chado.mage Tables
| Table / View | Referenced | Foreign Keys | Columns | Type | Comments |
|---|---|---|---|---|---|
| acquisition | 4 | 3 | 7 | Table | This represents the scanning of hybridized material. The output of this process is typically a digital image of an array. |
| acquisition_relationship | 0 | 3 | 6 | Table | Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this. |
| acquisitionprop | 0 | 2 | 5 | Table | Parameters associated with image acquisition. |
| arraydesign | 3 | 5 | 18 | Table | General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns). |
| arraydesignprop | 0 | 2 | 5 | Table | Extra array design properties that are not accounted for in arraydesign. |
| assay | 7 | 4 | 10 | Table | An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization. |
| assay_biomaterial | 0 | 3 | 5 | Table | A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays). |
| assay_project | 0 | 2 | 3 | Table | Link assays to projects. |
| assayprop | 0 | 2 | 5 | Table | Extra assay properties that are not accounted for in assay. |
| biomaterial | 7 | 3 | 6 | Table | A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table. |
| biomaterial_dbxref | 0 | 2 | 3 | Table | |
| biomaterial_relationship | 0 | 3 | 4 | Table | Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance. |
| biomaterial_treatment | 0 | 3 | 6 | Table | Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value). |
| biomaterialprop | 0 | 2 | 5 | Table | Extra biomaterial properties that are not accounted for in biomaterial. |
| channel | 2 | 0 | 3 | Table | Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one). |
| control | 0 | 3 | 8 | Table | |
| element | 3 | 4 | 5 | Table | Represents a feature of the array. This is typically a region of the array coated or bound to DNA. |
| element_relationship | 0 | 3 | 6 | Table | Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance. |
| elementresult | 2 | 2 | 4 | Table | An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit. |
| elementresult_relationship | 0 | 3 | 6 | Table | Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance. |
| magedocumentation | 0 | 2 | 5 | Table | |
| mageml | 1 | 0 | 3 | Table | This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables. |
| protocol | 6 | 3 | 9 | Table | Procedural notes on how data was prepared and processed. |
| protocolparam | 0 | 3 | 7 | Table | Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration. |
| quantification | 4 | 4 | 8 | Table | Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures. |
| quantification_relationship | 0 | 3 | 4 | Table | There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where. |
| quantificationprop | 0 | 2 | 5 | Table | Extra quantification properties that are not accounted for in quantification. |
| study | 3 | 3 | 6 | Table | |
| study_assay | 0 | 2 | 3 | Table | |
| studydesign | 2 | 1 | 3 | Table | |
| studydesignprop | 0 | 2 | 5 | Table | |
| studyfactor | 1 | 2 | 5 | Table | |
| studyfactorvalue | 0 | 2 | 6 | Table | |
| studyprop | 1 | 2 | 5 | Table | |
| studyprop_feature | 0 | 3 | 4 | Table | |
| treatment | 1 | 3 | 6 | Table | A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling. |