Obsolescence of Duplicated Classes, Properties and Instances

After last week’s tidying up, I identified a number of duplicated classes, properties and instances. I have spent some time this week resolving these duplications by obsoleting those terms from each pair of duplicates which seemed to have less impact on the ontology. A full description is present in the ontology, and is presented below. Also note I needed to create a new identifier to hold the new object property obsolete object property. Further information on its creation is at the end of this post.

  1. Clustering algorithm: The original label for this class was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM. As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. The version used in the obsoleted in version annotation was 0.3, as it is assumed that the next version number will be 0.3.
  2. is specified output of: There is an object property duplication for is specified output of, where one is from OBI and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete.
  3. .java file: The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of Programming language format this class was retained and SWO_0000585 deemed obsolete.
  4. TIFF (data file) and TIFF image (original file). Although these two labels may seem semantically different, they are both placed in the same location in the hierarchy, as children of data format specification. As such, they are duplicates rather than the former being a format and the latter an image itself. In fact, the latter’s label is unclear, as it seems to imply an image rather than a format. SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label ‘TIFF’, is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead.
  5. XML (data file and original file). SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. The version used in the obsoleted in version annotation was 0.3, as it is assumed that the next version number will be 0.3.
  6. html (data file and original file). There is one EDAM html class (EDAM:0002331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM:0002331 was retained and SWO_ 0000399 deemed obsolete, as EDAM:0002331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_ 0000399 were transferred to EDAM:0002331.
  7. JPEG (data file) and jpeg (original file). SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label ‘JPEG’, is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead.
  8. pdf (data file and original file). SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_ 0000652 were transferred to SWO_3000015. Please use SWO_ 3000015 instead.
  9. PNG (data file) and png image (original file). SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead.
  10. PostScript (data file) and ps image (original file). An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead.
  11. Information processing: Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead.
  12. is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead.
  13. Duplicated instances within organization: MathWorks (SWO_0000291 and SWO_9000002), Stanford University (SWO_0000431 and SWO_9000003). SWO_9000002 and SWO_9000003 were retained, while the others became instances of obsolete class. Please use SWO_9000002 and SWO_9000003.

New identifiers created:

  1. SWO_0004007: obsolete object property. Created to store those object properties which are no longer appropriate for use within SWO.
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