Help & Documentation

Parameters

There are various types of parameters. Most common are either “simpleParameter”, where single-value measurement data is submitted, or “procedureMetadata”, where information about experimental conditions or equipment used during the experiment.

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

Data parameters are annotated to Mammal Phenotype Ontology terms to facilitate data sharing. MP terms can be associated with biomedical ontology terms to aid in the identification of phenotypic mouse-models of human diseases.

Metadata

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.

Parameter name and version

The key part indicates the pipeline it is part of (IMPC), the procedure it belongs to (BWT – Body Weight), the id of this parameter (001), and finally the version of this parameter (001), IMPC_BWT_001_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.

The version is composed of a major and a minor version. 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.

Ontology annotation

Parameters with a tick for annotation will have their associated ontology terms used for annotating data. In IMPReSS, you can view the ontology terms associated to a 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].

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