Guidelines for new Biological Processes
Out of scope
- Processes, functions or components that describe mutants or diseases: e.g. "oncogenesis" is not a valid GO term because causing cancer is not the normal function of any gene.
Beginning and end
Every process should have a discrete beginning and end, and these should be clearly stated in the process term definition.
Collections of processes
The biological process ontology includes terms that represent collections of processes as well as terms that represent a specific, entire process. Generally, the former will have mainly is_a children, and the latter will have part_of children that represent subprocesses. Also see "is_a or part_of" below.
is_a or part_of
To determine whether a process term should be an is a or part of child of its parent, ask: is an instance of the child process an instance of the entire parent process? That is, does the whole process, from start to finish, take place? If yes, the child is is a; but if the process is only a portion of the parent process, the child is part of.
Draft guidelines Metabolic process should specify primary inputs and outputs, as appropriate.
- metabolic process: x metabolic process has primary input or output some x
- biosynthesis: x biosynthetic process has primary output some x
- catabolic process: x catabolic process has primary input some x
In cases when there are more than one pathway, we additionally have a relation 'has participant' or 'has intermediate', (or sometimes the pathway differs by the input or the output.)