Monoclonal antibodies (mAbs) are typically sourced in part from an animal (or human) that has been challenged with an antigen, the process of creating mAbs includes fusing these cells with additional myeloma cells. This makes them different from antibodies taken directly from a subject, such as via a sera sample. MAbs are considered distinct from that initial test subject. A particular cell line may also be tested more than once, sometimes after significant time has passed and the mAbs are now generations removed from the initial parent cell(s). The usual process of filtering by subject characteristics is not applicable to this type of data in a DataSpace.
There are two areas where data derived from assaying monoclonal antibodies (mAbs) can be incorporated into and viewed in the DataSpace application: on the "Learn About" page with other assays, and on a separate tab.
When the DataSpace contains MAb Assay data, click Monoclonal Antibodies to see the grid.
The mAb summary grid aggregates statistics for all mAb assay records for each mAb and mixture containing a mAb. There are three categories of columns in the grid:
Learn more about filtering below.
Hover over any column of data to reveal the (Filter) icon in the header. Click to set filters using checkboxes, or use the search box to narrow the list.
The static value columns (MAb/Mixture, Donor Species, Isotype, HXB2 Location, Antibody Binding Type) offer two lists when there are values both in and out of the current selection. For example, filtering the isotype column might look like this:
When you filter any one of the columns providing distinct count values, you see a panel for selecting among the other count column values simultaneously. For example, filtering the Viruses column looks like this:
The geometric mean Curve IC50 column filter offers a set of ranges of values as shown here:
After applying a few grid filters, you will notice that the filter panel on the right shows counts different from the original set of mAbs (inset on the left of this image):
Click Clear in the MAb filter panel to restart filtering from the full set of mAbs available.
When you have selected the subset you want, you can click Save to save this set of filters for finding this subset of mAbs. To learn more about saving groups, see the documentation for saving subject filters. Note that MAb filter groups and Subject filter groups are saved independently. You can only replace a MAb group with another MAb group.
When you have saved groups, you will see them on the home page of the DataSpace above any publicly shared Curated groups.
You can export unaggregated and filtered MAb data in either CSV format or Excel workbook format. Above the MAb Data grid, click either Export CSV or Export Excel.
Selecting rows prior to export is optional. If no rows are explicitly selected, all columns and rows are included in the export. If a subset of rows are selected, only data from these rows are included.
The Excel export includes the following sheets.
R reports for MAb data are created in LabKey (outside the DataSpace application). Up to 2 reports can be configured to show as buttons directly in above the Monoclonal antibodies grid.
An administrator or developer creates R reports for MAb data.
library(Rlabkey)
if (!is.null(labkey.url.params$"filteredKeysQuery")) {
labkey.keysQuery <- labkey.url.params$"filteredKeysQuery"
cat('Query name for filtered unique keys: ', labkey.keysQuery)
uniquekeys <- labkey.selectRows(baseUrl=labkey.url.base, folderPath=labkey.url.path, schemaName="cds", queryName=labkey.keysQuery)
cat('nn', 'Number of unique keys: ', nrow(uniquekeys), 'nn')
cat(length(names(uniquekeys)), 'Columns for unique keys:n')
names(uniquekeys)
} else {
print("Error: filteredKeysQuery param doesn't exist")
}
if (!is.null(labkey.url.params$"filteredDatasetQuery")) {
labkey.datasetQuery <- labkey.url.params$"filteredDatasetQuery"
cat('Query name for filtered dataset: ', labkey.datasetQuery)
filtereddataset <- labkey.selectRows(baseUrl=labkey.url.base, folderPath=labkey.url.path, schemaName="cds", queryName=labkey.datasetQuery)
cat('nn', 'Number of filtered data rows: ', nrow(filtereddataset), 'nn')
cat(length(names(filtereddataset)), 'Columns for dataset:n')
names(filtereddataset)
} else {
print("Error: filteredDatasetQuery param doesn't exist")
}
After creating your R Reports, notice the reportId shown in the URL (%3A represents the : symbol). Shown here, the report ID is 35:
Reports must be saved as Shared with all users to be available to DataSpace users.
Using module properties, an admin configures up to two R reports to display as buttons above the MAb grid.
When you return to the DataSpace application, you will see buttons for the two reports shown above the grid on the Monoclonal Antibodies tab. Use filtering as needed, then select the rows to plot. The box in the header is used to select all rows. Click one of the buttons to generate the report on the selected rows.
Viewing the report, click the button to return to the grid. Within this report, there are multiple tabs to view.
Another tab within the same report shows the curves for a specific MAb, with data in a grid below.
Pharmacokinetic (PK) data for mAbs can be plotted in the DataSpace using the PK MAb assay and a "Study hours" time dimension. PK data is often gathered over short intervals after infusion of a patient.
To plot PK data:
On the Learn About page, use the MAbs tab to see details about the monoclonal antibodies included in the DataSpace.
You can also click the Assays tab and scroll to see monoclonal antibody assay data that is available.
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