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  • Annotating and registering data with the Annotation Tool
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Make sure to follow the instructions on how to prepare your data for registration first.

Your administrator might have created a desktop shortcut to the Annotation Tool for convenience; if this is not the case, use Windows Explorer to locate the executable: by default, the Annotation Tool is installed in C:\oBIT\obit_annotation_tool. Please ask your administrator if you cannot find it.

AnnotationToolAdmin is used to set up the Annotation Tool on current machine, but can only be run by a local administrator. 

AnnotationToolUpdater is a tool that runs in the taskbar and can be used to check for and download Annotation Tool updates.

Double click on the AnnotationTool icon to start the Annotation Tool.


Even before the Annotation Tool main window is displayed, you are asked to login to openBIS. If the login succeeds, the Annotation Tool is started.

Annotation Tool explained

The main window of the Annotation tool is broken down into several panels that allow for inspection and annotation of the acquired datasets. The idea is to ensure that only consistent and annotated experiments can be sent for registration to openBIS.

In the following, we will discuss the various components of the Annotation Tool.

The Annotation Tool scans your user folder (e.g. D:\toOpenBIS\pontia) and displays the experiments in the data viewer ( 1 in a familiar form (here as an example for the BD LSRFortessa flow cytometer).

Each element in the data viewer tree has metadata associated, that is displayed in the metadata viewer ( 2 ) upon selection.

The Annotation Tool also performs validation on the content of the incoming folder, and lists all invalid datasets in ( 3 ); you must fix or remove any invalid datasets before registration is possible.

The openBIS panel ( 4 ) displays all entities you are permitted to access (currently, besides read-only viewing operations, the openBIS viewer also allows you to create new projects and tags).

openBIS currently does not yet support sub-projects. To circumvent this limitation, experiments can be tagged ( 5 ).

In the Annotations panel ( 6 ), you can associate additional metadata to the various experiments, and choose the target openBIS projects for registration. The selected target project can be associated to current experiment only, or to all projects at once.

When metadata is ready, you can clicks on Send to openBIS ( 7 ) and all data and associated metadata is sent to the the openBIS Data Store Server for registration.

At this point, you can log out and go home.

Once the data is registered in openBIS, you can work with it further.

Adding attachments

Files of type .pdf, .doc(x), .xls(x), .ppt(x), and .csv can be registered as attachments to experiments by copying them into the Experiment folder of a dataset.

Managing invalid datasets

Unexpected files or folder (or folder structures) are listed in the Invalid Data table.

Right-clicking on an entry gives you the following options:

  • Show in Windows Explorer: The file or folder will be selected in Windows Explorer and you can fix it manually.
  • Move to...: a file dialog will open and you can choose where to move it to. 
  • Delete: the file or folder will be deleted.

openBIS operations

The openBIS panel allows for some additional operations.

Creating a new project

Right-clicking on a space name offers the option to create a new project and a new tag associated to that space.

When choosing Create new project, an input dialog is shown for the new project name.

Choosing a default target project

A project can be made the default target for registration by right-clicking on the project name a selecting Set as default target project.

From next data scan, all experiments will automatically be assigned to the selected project.

Tagging

Creating new tags

New tags can be created in one of two ways. Right-clicking on a space name offers the option to create a new tag (and a new project, see Creating a new project above).

Alternatively, the Create new tag... button performs the same function.

Tag creation is similar to Project creation. You must specify a name and optionally a description and the tag will be registered in openBIS and added to the list for you to choose from.

Assigning tags to a project

One or more tags can be assigned to an Experiment by choosing them in the Tags viewer and dragging them to the Experiment tags field in the Data editor.

If more than one Experiment exists in the data viewer, you can decide whether you want to apply the tag(s) to just the selected one or all.

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