[Ontology-editors] Abductive reasoning

[Chris Mungall]

This came up on one of the trackers. Most of the reasoning we do (for  
checking parentage etc) is deductive. However, abductive reasoning has  
proven useful too. Mike has a paper on this.

The difference between deductive and abductive reasoning is explained  
nicely here:

http://en.wikipedia.org/wiki/Abductive_reasoning

Deductive reasoning is watertight. The OE reasoner performs deduction.  
It doesn't do abduction yet. For some of the xps (notably the  
regulation xps) I perform the additional abductive reasoning step  
outside oboedit.

Example of deduction. Given 3 assumptions:

[A1] regulation of A = any process that regulates A
[A2] regulation of B = any process that regulates B
[A3] A is_a B

The following fact is entailed:

[A4] regulation of A is_a regulation of B

Example of abductive reasoning. The 3 stated facts:

[A1] regulation of A = any process that regulates A
[A2] regulation of B = any process that regulates B
[A4] regulation of A is_a regulation of B

then A4 has possible explanation:

[A3] A is_a B

Note that A3 does not *necessarily* hold (to assume so would be a  
logical
fallacy as the wikipedia page suggests). However, with GO xps I  
believe it
holds enough of the time to make this a useful heuristic (David and  
Tanya
can confirm). For example, if the ontology has A1,A2 and A4 but not  
A3, we can make a pretty good bet that A3 should really be there.

Context:
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2087283&group_id=36855