The BioUML repository (or simply repository) is the central BioUML data storage place. Basically, all the data you work with in BioUML is stored in the repository. The repository has a hierarchical structure similar to file systems. In the BioUML user interface the repository tree is displayed in the repository pane.
Every item that appears in the BioUML repository is called data element (in the 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). A data collection is a data element which can store other data elements. So, practically every expandable folder you can see in the repository pane is a data collection. Please, note that for some collections their child elements 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 the 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.
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 the Filter table analysis method. To find it, you should navigate to the 'analyses' root collection, find the 'Methods' collection inside it, then the 'Data' collection and finally the 'Filter table' element.