The Alternative Pipeline contains the same procedures as the standard pipeline without the constraint on when the procedure should be performed. It is intended for capturing data on animals that cannot continue on the standard pipeline due to welfare issues. Control data is not required but can be submitted. These animals are expected to have submissions to the Welfare procedure with an appropriate Welfare Status and after the date for the Welfare procedure all data should be submitted to the Alternative Pipeline. This data will not undergo the standard QC process.
A Parameter that has Annotation ticked means that an ontology annotation will be automatically associated with the data submitted for a Parameter if the data is found to be significantly different when compared to the baseline. Automated annotation of data is required for high-throughput phenotyping.
Data Coordination Center. Data from mouse experiments will be uploaded to and stored in the DCC. No data is submitted to IMPReSS. Published data will be displayed on http://www.mousephenotype.org.
A derived parameter is one that is calculated using the values of other parameters. For example, Respiratory Exchange Ratio is calculated by dividing the parameter "Carbon Dioxide Production" by "Oxygen Consumption". The formula used to calculate a derived parameter is shown on IMPReSS.
International Mouse Phenotyping Consortium. Please visit http://www.mousephenotype.org/.
International Mouse Phenotyping Resource of Standardised Screens. IMPReSS is a database containing the definition of experimental Procedures done on mice in order to identify phenotypes arising from targetted gene knockouts. Experimental definitions and the parameters measured in the experiments can be viewed on this website and can also be obtained from the IMPReSS database using its Web Service machine interface (see Web Service). IMPReSS does not receive or display data from experiments. Experimental data should be submitted to the DCC (see DCC).
If a parameter requires multiple readings to be obtained then it is Incremental. There are two types of increments measured in IMPReSS - simple repeats and defined increments. A simple repeat is taken any number of times but a minimum number of readings need to be obtained for the data to be accepted. Defined increments are measurements that must be taken at specific intervals such as t=0, t=15, t=30, t=45, t=60 seconds.
If a Procedure is marked as Mandatory then it must be submitted to the DCC. If it is not marked as Mandatory then it is optional. Optional procedures are not required to be submitted but it is recommended to submit them.
A Parameter that has Media ticked means that an image or video clip can be submitted with the data.
A Metadata parameter is not for collecting experimental values but for collecting information about the conditions the experiment was done under or about the equipment used. Equipment Manufacturer, Experimenter ID and Period Of falting are examples of Metadata Parameters.
If the results of an experiment or observation can be defined into an enumerated set of values then these can be submitted as Option values. e.g. Yes/No.
A parameter is a measurement obtained during an experiment. Also see Parameter Type. Most parameters are measured parameters e.g. Body Weight. Some Parameters are Derived (see Derived Parameter) and some are Metadata (see Metadata Parameter). A Parameter's value needs to be of a certain data type like FLOAT (floating point number like 30.6) for Body Weight, and they can also have a unit, e.g. g (grams), if necessary. A parameter can be optional or required for upload (see Req. Upload). Optional parameters do not need to be submitted when sending data to the DCC but it is recommended to capture them. A parameter can have enumerated values submitted for it if it has Options (see Option). A parameter can also have multiple values submitted for it if is an Increment parameter (see Increment). Media such as images or video can also be submitted as part of the data submission if the Media tick is present (see Media).
Parameter Data Type
The data type of a parameter in IMPReSS can be any one of TEXT, INT, FLOAT, BOOL, IMAGE or DATETIME. The parameter data type will aid in the valid comparison of data and the automated validation of submitted data so if we expect a floating point number and we are given a boolean then the Data Wranglers can notified about the error and investigate it.
The type of a parameter is either Measured (a measurement/observation), Derived (requiring other measured parameters to calculate its value) or Metadata (data providing information about experimental conditions or the equipment used). Metadata is used to ensure that comparison across different datasets is consistent across equipment, experimental conditions and the environment the experiment was conducted in.
A collection of Procedures (experiments) that need to be done to the mice in a defined sequence.
A procedure is an experiment that is done during a certain week and in the way defined in the Protocol (see Protocol).
The definition of how a Procedure (experiment) should be carried out as well as what parameters should be measured.
Quality Control is an important part of ensuring that data submitted to the DCC is valid. There is an automated processing pipeline and a manual pipeline where data will be statistically analyzed and verified by Data Wranglers.
See Required For Upload.
Required For Data Analysis
Only Metadata Parameters are flagged as Required for Data Analysis. Metadata Parameters which can significantly alter the measurements of a Procedure are set to Required For Data Analysis, but if the parameter is not Required For Upload then you are not required to submit data for it, though this is recommended. If a parameter is set as Required For Data Analysis then the data will automatically be split by it to identify if the difference is significant when viewing data in the DCC.
Required For Upload
If a Parameter has a tick for "Req. Upload" then it must be submitted to the DCC as part of the data submitted for the Procedure or it will not be accepted. If there are valid reasons for missing data then this can be handled separately. Some parameters are optional. Optional parameters do not need to be submitted when sending data to the DCC but it is recommended to capture them.
IMPReSS has a RESTful web service machine interface. The API can be accessed here: http://www.mousephenotype.org/help/impress/