openBIS Importer Toolset
Abstract
The openBIS Importer Toolset (oBIT) is a set of tools to streamline registration of acquired data and metadata into openBIS and extend openBIS via custom views and apps for working with data.
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Description
openBIS is an extensible, open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. It enables users to collect, integrate, share, publish data and to connect to data processing pipelines.
oBIT is a tightly integrated collection of tools that allows for the semi-automated, semi-unsupervised registration of annotated datasets into openBIS directly from the acquisition stations.
Flow chart
The initial goal of the openBIS Importer Toolset was to offer optimized workflows for registering data into openBIS from shared acquisition stations. With time, it is also progressively extending openBIS itself with custom data viewers and server-side core plug-ins packaged into two official openBIS core technologies. Soon, two new official openBIS core technology for flow cytometry and microscopy will be released along with openBIS.
The openBIS Importer Toolset relies on two components that are installed and configured on the acquisition machine: the Annotation Tool and Datamover as a Windows Service; and on a third one: a hardware class-specific openBIS dropbox core plug-in that is on the remote data store server.
Data to be registered is directly saved or exported into a specified user folder at the end of an acquisition round.
When the data is ready to be registered, the user launches the Annotation Tool that scans the data and allows the user to add custom and optional annotations. Data and metadata in the form of an XML file are then moved to a folder that is monitored by Datamover, a background service that checks for new data periodically and moves it to the dropbox folder on the data store server after a validation step.
On the data store server (one of the two server components of openBIS), a dropbox core-plugin registers the data to openBIS using the annotations provided in the XML file.
Most of this is transparent to the user, who only needs to interact with one tool: the Annotation Tool.