You are here
When you click through to the Parameters of a Procedure or view its’ Protocol you will see a list of Parameters like in the figure below.
Figure 1: Parameters of the IMPC Body Weight Procedure.
The Parameters table shows information about each Parameter such as:
- Parameter Name and Key
The Key parts indicate the Pipeline it originates from (IMPC), the Procedure Type it belongs to (BWT – Body Weight), the id of this parameter (001), and finally the version of this parameter (001). There is no way to identify which version of the Procedure or the Pipeline it came from by its key because the same parameters can be found in different versions.
- Parameter Version
This is composed of a major version and minor version parts. When a Parameter is first created it starts as version 1.0. If the Parameter has had a minor change happen to it, such as a spelling correction, then the minor version is incremented, becoming 1.1. A major change leads to the creation of a new version of the Parameter with a new key such as IMPC_BWT_001_002 indicating that it is a new version, and the version will show as 2.0. It is important to keep track of which version of a Parameter (or Procedure/Pipeline) is being used in any Procedure to make sure parameters can be compared.
- Parameter Type
There are various types of Parameter but most are either "simpleParameter" where single-value measurement data is submitted, or "procedureMetadata" where information about experimental conditions or equipment used during the experiment. The type of the parameter is important for correctly structuring the XML that represents the data you send to the DCC. Here are the different types of Parameters:
- simpleParameter for single-value measurements
- procedureMetadata for single-value metadata
- seriesParameter for simple incremental measurements
- mediaParameter for image/video data
- seriesMediaParameter for incremental image/video data
- mediaSampleParameter for annotated image data
- ontologyParameter for values which are ontology terms
- Required For Upload
If a Parameter’s data must be submitted as part of the Procedure to the DCC, it is marked as required for upload.
- Required For Data Analysis
Some Parameters can influence the outcome of the rest of the data so when the data is observed and analysed it is grouped by the value of such Parameters that are marked as Required For Data Analysis. For example, the Parameter Grid Model is marked as Required For Data Analysis because data obtained with one type of grid will give different results to data obtained with a different type of grid, so the two sets cannot be comparable, and so the data must be split between data obtained using the HMGU plate and data obtained using a non-HMGU plate.
Parameters with a tick for annotation will have their associated ontology terms used for annotating data. To view the ontology terms you need to click the name of the parameter. High-throughput ontology annotation allows phenodeviants to be automatically annotated with an ontology based on their outcome, so if a significant number of mice with a particular mutation show an inability to grip the grid properly then they will be annotated with the ontology: Decreased Grip Strength [MP:0010053].
- Incremental Parameters
Incremental Parameters have more than one value submitted for them. If the Parameter is an incremental Parameter then this field will display one of two things – either it will mention the minimum number of simple repeats that need to be submitted for it or it will list defined incremental categories (1, 2, 3) that must be submitted.
- Parameter Options
If a Parameter has Options then the only allowed values that can be submitted for this Parameter are listed here. This ensures data consistency.
- Parameter Ontology Options
Ontology Options are like Parameter Option except the submitted values are ontology terms and more than one term can be submitted. Ontology Options are relevant to some types of data such as describing observations in the Gross Pathology Procedure.
- Derived Parameters
If this field is not empty then it is a derived Parameter. The field will display the formula used to calculate the value of this parameter based on the values of other Parameters. You are not required to upload values for this Parameter since the DCC do the calculation on their side but if you do submit a value it will be checked against the DCC-calculated version.
- Parameter Unit
The expected unit of the data submitted for the Parameter. If you find your data does not match the unit expected then you must convert it on your side before submitting it to the DCC
- Parameter DataType
This shows the expected data type of the submitted value.
- FLOAT is a real number such as 21.6
- INT is an integer or whole number such as 67
- BOOL expects a "true" or "false" value
- DATETIME allows for dates in the strict XSD/W3C format "YYYY-MM-DDTHH:MM:SSZ" or "YYYY-MM-DDThh:mm:ss+hh:mm", and in the default UTC timezone, regardless of your relative location
- DATE in the format "YYYY-MM-DD"
- TIME in the format "hh:mm:ss"
- IMAGE expects a static or moving image/video clip to be submitted
- TEXT is a data type which is used to capture words or other miscellaneous values
Clicking the Measured Parameters name hyperlink will take you to a page where you can view the parameter's associated ontology annotations, if there are any. Metadata Parameters are not clickable as there are no ontology annotations for metadata.