How to annotate HCS data

Hi,

I would like to be helped regarding the following.

I would like to know HOW can be added columns to an existing table
and once the column is added how can be automatically be filled by data
according to what is on the same row of another specific column (which
can be different among different rows).

As an example, I have data obtained from analysis of high content
screening images (a lot of data points with for example values of cell
area, cell intensity, nuclear area, nuclear intensity, etc for each
analyzed cell) and for each data point a well column and row is
indicated. I would like to add a column for example with the title
treatment, another with the title cell type, another with the title
concentration, another with the title time, etc... which should change
their values for each row (according to the column and row indicated in
the columns row and column). Can I somehow
provide the information about what is each column and row via a template
in excel that will serve as guide for adding the values to my original
table?

How can be done it alternatively in automated way using KNIME.

Please give me detailed instructions.

Thanks and regards,

Leo

Hi Leo, Let me try to answer you question before the HCS people start jumping in. For me it sounds like basic KNIME data preprocessing where you can use for example the Rule Engine, Constant Value, Java Snippet, etc. node to append new columns. Furthermore, KNIME can read XLS sources directly and process them of course. If you provide us with a more detailed example we might be able to help you with your workflow. I also would like to mention our learning hub and YouTube channel as a good starting point.

Hi Leo,

I agree, this seems to a basic KNIME task.

Anyhow, we created some of the HCS nodes to do exactly what you would like to do (as far as I understood) with only a few nodes and without reshaping data in between.

I saw, that our example workflow for the HCS-Tools got lost somehow. I will provide a new one soon but I can already send you an example via email if you like (niederle #AT# mpi-cbg.de).

 

Dear all,

Please find attached the file that needs to be annotated and the file that could serve as a template for defining how to annotate. I will appreciate whether somebody can send me a workflow showing how to automatically manipulate the "example to be annotated.csv" file to add to it the corresponding columns, filling each of their rows as established by the relation between well and annotation in the auxiliary file "example of template for annotation.csv".

Thanks and best regards!

Leo 

Hi Leo,

I created a little workflow which does what you need (hopefully). I've attached the workflow. To annotate the data I created an Exel file with a layout sheet which follows a certain formatting (described in the help of the nodes "Join Layout"/"Load Layout"). You can find it in the "data" section within the Zip archive.

The KNIME-basic-solution would be as simple as this solution. The advantage of using the HCS-nodes is that it's pretty easy to design the layout file. Whatever you want to annotate you can put as several layers in a plate format (in you case layers are: Status, Compound, Cells). You would not need to bring it to a format you provided as template. You can use any Excel file as long as the layout sheet follows the formatting.

Just contact me if there are any questions left!

Antje

Dear Sir,

I appreciate your help.

I have tried your workflow but it seems that I need some plug ins that are not installed in my KNIME. Would you help me guiding me how to install them? Where can I find them?

I have made a search and I found a lot of plug ins and I'm very confused about which ones are those I need.

Nevertheless, what I found I also don't know how to download and install.

Thanks and best regards,

Leo

Hi Leo,

yes, you need to install the HCS-Tools plugin.

From Help > "Install New software" select the following update site:

Trusted Community Contributions - http://tech.knime.org/update/community-contributions/trusted/2.9/

Expand: Bioinformatics & NGS

Select HCS-Tools

and follow the installation process.

Does it help?

Hi,

Before I saw your message I went to File>Install KNIME extensions.

Then I selected all and installed.

I think it worked. I need to check the output.

Let me know if anyway I need to do what you said in Help or if it is enough/the same what I did in File.

Thanks and regards,

Leo

Hi Leo,

the way you did it might have installed a lot of extensions you won't need. But theoretically it should work now :-)