PUMAdb : Experiment Annotation Help
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Related Help Documents
- Procedural Details Batch Procedure: Describes how to enter procedural details into the database for multiple procedures.
- Experiment Sets: Information about the tools available in PUMAdb to annotate experiment sets.
- Protocols: Information about protocol entry and editing.
Experiment annotation in PUMAdb allows users to enter details of a sample's history into the database. This may include the details of the biological samples that were used in the experiment, how the samples were processed, or how they were analyzed.In PUMAdb, experiments are annotated in a hierarchical fashion: first they are assigned to Experiment Types, then the whole process of how the experiment was performed is broken up into individual steps (called Procedures), and finally the details of each step is captured in one of two ways: either as a free text description (Protocols) or as a collection of Parameters and their values. Together, the experiment type, procedures and parameters create a framework to capture the details of how an experiment was performed, which are represented by the values of the parameters.
Experiment annotation can be entered for a single experiment (from the main page follow: 'Advanced Search' -> 'Display Data' -> 'Edit' experiment icon -> 'Associate Procedural Information'), or for a batch of experiments (from the main page: Enter Procedural Information).
Experiment Types describe major types of microarray studies, such as Chromatin IP or Expression (Type I). Each experiment type is modeled as an ordered set of procedures, e.g. Expression (Type I) contains the procedures:You can display the currently available List of Experiment Types from the PUMAdb main page.
- 1, Biological Sample
- 2, Growth Conditions
- 3, RNA Extraction
- ...
Experiment Types are created by PUMAdb curators. If you are doing a new type of experiment, please contact them at array@princeton.edu.
Procedures describe the general steps that are performed during a microarray experiment, such as growth conditions, hybridization conditions, the biological sample itself, etc. The currently available List of Procedures can be accessed via the PUMAdb main page. The actual details of a procedure can be entered into the database either as a collection of parameters - together with their values - or as a free text description of the procedure, a protocol.Procedures are created by PUMAdb curators in cooperation with users. If you need a new procedure, please contact curators at array@princeton.edu.
The details of how a procedure was performed is entered in the database as a list of parameters and their values. The parameters are part of the general model of an experiment, while the values represent how the experiment was actually performed. Examples of parameters in the procedure hybridization, e.g., include temperature, hybridization date, duration, etc.The currently available List of Parameters can be accessed from the PUMAdb main page.
If you need a new parameter, that please contact the PUMAdb curators at array@princeton.edu.
In addition, parameters are also used for annotating sets of experiments. Parameters existing within an experiment type form a pool of experimental factors available for annotating experiment sets. (See PUMAdb Help: Experiment Sets for more details on sets.)
Protocols are free text descriptions of procedures (see the separate page for PUMAdb Help: Protocols for more details). Protocols are an alternative to parameters and their values for capturing details of a procedure.Protocols can be created by you: Enter Protocol and you can list them: List Protocols from the PUMAdb main page.