Simple Assay Module

 

SAM is the module for the Generic Study Capture Framework that stores clinical measurement assays. Clinical measurements are simple measurements that typically consist of only one figure per sample per measurement. For instance, the blood glucose level of a certain sample could be one measurement within a clinical measurement assay.  We can use it for saving information about assays and sub-assays related to a given study. After creating a study with the Generic Study Capture Framework the user will be redirected to the Simple Assay Module for creating the assays and saving the data related to each assay.

Two essential kinds of information can be saved in SAM : the sub-assays and the assays. Two importers are available from this module for creating and saving the data related to the assays and sub-assays. See the importer's details bellow.

SAM Data Model

The Simple Assay Module has only four different domain classes: SimpleAssay, SimpleAssayMeasurement, SimpleAssayMeasurementType, and SimpleAssaySample. The classes are described below:

 

The UML graph:

 

 

 

 

The SimpleAssay attributes:
- name : the name of the corresponding SimpleAssay
- isNew : a boolean for defining if the simple assay is new or not
- externalStudyID : the ID of the study in which the simple assay is present
- externalAssayID : the ID of the sample in which the simple assay is present

The SimpleAssayMeasurement attributes:
- assay : the SimpleAssay related to
- type : the SimpleAssayMeasurementType related to
- sample : the SimpleAssaySample related to
- value : the actual value of this measurement

The SimpleAssayMeasurementType attributes:
- name : the name of the subassay
- sop :
- unit : the unit for the measurement
- referenceValues :
- detectableLimit :
- correctionMethod :
- isDrug : is the measurement a drug ?
- isIntake : is the measurement an intake ?
- inSerum : is the measurement in serum ?
- is New : is the measurement new ?

The SimpleAssaySample attributes:
- assay : the SimpleAssay related to
- externalSampleID : identifier of sample domain object in GSCF
- subject : the subject linked to
- startTime : the start time of the assay
- name : the name
- material : the material used for the assay
- event :
- info :

 

 

SAM importers

 

For creating and saving new assays and sub-assays to the Simple Assay Module's database, you can use two different importers: the assay importer and the sub-assay importer.

 

Sub-Assay importer

The user can create and add sub-assays to the database using the sub-assay importer. It is possible to import an Excel file or to enter or copy and past a tab delimited plain text directly into the text area shown in the importer. After that the user can create and save assay data.

The sub-assay importer is organized in three steps using a web flow:

1 - Import Data: you can either choose an Excel file or paste your data into the available text area. The added data will be parsed and the information needed will be extracted for creating and saving the data.

2 - Show Data: here the user will check the data and choose the corresponding fields for a correct import. If the parsing get wrong or if the user want to change any information he can do it here. Also we can define the different attributes for each sub-assays.

3 - Done: your data is saved into the database, you can visualize the created sub-assays from the menu selecting the item named "SubAssays List". The program will check the integrity of your data and if everything goes weal the data will be saved into the database. The program will check if all of the mandatory fields for a sub-assay are present and if the sub-assay already exists or not.

 

 

 

Assay importer

The assay importer is using the same architecture as the sub-assay importer. From there it is possible to add assay data after choosing the corresponding study and sample. Data can be saved using an Excel file or paste directly into the text area. A connection to a running GSCF version is needed here. Hidden from the user, the study and the sample information are fetched from GSCF using a REST communication process. See bellow for more information about the REST services.

The different steps for the assay importer

1 - Select Study: Select the study where you want to add assay data.
2 - Select Sample: Select the sample related to the study where you want to add assay data.
3 - Select Layout: Select the layout for the view. Two layouts are available here : the Sample layout or the Subject layout. The selection of the layout depend on the format of your data. If the first column contains the subject's names you have to choose 'Subject Layout' or if the first column contains the sample's names, you have to choose 'Sample Layout'.
4 - Input Assay Data: For the input the user can choose either an Excel sheet or paste the data into the available text area.
5 - Select Data: The parsed data is showed and the user can correct it if there is any error.   
6 - Show Data: Here the selected data is showed for a last time for checking, if everything is correct the data will be saved to the database by clicking the 'next' button.
7 - Done: Your assay is saved into the database, you can visualize it by clicking "Assays List". The program will check the integrity of the data. If the data already exists the user will be informed and asked to correct the input.