Repository

BioUML repository (or simply repository) is the central BioUML data storage place. Basically everything you're working with in BioUML is stored in the repository. Repository has the hierarchical structure similar to file systems. In BioUML user interface repository tree is displayed in the repository pane.

Every item which appears in BioUML repository is called data element (in BioUML code it's the class implementing the DataElement interface). An important kind of data elements is data collection (in BioUML code it's the DataCollection implementors). Data collection is the data element which can store another data elements. So practically every expandable folder you can see in repository pane is data collection. Please note that for some collections their children are hidden from the repository tree. For example, tables are collections of their rows, but rows aren't shown in the tree.

On the top level repository consists of several root folders. The most common ones are:

• databases: this data collection contains preinstalled or user-defined modules.
• data: this data collection contains user projects and public examples.
• analyses: this data collection contains predefined analysis methods, workflows and so on.
• users: this data collection contains available user groups.

Other collections may exist depending on BioUML installation and perspective selected. Usually each repository pane tab displays single root collection. Some technical root collections might be hidden from user interface, but accessible programmatically (via JavaScript and so on).

Every data element in the repository is identified by complete name or path, which contains a slash-separated chain of collections you have to visit in order to find the given element. For example, analyses/Methods/Data/Filter table is the path to Filter table analysis method. To find it, you should navigate to 'analyses' root collection, find 'Methods' collection inside it, then 'Data' collection and finally 'Filter table' element.