Definition and ID changes

I’ve recently been adding more natural language definitions. Mainly, the definitions were for higher level terms; while I am interested in adding definitions for terms such as “R”, the higher level ones are being completed first so as to provide clarity of intent. I’ll add to this document as I put in further definitions and other related changes in the next week or so.

  • Added definitions: followed by; directly followed by; has clause; has declared status; is alternative format of; is version of; input of; output of; directly preceded by; has website homepage; has download location; release candidate; attribution clause; attribution required; derivatives clause; derivative code linked same license; restrictions on derivative software; no restrictions on derivative software; derivative code same license;
  • Modified definitions for: has interface, is about; has part; has version; development status; generalization specification; ensemble specification; single generalization specification; clustering specification; pattern specification; predictive model specification; probability distribution specification.
  • Refactored external IDs (see https://code.google.com/p/obo-relations/wiki/ROAndBFO):
    • precedes / preceded_by:  We linked these RO classes using the URIs http://www.obofoundry.org/ro.owl/ro#precedes and ro#preceded_by (and used our own labels “followed by” and “preceded by”). These URIs used within SWO were outdated – they are actually BFO IDs http://purl.obolibrary.org/obo/BFO_0000060 (preceded_by) and BFO_0000063 (precedes). This is because RO makes use of BFO relations that are either uncontroversial (non-temporalized) parts of BFO2, or that will be incorporated in the future. The URIs have been changed accordingly in SWO via Protege refactoring.
    • participates_in / has_participant: In previous versions of RO they made use of unofficial non-temporalized BFO relations. To avoid potential clashes with temporalized relations with different meanings, they have since decided to create separate IDs with RO prefixes. These are available for participates_in (RO_0000056) and has_participant (RO_0000057). SWO was updated to reflect this. This required the obsoleting of SWO_9000059 (our own version of has_participant, “has participant”) and its replacement with RO_0000057. participates_in was already used within SWO correctly used the RO ID, with our own label of “participates in”.
    • has role: This object property currently has the URI of http://purl.obolibrary.org/obo/OBI_0000316, however this class is now obsolete in OBI. We have therefore refactored the URI, replacing it with the equivalent RO term http://purl.obolibrary.org/obo/RO_0000087. There seems to be no definition available from RO for this term, so we have not put a definition into SWO at this time.
  • External Classes without external definitions: The following classes do not have definitions within SWO as they have no definitions in their parent ontology: data processing algorithm execution, data visualization algorithm execution, has role.

Hierarchy Changes

  • derivative software and no derivative software: These two classes have been placed, seemingly mistakenly, as children of Restrictions on derivative software. The new structure has these two classes as the direct and only children of Derivatives clause. Then, the children of derivative software would be the both no restrictions on derivatives and restrictions on derivatives. Also, to make it clear when the classes are out of context (e.g. being discussed in a paper or somewhere else that isn’t within the ontology hierarchy itself), the labels for these classes have been changed so that it is clear these entities do not refer to software items themselves, but to clauses of software licenses. Therefore the new names for these classes are derivative software allowed and derivative software not allowed.
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