Wednesday, March 01, 2006
Generative Methodology Glass Bead Games
On the limits of the OWL standard à [184]
Reading material [1]
Reading material [2]
Reading material [3]
Summary of the discussion up to this point à [186]
On ontological modeling of biological expression
On Formal verses Natural systems à [206]
Hi Paul,
I think the point I am trying to make is that what we call pathways to the largest extent are artifacts created by humans to reduce complexity and be able to discuss complex phenomena.
Because of this, a solution for mapping pathways to each other is hard to get with OWL, as pathways will differ a little from each other and OWL anyways seems to have problems describing the structure of a relationship of three or more items to each other. Technically a mapping could approximately be achieved by comparing elements in the pathways, and maybe structural features.
Otherwise, it can be achieved by consent and agreement between the people defining them. I think that it is possible to come up with such an agreement, and that is where ontologies can be useful, as they formalize the process.
This is exactly why GO is so successful: GO does not represent the only, or best description of protein function. But it represents a common denominator which is accepted by many people, and thus can be used to compare statements about proteins created by many people.
As with GO, a repository of pathways, which could use BioPax as representation model, could work if there was someone editing and curating it, avoiding double submissions that only slightly differ, extending existing pathways according to the current state of knowledge, and keeping it consistent. Reactome seems to be operating like that, and would be a good example.
Progress is possible. Only for this special corner of our domain, OWL might not be the right tool. In general is as fine as many other things, I guess. So there are paths forward, or maybe even pathways...
Friendly greetings
Frank