OBO round trip - Revision history

Akivela: /* OBO-Wandora-OBO round trip results */

2008-08-21T18:35:30Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-08-21T18:35:19Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-08-21T18:33:52Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-08-21T18:31:04Z

‎OBO-Wandora-OBO round trip results

Akivela at 18:29, 21 August 2008

2008-08-21T18:29:53Z

Akivela: /* OBO-Wandora-OBO round trip results */

2008-04-22T15:47:50Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-02-04T21:12:48Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-01-29T10:37:59Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-01-28T19:20:00Z

‎OBO-Wandora-OBO round trip results

Akivela: /* OBO-Wandora-OBO round trip results */

2008-01-28T19:19:17Z

‎OBO-Wandora-OBO round trip results

← Older revision		Revision as of 18:35, 21 August 2008
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	relationship: has_quality SO:0001183 ! morpholino		relationship: has_quality SO:0001183 ! morpholino

−	More detailed comparison of original and Wandora roundtripped OBO ontologies is found in MSc Theses Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon], 2008. (in Finnish). (English ~~Abstract~~ is also available: [http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf Converting OBO ontologies to Topic Maps]).	+	More detailed comparison of original and Wandora roundtripped OBO ontologies is found in MSc Theses Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon], 2008. (in Finnish). (English abstract is also available: [http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf Converting OBO ontologies to Topic Maps]).

← Older revision		Revision as of 18:35, 21 August 2008
Line 44:		Line 44:
	relationship: has_quality SO:0001183 ! morpholino		relationship: has_quality SO:0001183 ! morpholino

−	More detailed comparison of original and Wandora roundtripped OBO ontologies is found in Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]~~. MSc Theses~~, 2008. (in Finnish). (English Abstract: [http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf Converting OBO ontologies to Topic Maps]).	+	More detailed comparison of original and Wandora roundtripped OBO ontologies is found in MSc Theses Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon], 2008. (in Finnish). (English Abstract is also available: [http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf Converting OBO ontologies to Topic Maps]).

← Older revision		Revision as of 18:33, 21 August 2008
Line 43:		Line 43:
	intersection_of: has_quality SO:0001183 ! morpholino		intersection_of: has_quality SO:0001183 ! morpholino
	relationship: has_quality SO:0001183 ! morpholino		relationship: has_quality SO:0001183 ! morpholino
		+
		+	More detailed comparison of original and Wandora roundtripped OBO ontologies is found in Kivelä A.: [http://www.wandora.org/wandora/download/other/gradu_kivela.pdf OBO-ontologioiden kuvaaminen Topic Map-muotoon]. MSc Theses, 2008. (in Finnish). (English Abstract: [http://www.wandora.org/wandora/download/other/gradu_kivela_abstract_en.pdf Converting OBO ontologies to Topic Maps]).

@@ Line 17: / Line 17: @@
    id: ENVO:00000004
    synonym: "administrative division" RELATED [ADL:FTT, Getty:TGN]
 In '''po_temporal.obo''' empty definition origin descriptions do not survive round trip. Original OBO ontology contains for example:

← Older revision		Revision as of 18:29, 21 August 2008
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−	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 [http://www.oboedit.org OBOEdit].	+	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 with the '''obodiff''' application shipped with the [http://www.oboedit.org OBOEdit] for example.

	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.

@@ Line 5: / Line 5: @@
 == 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 with '''obodiff''' gives a [http://www.wandora.org/wandora/download/other/round_trip_compare_results.txt result file]. Some observations about results follow.
+Round tripping current (2008-01-22) OBO ontologies available at [http://www.obofoundry.org OBO Foundry], and comparing round tripped ontologies to original ontologies with '''obodiff''' gives a [http://www.wandora.org/wandora/download/other/round_trip_compare_results.txt result file]. Some observations follow.
 Synonym differences on '''envo.obo''' are due to a design decision where Wandora's OBO export tries to collapse all identical synonyms into a single synonym with several origin definitions. The original '''envo.obo''' contains identical synonyms such as:

@@ Line 7: / Line 7: @@
 Round tripping current (2008-01-22) OBO ontologies available at [http://www.obofoundry.org OBO Foundry], and comparing round tripped ontologies to original ontologies with '''obodiff''' gives a [http://www.wandora.org/wandora/download/other/round_trip_compare_results.txt result file]. Some observations 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:
+Synonym differences on '''envo.obo''' are due to a design decision where Wandora's OBO export tries to collapse all identical synonyms into a single synonym with several origin definitions. The original '''envo.obo''' contains identical synonyms such as:
    id: ENVO:00000004

@@ Line 30: / Line 30: @@
    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''':
+Completeness status changes at '''so.obo''' and '''fly_anatomy.obo''' seem to be due to a 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

@@ Line 33: / Line 33: @@
    id: SO:0000034
    intersection_of: has_quality SO:0001183 ! morpholino
    relationship: has_quality SO:0001183 ! implied link automatically realized ! morpholino
@@ Line 39: / Line 41: @@
    id: SO:0000034
    intersection_of: has_quality SO:0001183 ! morpholino
    relationship: has_quality SO:0001183 ! morpholino