Measurement Edit
Excel file support
The data manager now supports measurement registration and updates with Excel files (*.xlsx).
Only requirement: metadata must be in the first sheet of your workbook.
To edit measurement metadata, start by navigating into the measurement summary view.
Once within the measurement summary view, measurements can be edited via the following steps:
- Select the tab containing the registered metadata of the domain of interest.
- Download the measurement metadata
- Prepare the edits of the downloaded domain specific metadata sheet
- Upload the edited metadata sheet via the edit measurement dialog
Additionally, within the measurement summary view you're also able to delete measurement metadata.
Project role
Should you not see the edit, deletion and download buttons, please make sure that you have been granted the "write" or "admin" role to the project by its owner or an admin!
Download Metadata
Proteomics
Start by selecting the Proteomics Tab within the measurement metadata tab sheet.
Press the "Download Metadata" button, which will download the metadata for all your proteomic measurements in a xlsx file.
Genomics
Start by selecting the Genomics Tab within the measurement metadata tab sheet.
Press the "Download Metadata" button, which will download the metadata for all your genomic measurements in a xlsx file.
Prepare Metadata
Proteomics
Start by opening the downloaded proteomics measurement metadata xlsx file containing the domain specific metadata sheet.
The xlsx lists the registered measurements according to their measurement Ids with the provided property values during the registration.
Fixed Properties
Specific measurement properties such as Measurement Id cannot be changed after a measurement has been registered. Cells of these properties are marked as grey, meaning changes to these cells will be ignored. Errors made within these cells require a deletion and reregistration of the measurement metadata in question.
Within this sheet make the necessary property changes for the measurements.
Finally, use your workbook directly (xlsx file) or export the sheet into a tab seperated UTF-16BE Unicode Text (*.txt) text file.
Notes: The "Instrument" column expects an ontology CURIE of the instrument. You can use our ontology search to find the CURIE
The "Organisation Id" column expects the full RoR Id URL of the organisation. Use the ROR registry search to determine the URL of the organisation RoR Id.
Finally, upload the exported text file into the data manager application.
Genomics
Start by opening the downloaded proteomics measurement metadata xlsx file containing the domain specific metadata sheet.
The xlsx file lists the registered measurements according to their measurement Ids with the provided property values during the registration.
Fixed Properties
Specific measurement properties such as Measurement Id cannot be changed after a measurement has been registered. Cells of these properties are marked as grey, meaning changes to these cells will be ignored. Errors made within these cells require a deletion and reregistration of the measurement metadata in question.
Within this sheet make the necessary property changes for the measurements.
Finally, use your workbook directly (xlsx file) or export the sheet into a tab seperated UTF-16BE Unicode Text (*.txt) text file.
Notes: The "Instrument" column expects an ontology CURIE of the instrument. You can use our ontology search to find the CURIE
The "Organisation Id" column expects the full RoR Id URL of the organisation. Use the ROR registry search to determine the URL of the organisation RoR Id.
Finally, upload the exported text file into the data manager application.
Upload Metadata
Once the measurement metadata has been prepared according to the domain specifications, the exported txt file can be uploaded into the data manager application.
To start the update process press the "Edit" button within the measurement summary view.
This will open the measurement edit dialog with which the edited metadata can be uploaded.
Within the dialog you are able to upload your measurement files either via clicking the upload files button and selecting the files of interest in your file system
or by drag and dropping the files into the dashed box saying "drop your files here".
Should you have uploaded one or more files by accident, you can easily delete them via a press of the cross icon next to their respective file names
File constraints
Please adhere to the file format and maximum file size outlined in the dialog. Currently, we support the txt, tsv or xlsx file formats with a maximum file size of 16Mb
The edit dialog will validate the provided metadata information and show invalid properties below the file name.
Once all metadata properties are valid, upload the measurement metadata files to the experiment via pressing the "Save" button on the bottom right of the dialog. The changed measurement metadata will be shown in the grid within their domain specific tab in the measurement summary view.
Delete Metadata
To delete measurement metadata, start by navigating into the measurement summary view.
Once within the measurement summary view, start the measurement metadata deletion process by selecting the measurements within the domain of interest.
Alternatively, can also select all measurements of a domain via a press of the checkbox within the column header.
You are also able to use the Search field above to filter measurements before selection. Keep in mind that changing the filter will reset the selection of measurements.
Domain Specific Selection
The selected measurements are reset if a different domain tab is clicked. Therefore, delete the measurements for each domain individually.
Afterwards, press the "Delete" button to start the measurement deletion. A dialog will open asking you to confirm the deletion and informing you about the number and domain of the measurements that will be deleted.
Press the "Confirm" button to trigger the measurement deletion.
If all measurements for a specific domain have been deleted, the domain specific tab will disappear as well until new measurements are registered.
Attached Raw Data
Keep in mind, that measurements can only be deleted if they have no raw data attached to them. Otherwise, you need to delete the raw data before the measurement can be deleted.