July 4, 2012 Leave a comment
Can we query for connections between FMA and GO? This should be
possible by using a combination of
- Axioms linking GO and Uberon (x-metazoan-anatomy)
- Axioms linking FMA and Uberon (uberon-to-fma)
This may seem like more components than is necessary. However,
remember that GO is a multi-species ontology, and “heart development”
in GO covers not only vertebrate hearts, but also (perhaps
controversially) drosophila “hearts”. In contrast, the FMA class for
“heart” represents a canonical adult human heart. This is why we have
to go via Uberon, which covers similar taxonomic territory to GO. The
uberon class called “heart” covers all hearts.
GO to metazoan anatomical structures
http://purl.obolibrary.org/obo/go/extensions/x-metazoan-anatomy.owl contains axioms of the form:
'heart EquivalentTo 'anatomical structure morphogenesis' and
'results in morphogenesis of' some uberon:heart
(note that sub-properties of ‘results in developmental progression of’
are used here)
Generic metazoan anatomy to FMA
http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl contains axioms of the form:
fma:heart EquivalentTo uberon:heart and part_of some 'Homo sapiens'
GO to FMA
Note that there is no existential dependence between go ‘heart
development’ and fma:heart. This is as it should be – if there were no
human hearts then there would still be heart development
processes. This issue is touched in Chimezie Ogbuji‘s presentation at DILS 2012.
This lack of existential dependence has consequences for querying
connections. An OWL query for:
?p SubClassOf ‘results in developmental progression of’ some ?u
Will return GO-Uberon connections only.
We must perform a join in order to get what we want:
?p SubClassOf ‘results in developmental progression of’ some ?u,
?a SubClassOf ?u,
?a part_of some ‘Homo sapiens’
Actually executing this query is not straightforward. Ideally we would
have a way of using OWL syntax, such as the above. To get complete
results, either EL++ or RL reasoning is required. In the next post I’ll present some possible options for issuing this query.