- All Implemented Interfaces:
- OBOExceptionHandler, OWLRenderer
public class OBOFlatFileRenderer
extends AbstractOWLRenderer
implements OBOExceptionHandler
Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 17, 2008
Renders OBO 1.2 flat file format.
OBO 1.2 is a subset of OWL, so a rendering of an arbitrary OWL ontology may be incomplete in OBO.
Several features are currently not implemented:
- Exception handling for unsupported constructs - these are currently reported in stderr
- axiom annotations (these might be serialisable as inline comments - although OBO parsers provide no
guarantees these will be roundtripped)
- anonymous classes/properties - it is not clear what this means in OBO
- datatype restrictions
- namespace and derived tags for relationships etc - it is not clear what this means in OBO
- preservation of ordering on roundtripping exercises
- Stanzas are ordered (classes, obj/data props then instances)
- Entities are ordered by ID in each Stanza type
- OBO tags are ordered WRT the OBO specifications
Additional points:
- cardinality is expressed as an '=' separated tag value pair in [1] and underspecified in [2]. OBOEdit 2
does not parse this (at the time of writing) so this has been changed to standard TVP syntax
- OBO 1.2 currently specifies pairwise disjointness which this renderer follows so files may get large
- Exceptions are caught along the way and then wrapped in an OBOStorageIncompleteException which is thrown
after serialisation ends
References:
[1] http://www.cs.man.ac.uk/~horrocks/obo/
[2] http://www.geneontology.org/GO.format.obo-1_2.shtml