All of these structural aspects of an organisation can, like the organisation itself, be addressed and involved in workflow in the same way as a trust group, or member of a trust group. In fact every concept (node) in the Ontology is a trust group that has members and a direction it's evolving towards.
This structure can change according to the needs of specific groups, for example, an individual member or project will most likely not require separate departments. And in some cases there can be more appropriate words for the structural categories, for example, in the context of Self organisation, the category that's normally called a "department" is called "area of focus". Groups can use splitting & merging processes to change the granularity or diversity of an operating system "in the field".
Organisations have members, resources, roles, departments, projects, tasks and activities amongst many other kinds of records and aspects of structure. They also have some key documents such as a charter, a manifesto, a best practices document and an alignment statement.
The standard "top-down" method of organisation is showing itself to be very flawed and inadequate. At the project management scale it's resulting in many failed or stagnant projects, and for those that do succeed, they do so only far beyond the original budgets and time-lines more often than not. At the large-scale of nations and the planet the top-down system is resulting in corruption, extreme inefficiency and devastation of the environment.
A new structure is emerging which has been called many names such panarchy, holacracy and bottom-up. This structure results in efficiency, fairness and flexibility. At Organic Design we talk about it in our manifesto, and we see it emerging in literally thousands of internet projects around the world. These principles are seen emerging in the new "Agile" project management paradigm, and are even starting to become used at the scale of nations.
Soon this method of organisation will crystallise into an Internet standard so that any projects, organisations and societies around the world can work in a common way allowing widespread alignment to occur.