The checklist says "Is topology rooted or not?" but what one really needs to know is whether the root implied by the representation is known (or believed) to be the biologically meaningful root. That is, some representations are either unrooted or are documented to give no meaning to the representation-level root, so if that root is the "real" one this fact needs to be signalled. Similarly, @root=true on a node in NeXML does not imply that the specified node is a biological root.
The true root might even be known and known not to be the root of the tree in the representation, so the real question ought to be, "If known, which node is the biological root"? Or if you want to rule that out possibility, the question ought to be "Is the representation-level root the biological root"? yes/no/unknown. Or something like that.
The checklist says "Is topology rooted or not?" but what one really needs to know is whether the root implied by the representation is known (or believed) to be the biologically meaningful root. That is, some representations are either unrooted or are documented to give no meaning to the representation-level root, so if that root is the "real" one this fact needs to be signalled. Similarly, @root=true on a node in NeXML does not imply that the specified node is a biological root.
The true root might even be known and known not to be the root of the tree in the representation, so the real question ought to be, "If known, which node is the biological root"? Or if you want to rule that out possibility, the question ought to be "Is the representation-level root the biological root"? yes/no/unknown. Or something like that.