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OWL Lite encoding of bio-ontologies.

stuart at inf.ed.ac.uk stuart at inf.ed.ac.uk
Thu Jan 22 04:22:49 PST 2004


Thomas, that's a good question, the answer is quite long I'm afraid.
Our work is mostly on OBO, but similar issues arise.

>> 3: The meaning of logical relations in bio-ontologies needs to be made
>> consistent with OWL and RDFS.
>
> Could you expand on this? Are there plans to address this?
>
> What would actually be lost at the semantic level by encoding the
> current bio-ontologies in the OWL Lite sublanguage (known to have
> decidable reasoning, and usable inference systems, e.g. RACER)?

First there is a syntactic problem with the IDs of GO terms. These are
used as local names in the XML/RDF syntax:
<go:term rdf:about="http://www.geneontology.org/go#GO:0003673" 
                                                   ^^^^^^^^^^^
            n_associations="0">
            <go:accession>GO:0003673</go:accession>
            <go:name>Gene_Ontology</go:name>
</go:term>

but the XML spec for Qnames does not allow ':' to occur, so
http:..../go#GO:0003673 causes problems under current standards.
One solution would be to used the concept name as the term:
<go:term rdf:about="http://www.geneontology.org/go#GeneOntology"  ...
but these need to be unique, and this would be a problem for OBO
ontologies.

Second there are semantic problems for OBO anatomies (GO is much
better stuctured). 
To use the DL reasoners both is_a and part_of need to be translated
into properly defined relations. is_a maps to rdfs:subClassOf, but
part_of is more complex. (part_of A B) might mean some B's have A's as
parts, or all B's have A's as parts, the problem is to define how the
instances of A and B relate to each other. A DL solution would be
along these lines (example from Drosophila ontology) - define 
AdultHeartMuscle and AdultAorticFunnel to be parts of the AdultHeart:

AdultHeartMuscle := (allValuesFrom part_of AdultHeart)
AdultAorticFunnel := (allValuesFrom part_of AdultHeart)

but we need to distinguish further between these. The ontology says 
AdultHeartMuscle isa AdultVisceralMuscle so we can write:
AdultHeartMuscle := (allValuesFrom part_of AdultHeart) and AdultVisceralMuscle

however there is no more information about AdultAorticFunnel in the
ontology, and therefore some additional knowledge and analysis must be provided
manually to get the right result from a DL classifier. There's a paper
on the migration problem as it applies to GO by Wroe et al 
http://www.smi.stanford.edu/projects/helix/psb03/wroe.doc
I guess the DL folks can give an update about the prospects for analysing GO
in this way. 

An alternative, which gives some of the same benefits, is to keep
part-of as a relation between classes (as it currently is in GO and
OBO) and define the alternative interpretations in first-order logic.
Basically the idea is to define partOf, and state the additional properties of
the partOf relation, e.g. given (partOf Part Whole) do sub-types of the
Whole have the Part as well?, is the Part a direct part of the Whole?
etc. There are only a small number of modelling decisions to be made
in converting to this ontology. This is an OWL-Full solution, more
details can be found here: 
http://www.aiai.ed.ac.uk/resources/go/
http://www-smi.stanford.edu/projects/helix/psb04/aitken.pdf

However, DL reasoners can't be used for reasoning as we don't use
property restrictions to encode the meaning. Fortunately, the Jena toolkit
provides a rule-based reasoner and the useful inferences can be coded
as rules. 

You mention OWL-Lite, but note that relations in OWL-Lite are between
individuals, not classes as is the case for GO's part_of. (so you need
either a DL or Full solution).
Hope this helps.....
Stuart

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