Assay Data such as Tm and ELISA values that are recorded in .csv or Excel files can be imported into Biologics and appended to your annotated sequences. This article describes how to import Assay Data and then Filter upon the results. Related Article: How do I filter my results?
The other videos in our Getting Started series may also be useful, linked here.
Jump to:
- Adding Assay Data
- How to Filter on added Assay Data
- Examples of Filtering on Assay Data
-
Troubleshooting Tips
Adding Assay Data
To add assay data into your results table, open a Biologics Annotator Result document in the Files table, click Add Metadata > Add Assay Data and follow the prompts to upload your assay data file.
Note that we only support Excel Workbook (*.xlsx). Excel 97-2003 Workbook (*.xls) and CSV (Comma delimited)(*.csv) type files.
To append the assay data into your results document, choose the columns to match the rows by in the dropdown for both the Biologics Annotator Result and assay data documents. In the following example, the rows will be matched on the "Name" column header of both 17 sequences Annotated & Clustered (Biologics Annotator Result document) and Llama VHH assay data.xlsx (assay data document).
Check the preview to make sure that the rows are matched correctly. To exclude the addition of a selected number of columns from your assay data, deselect the appropriate columns by clicking the check box of the column header. Once the options are set click the Add Assay Data button to add your assay data into the results table.
The imported assay data will be appended to the right end of the results table. To view the added assay data, scroll the table to the far right and the appended columns will be grouped under the assay data file name column header.
You can also jump to the Assay Data columns by navigating to the Assay Data section in Table Preferences and clicking the Focus Column button that pops up when mousing over a column heading:
Handy Tip: The Name Schemes feature can be used to extract parts of file names, such as Sample or Well ID into different columns in your result table. These Name Scheme columns can then be used as matching columns to match to a column in your assay data file.
Filtering on added Assay Data
The Biologics Annotator Result table with added assay data can be filtered using SQL search queries. You can right click on any assay data value and select "Filter" to quickly add it to the filter bar.
You can then edit this filter using standard SQL syntax or add more filters to further narrow down your search space. See our main article Filtering your sequences for examples of how the syntax works.
You can also type in your own custom filters using this format:
"FileName:Column" comparative operator
Once you have inputted your filter syntax, hit Enter or click the Filter button.
Examples of Filtering on Assay Data
To search for sequences that meet the condition of having a Solubility level of more than 100 mg/mL, use an SQL filter query in the form:
"310718 Isoelectric and solubility:Solubility (mg/mL)" > 100
In the example below, 310718 Isoelectric and solubility is the File name, Solubility (mg/mL) is the field we are filtering on, > is the operator, and 100 is the value.
Note that single quotes are only used for column type STRING.
To learn more about filtering please refer to the following article.
Troubleshooting Tips
We recommend avoiding newline, tab, or return characters in column headers. The characters . (fullstop) : (colon) / (forward slash) \ (backslash) and ` (back tick) act a little odd but we do handle them. There are more details below.
White space characters in column headers:
Characters that will cause import issues include whitespace characters such as tab, newline, vertical tab, form feed and return.
It is okay to use regular spaces in column names. These will import correctly, however you will need to make sure that your header name is surrounded by single quotes in the filter box when filtering on that column. This is handled automatically when you add a filter by right clicking on a table cell.
Special characters in column headers (Excel files):
Some characters in assay data or cherry pick headers get replaced with underscores behind the scenes. These characters are:
. (fullstop) : (colon) / (forward slash) \ (backslash) and ` (back tick) .
You can still use these characters in all excel file headers, EXCEPT for the match column.
Using these characters will affect syntax when filtering on the affected columns. For example I have an assay data column called HEK Titer (mg/L) in the group Biophysical Assays . In the filter it is represented in the format [‘ASSAY_DATA_Group_Name:Column Name’]
[‘ASSAY_DATA_Biophysical_
where ASSAY_DATA_ is a standard prefix for assay data columns, and the square brackets [] are standard to show that you are referring to a column name.
As you can see above, spaces in the column group name (file name) also get replaced with underscores.
Special characters in column headers (CSV files):
Some non-whitespace characters will also cause an import issue with CSV file headers. These characters are:
. (fullstop) : (colon) / (forward slash) \ (backslash) and ` (back tick) .
Hidden Columns and other Excel formatting
Generally Biologics ignores any complex Excel cell formatting. Hidden columns are added by default. You can unselect specific columns in the Add Assay Data options if you don't wish them to be imported.