OBO round trip
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OBO round trip uses tool's own internal topic map for OBO-topic map-OBO conversion and leaves the current topic map untouched in Wandora. | OBO round trip uses tool's own internal topic map for OBO-topic map-OBO conversion and leaves the current topic map untouched in Wandora. | ||
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| + | == OBO-Wandora-OBO round trip results == | ||
Round tripping current (2008-01-22) OBO ontologies available at [http://www.obofoundry.org OBO Foundry], and comparing round tripped ontologies to original ontologies gives a [http://www.wandora.org/wandora/download/other/round_trip_compare_results.txt result file]. Some notes about the results: | Round tripping current (2008-01-22) OBO ontologies available at [http://www.obofoundry.org OBO Foundry], and comparing round tripped ontologies to original ontologies gives a [http://www.wandora.org/wandora/download/other/round_trip_compare_results.txt result file]. Some notes about the results: | ||
Revision as of 22:13, 28 January 2008
OBO round trip is a special import-export tool found in File > Export > OBO round trip.... Tool is used to test how OBO flat file ontologies convert to topic maps and back again to OBO ontologies. Tool can round trip several ontologies at once. Round tripped OBO files are stored to wandora_round_trip folder beside original OBO files. Conversion cycle should not loose or add any information to ontologies. Conversion changes can be tracked for example with the obodiff application shipped with the OBOEdit.
OBO round trip uses tool's own internal topic map for OBO-topic map-OBO conversion and leaves the current topic map untouched in Wandora.
OBO-Wandora-OBO round trip results
Round tripping current (2008-01-22) OBO ontologies available at OBO Foundry, and comparing round tripped ontologies to original ontologies gives a result file. Some notes about the results:
Synonym differences on envo.obo are due to a design decision where OBO export tries to collapse all identical synonyms into a single synonym with several origin definitions. envo.obo contains identical synonyms such as:
id: ENVO:00000004 synonym: "administrative division" RELATED [ADL:FTT] synonym: "administrative division" RELATED [Getty:TGN]
Wandora round tripped ontology contains these synonyms collapsed into a single synonym specification:
id: ENVO:00000004 synonym: "administrative division" RELATED [ADL:FTT, Getty:TGN]
It looks like Wandora doesn't handle all escaped characters right. Look at FIX:0001087 in fix.obo for example. Backslash in { and } has duplicated. Have to fix this!!!
In po_temporal.obo empty definition origin descriptions do not survive round trip. Original OBO ontology contains for example:
id: PO:0001027 def: "OBSOLETE. The meristematic zone is formed" [GR:ap ""]
This is round tripped to:
id: PO:0001027 def: "OBSOLETE. The meristematic zone is formed" [GR:ap]
Completeness status changes at so.obo and fly_anatomy.obo are due to duplicate relationship definition. Same relationship is defined with modified relationship and exact relationship term such as part_of. For example in original so.obo:
id: SO:0000034 intersection_of: has_quality SO:0001183 ! morpholino relationship: has_quality SO:0001183 ! implied link automatically realized ! morpholino
has round tripped to
id: SO:0000034 intersection_of: has_quality SO:0001183 ! morpholino relationship: has_quality SO:0001183 ! morpholino
