pk | Accession Number | serial | false | |
| provider_con_fk | Data Provider | int | false | the researcher that provided the array info it is important to destinquish between this and the rw_groupname because if data is imported from another DB then the owner of the data will not be the individual that submitted it. |
| Primary Key Information |
|---|
| Column Name |
| pba_pk |
| Foreign Key Information | |||
|---|---|---|---|
| Column Name | Foreign Table | Primary Key in Foreign Table | Foreign Key Type |
| array_fk | Array | array_pk | MANY_TO_ONE |
| provider_con_fk | Contact | con_pk | MANY_TO_ONE |
| Unique Column Information |
|---|
| Column Names |
| Index Information | |
|---|---|
| Name | Column Name |
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