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NCI Extensions to Protégé

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This page is meant as an explanation of the NCI Protégé Extensions, why they were implemented and what they do.

The Editor's Guide for the most recent version of the NCI Protégé extensions can be found on GForge. This provides the user with instructions on how to edit within the NCI Edit tab, how to do searches using the Advanced Search tab, how to handle workflow, pull reports, etc.

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  • Each concept must have one and only one NCI/PT Full-Syn
  • Each concept must have one and only one Preferred_Name
  • HD, AQ and PT are equivalent Full-Syn term types. (i.e. an NCI/AQ can take the place of an NCI/PT)
  • NCI/PT value must match the Preferred_Name
  • Properties cannot be duplicated within a concept
  • Roles cannot be duplicated within a concept
  • Role groups cannot be duplicated within a concept
  • Superclasses cannot be duplicated within a concept
  • The last superclass of a concept cannot be deleted
  • Cannot create a restriction pointed at a retired, pre-retired, or pre-merged class
  • If concept has Def_Curator property present, only authorized users can create, modify or delete the DEFINITION
  • If concept has Def_Curator property present, only authorized users can modify or delete the Def_Curator
  • Def_Curators must exist in a configuration file. No "dummy" Def_Curators
  • Each DEFINITION must have 1 review date, 1 review name, 0 or 1 attributes, and no source
  • Only single spaces allowed in a DEFINITION unless preceeded by !, ? or .
  • No leading or trailing spaces allowed in properties
  • Only single spaces allowed between tokens in properties (except for DEFINITION)
  • Properties cannot include the characters :,!,? or @ (except for DEFINITION which allows ! and ?)

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Retire

  • Pre-retired concepts are retired under the preretired_concepts bin
  • Pre-retire process forces dependent classes to be fixed (children retreed, incoming roles re-pointed)
  • Pre-retire concept must have and Editor_Note added explaining the retirement
  • Only the lead editor may do the final retire on a concept
  • Only the lead editor may edit retired concepts
  • Roles in the retiring concept converted to annotation properties called OLD_ROLE
  • Retiring concept deprecated using owl:deprecatedClass

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Merge

  • Pre-merge retiring concepts are double-treed under premerged_concepts bin
  • Pre-merge identifying properties (Merge_From, Merge_To) are added to the surviving and retiring concepts
  • Pre-merge retiring concept must have an Editor_Note added explaining the merge
  • Only the lead editor may do the final merge on a concept
  • Non-redundant roles and properties of the retiring concept are added to the surviving concept
  • Non-redundant incoming roles pointed at the retiring concept are re-pointed at the surviving concept
  • Roles in the retiring concept converted to annotation properties called OLD_ROLE
  • Retiring concept deprecated using owl:deprecatedClass

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