Processed data upload

Topics in this page:

• Start the upload process

• Interactive upload

  • Step 1: Add project-related information

  • Step 2: Check compound information in the registration

  • Step 3: Standardize processed data types

  • Step 4: Confirm standardized processed data

• Semi-automatic upload

• Automatic upload

Data files can be uploaded interactively, semi-automatically and automatically. The route of the upload is chosen by the software after checking the selected excel file for specific sheets. On this page you will read about the interactive and the semi-automatic upload. Please read the administration guide about automatic upload.

Start the upload process

On the Tasks tab click on the Add New Task button. A file-drop area is shown where you can drag & drop a file. Alternatively, click on the area to open a File Open window to browse in your computer's folders.

{info} Template file download

Under the drop area you find the download link to the easy-digest template file that enables you to use the semi-automatic and the automatic upload feature. Currently no user-defined template files can be subject for the auto-upload. An example template is available too, which shows a correctly filled in ready-to-go Excel file.

When the file is selected, the upload process is directed towards the appropriate path based on the presence of predefined sheets in the Excel file (see details below). If no required sheets are found in the file, you will be forwarded to the interactive upload process.

Interactive upload

Step 1: Add project-related information

Fill in the project-related form in the data capture panel providing the required and optional data as requested by the form.

Required fields are Project Abbreviation (Project Title is filled in based on your project selection), Task ID, Task Title and the Task Owner Group (if applicable). The Project Abbreviation has to be selected from a list of existing projects which has to be set up within Synergy. Contact your administrator if you don't find a matching project ID. These data is needed to identify the task precisely, so fill in carefully.

Filling in the Laboratory Notebook ID and Laboratory Notebook Page Nr/Link, personnel and date of the experiment is optional.

Click the Next step button to proceed.

{info} Requirements for the uploaded file

File and table format requirements

• the file format: Microsoft Excel Open XML file (file extension **.xlsx** )

• the processed data is found in the first sheet of the file

• the first column (Column A) contains the entity description (the ID of the compound used in a registration system)

• the first row (Row 1) contains information on the assay and parameter types allowing the user to interpret the data

• cells referenced by Row 1 and Column A contain the processed data

The uploaded file is checked for empty rows or columns, and will be removed during the upload process.

Step 2: Check compound information in the registration

All compounds will be matched for entity descriptions present in the compound registration database.

Entity statuses that do not match a registration system ID are highlighted in red at the top of table.

To include data to be uploaded, check the tickbox next to the compunds ID; to include all unregistered , select the checkbox in the header row.

In case you made only a typo in the compound's name, correct the Excel file and re-upload it.

Click the Next step button to proceed.

{primary} No registration action

Please note, that this action only marks the Assay data to be uploaded, the compounds will not be registered in the connected registration system.

Step 3: Standardize processed data types

You can standardize the processed data by assigning to it a combination of

• a protocol and

• a processed data result type

by choosing the appropriate values from the drop-down boxes of the data standardization panel.

You may ignore a column; the data for ignored content will not be uploaded. Click the eye icon next to the header of the column to toggle ignore/include.

Heading titles

1. The selected protocol's and parameter’s abbreviations are used to create a standardized heading title, in the form of [Protocol Abbreviation .ResultTypeAbbreviation]. In this step you will see the original content on the bottom and the standardized content on the top in the header of the data table.

2. Ignored : will be displayed in the upper section of the data table header.

If a value falls out of the expected range as defined by the admin, the lower section of the cell will display "out of range".

Click the Next step button to proceed after all columns have been mapped or ignored. Feedback and warnings

• Red highlighted columns warn you about attempting to standardize two columns identically in the same file. If you have multiple data columns that represent the same type of value from the same types of procedures and result type in the Excel file, consider splitting the Excel file and upload them separately. Alternatively, you can create multiple data upload tasks and ignore the columns in a pattern that will allow the population of all data from the original file.

• You may not proceed without mapping all columns. Clicking the Save as draft or Next step buttons will give you a warning.

Suggestion for speeding up standardization

If you standardized a particular phrase given as a header title in an Excel file, Assay will offer this standardization as default next time the same header title turns up. The user still needs to check if this standardization is correct, as t he suggestion is always based on the last standardization used for that particular header title.

Step 4: Confirm standardized processed data

You can reexamine here if everything is standardized as intended.

Clicking on the Confirm & Save button saves the task in the database.

By confirming the data, t he data in the task will be available for aggregation and search. You will be forwarded to the Tasks tab.

{info} CRO restrictions

A user assigned as a member of a CRO group will see a Submit button instead of a Confirm button. The uploaded task has to be reviewed and confirmed by an authorized user of the requester side.

Semi-automatic upload

If your opened file contains the specific file structure needed for the semi-automatic upload, your file will be processed and uploaded. If the upload went smooth and without problems, the Task tab will open up containing your last uploaded file in the list with Confirmed status.

The minimum information to induce semi-automatic upload is on the Task and the Processed Data sheet. Without these you will be directed to interactive upload.

Download the pre-filled template file here: template_example.xlsx

Automatic upload

Files from a shared folder (currently a Google Drive folder) can be uploaded automatically. All you have to do is to upload the data files (in the above mentioned template format) to the Drive folder set up by your system administrator. Please read more details in the Administration guide.