Package owltools.io

IO - Input/Output

See: Description

Interface Summary

Interface	Description
GraphReader
GraphRenderer

Class Summary

Class	Description
AbstractClosureReader
AbstractClosureRenderer	Renders the graph closure - i.e.
AbstractRenderer	Renders the graph closure - i.e.
CatalogXmlIRIMapper	OWLOntologyIRIMapper using the mappings from a catalog.xml file.
ChadoGraphClosureRenderer	implements a graph closure writer suitable for imports into Chado; in particular: all identifiers are translated to OBO IDs relationship chains of length > 1 are ignored SUBCLASS is written as is_a, and only existential restrictions are emitted
ClassExpressionGraphClosureRenderer	Writes graph closure as class expressions
CompactGraphClosureReader	Note that the ontology must be loaded prior to restored a closure table
CompactGraphClosureRenderer	Similar to GraphClosureRenderer, writes in a more compact format
EdgeTableRenderer	renders all edges in a simple TSV format
GeneralObjectDeserializer	Use this class to create a general object-tree using the Gson parser (see http://code.google.com/p/google-gson/).
GMTParser	reads in a table (e.g.
GraphClosureRenderer
ImportClosureSlurper
InferredParentRenderer	Renders the most specific parent over a set of Objectproperties using an extended reasoner.
LocalMirrorIRIMapper	This mapper allows for IRI resolution based on matching *parts* of URIs.
OWLGsonParser	Counterpart to OWLGsonRenderer UNTESTED
OWLGsonRenderer
OWLJSONFormat
OWLPrettyPrinter	Use a OWLGraphWrapper or OWLGraphWrapperExtended to render OWLAxiom, OWLGraphEdge, or OWLQuantifiedProperty in better human readable form. Hint: Every OWLGraphWrapper is also a OWLGraphWrapperExtended.
ParserWrapper	Convenience class wrapping org.oboformat that abstracts away underlying details of ontology format or location
ParserWrapper.OboAndOwlNameProvider	Provide names for the OBOFormatWriter using an OBODoc first and an OWLGraphWrapper as secondary.
ParserWrapper.OWLGraphWrapperNameProvider	Provide names for the OBOFormatWriter using an OWLGraphWrapper.
StanzaToOWLConverter	reads in a stanza-formatted file (e.g.
TableRenderer	Renders the graph closure - i.e.
TableToAxiomConverter	reads in a table (e.g.

Package owltools.io Description

IO - Input/Output

lightweight wrapper that abstracts away from whether source ontology is obo format or owl