OBO-Edit:Reasoner Benchmarks

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Revision as of 12:51, 16 November 2008 by Cjm (talk | contribs) (→‎Results)
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OBO-Edit Native Reasoners

oboedit_fcr

OBO-Edit Forward Chaining Reasoner. Fast, but only uses the following rules:

  • Transitivity
  • Propagation over/under is_a
  • Intersection_of

John wrote this first in OE1, and then abandoned it. Can still be used for so-xp, and is suitable for certain purposes such as finding trivial redundancies by transitivity, but not recommended in general

oboedit_lpr

LinkPileReasoner (LPR). Successor to FCR.

Rules:

BUGS: there are certain edge cases involving sub-relations and transitivity that do not work. This bug was discovered after John left. The code is difficult to maintain so this reasoner will eventually be abandoned in favour of the RBR (Developer notes: this appears to be due to the fact that sub-relations are computed on the fly rather than cached)

oboedit_rbr

RuleBasedReasoner. Successor to LPR.

The internal design of the RBR is highly simplified compared to the LPR. It was written entirely by cjm. Note the profile is the same as for the LPR, however, the LPR bug does not arise due to the design of the RBR.

Note that the RBR is currently slow for incremental reasoning. This is because it checks all links after any links are added or deleted. This can easily be fixed in future versions. When it is, the LPR will probably be retired altogether.

OWL/DL reasoners

OWL Reasoners are superior to OE reasoners in that they can make use of more expressive constructs, such as complementOf (negation) and universal restrictions (all-only links). However, these constructs are not currently permitted in the OBO 1.2 language.

Some OWL reasoners only recently included transitive_over and arbitrary Relation_composition. They do not allow relation intersections.

Note that OWL reasoners will not allow you to ask questions of the form "what is the heart ventricle part_of?". To allow this we perform an extra step of materializing all transitive relation x class pairs (e.g. "heart part"). This leads to worse performance.

The two main open source OWL reasoners are FaCT++ and Pellet

owlapi_pellet

Pellet executed via the OWLAPI (1.2)

owlapi_pellet_mr

As above, with all class x relation pairs materialized.

owlapi_factpp

FaCT++ executed via the OWLAPI (1.2)

owlapi_factpp_mr

As above, with all class x relation pairs materialized.

pellet

Pellet 2.0 executed directly

oboedit_pwr

OBO-Edit pellet-wrapped reasoner. Pellet, executed with OE using a java object level bridge. Performs the class x relation materialization.

Needs updated to the latest Pellet API. May be discontinued in favour of an OWLAPI bridge

Database Reasoners

These reasoners use essentially the same procedure as the oboedit RBR. However, inferred links are backed by a relational database rather than in-memory. As such they tend to be slower, but are not-memory bound. These are also a good choice when the inferred graph needs to be stored in a database, to allow for advanced queries on annotations.

obdsql

Runs off of the OBD SQL schema. See OBD

Uses: Postgres 8.3

  • Transitivity
  • Propagation over/under is_a
  • Subrelations
  • Intersection_of

godb

Uses: MySQL 5

Relatively limited set of rules:

Will be extended in future

blipkit

Backed by a prolog database


Results

See reasoner-benchmarks for the raw data.

The following ontologies were used:

Methods

The reasoner-benchmarks.pl script was used