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Notes on NEMO Ontology "Annotation" (i.e., properties used to annotate concepts)

Created:  05/23/2009 (GF) XXXXXXXXXXX

Updated:  09/01/2009 (PL)

NEMO.owl version 0.90

NEMO will use one annotation ontology called:http://nemo.nic.uoregon.edu/ontologies/NEMO_annotation_properties.owl

...which is derived (but NOT imported) from the two NIF annotation ontologies:

http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl
http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl

NEMO annotations will be a closed set, meaning, ALL annotations used by NEMO will be from nemo_annotation_properties.owl, and no other annotation ontology (not core, not dc, not nif_annot).  The only exception might be rdfs:label, which is used to facilitate visualization of the ontology.

The following annotation fields are the ONLY ones used for NEMO.  BOLD indicates only one entry is allowed.

REQUIRED annotation properties:

  • NEMO_annotation_properties:hasURI -- This property defines the NEMO URI for a concept. The URI is a non-human-readable label that also provides a stable web address for accessing the concept.
  • NEMO_annotation_properties:label -- An underscore-delimited, human-readable label for a concept [GF: should we change this to "preferredLabel" to be less ambiguous, redundant?]
    • Equivalent to rdfs:label and core:prefLabel.
    • We are re-creating NEMO_annotation_properties:label to keep all annotation properties for NEMO closed.
  • NEMO_annotation_properties:createdDate -- [YYYY-MM-DD] The date when the current concept was created.
  • NEMO_annotation_properties:curator -- This property defines the NEMO ontology curators who've contributed to the definition of a class.  More than one instance of this property is valid.  In the case of multiple curators, the individual curator name may also be associated with the definition, if that person was primarily responsible for it.
    • Range-restriction:  NEMO_annotation_properties:NEMO_curator.  
      • NEMO_curator enumerates the valid set of individuals designated as NEMO curators, which currently is {Gwen_Frishkoff, Paea_LePendu, Haishan_Liu, Dejing_Dou}.  Altogether, this set is also called the NEMO_OTF (“ontology task force”).
      • GF Note: we need to add NEMO_Consortium!! Also, individual members of consortium + their "point people"...
  • NEMO_annotation_properties:hasNamespace -- This property defines the NEMO namespace for a concept.
    • Range-restriction:  NEMO_annotation_properties:NEMO_namespace.
      • NEMO_namespace enumerates the valid set of individuals designated as NEMO namespaces which currently is {NEMO_spatial, NEMO_temporal, NEMO_functional, NEMO_erp, NEMO_data}.
  • NEMO_annotation_properties:definition - A natural language definition that adheres to Aristotelian constraints.
    • Equivalent to core:definition.
    • We are re-creating NEMO_annotation_properties:definition to keep all annotation properties for NEMO closed.
  • NEMO_annotation_properties:hasCurationStatus -- This provides specific info on the level of curation a given class has received and is specifically design to promote automated reporting on the status of classes in an ontology.  It is likely some classes will require more than one instance of this property to fully describe their status.   Is a type of skos_editorial_note.
    • Range-restriction:  NEMO_annotation_properties:curation_status.  The set of valid curation_status fields are as follows:
      • limbo_class (resp., limbo_property) -- Indicates a class (resp., property) has been created by curators but has not been assigned to a superclass and therefore has an uncertain place within the ontology class hierarchy. By implication, the class has no definition or one that is minimally specified.
        • By implication, the next steps required are to: identify a valid definitionSource, specify the definitionSource, update the hasCurationStatus from limbo_class to definition_incomplete or pending_final_vetting.
      • definition_incomplete -- Indicates a class has been assigned to a superclass and therefore has a clear place within the ontology class hierarchy and at least a minimal definition. However, the definition may require considerable amending before it complies with Aristotelian/OBO requirements for a good, noncircular definition.
        • By implication, the next steps required are to: verify the definition adheres to Aristotelian constraints, update hasCurationStatus from definition_incomplete to pending_final_vetting.
      • pending_final_vetting -- Indicates a class needs to be vetted by two or more NEMO curation authorities.
        • By implication, the next steps required are to: vet the definition among NEMO consortium members, update hasCurationStatus from pending_final_vetting curation_complete.
      • curation_complete -- Indicates a class has been fully vetted by NEMO curation authorities and deemed ready for use.

OPTIONAL annotation properties (main ones highlighted):

  • NEMO_annotation_properties:modifiedDate -- [YYYY-MM-DD] The date when the current concept was last updated.
  • NEMO_annotation_properties:synonym - A lexical variant carrying the same latent semantic value.
  • NEMO_annotation_properties:acronym - A synonym consisting of a sequence of letters typically taken from the beginning of words of which either the preferred label or another synonym are composed.
  • NEMO_annotation_properties:definitionSource -- A traceable source for the current definition.
    • In free-form text, a source could be a person's name, a URI, an informal publication reference, a PubMed ID, whatever most succinctly identifies a source.
    • We originally had an EnumerationClass of Definition_Sources but decided that was too restrictive.
  • NEMO_annotation_properties:example -- An example of a given concept.  
    • Equivalent to core:example.
    • We are re-creating NEMO_annotation_properties:example to keep all annotation properties for NEMO closed.
  • NEMO_annotation_properties:usageNote -- Supplies some, possibly partial, information about the intended meaning of a concept, especially as an indication of how the use of a concept is limited in indexing practice.
  • NEMO_annotation_properties:comment -- A general comment.
    • Please consider using editorialNote, historyNote or changeNote before attemping to apply a general comment. [GF: I think we should revisit this issue... Might be better to use comment to cover all of these?]
    • We are re-creating NEMO_annotation_properties:comment to keep all annotation properties for NEMO closed.  Otherwise, we consider NEMO_annotation_properties:comment to be equivalent to rdfs:comment and core:note.
    • NEMO initially used comments to store temporary definitions. The proper method is to now use NEMO_annotation_properties:tempDefinition for that purpose.
  • NEMO_annotation_properties:historyNote - Describes significant changes or historical justification for the current version of a concept.
  • NEMO_annotation_properties:changeNote - Documents fine-grained changes to a concept, for the purposes of administration and maintenance.
  • NEMO_annotation_properties:editorialNote - Supplies information that is an aid to administrative housekeeping, such as reminders of editorial work still to be done, or warnings in the event that future editorial changes might be made.
  • NEMO_annotation_properties:tempDefinition - A definition specifically declared to be temporary and in the midst of more detailed curation efforts.
  • NEMO_annotation_properties:_deprecated - A graveyard for deprecated classes.
  • NEMO_annotation_properties:_deprecatedProperty - A graveyard for deprecated properties.
  • NEMO_annotation_properties:_limbo - A class that has been created by curators but has not been assigned to a superclass and therefore has an uncertain place within the ontology class hierarchy. By implication, the class has no definition or one that is minimally specified.
  • NEMO_annotation_properties:_limboProperty - A property that has been created by curators but has an uncertain place within the ontology. By implication, the property has no definition or one that is minimally specified.

TECHNICAL NOTES:

AnnotationType -- A category designed to help data processing systems automatically determine how to process a given annotation.

  • AnnotationProperty types are recommended by Alan Ruttenberg (2007-05-20) for representing fixed enumeration class instances for ontology class annotation.
  • This is required, since sub-classing AnnotationProperties is not allowed in OWL-DL.  Using this descriptive metadata AnnotationProperties, we can construct a chained code representation of a classification graph for AnnotationProperities very likely to be useful for information systems built to parse and process OWL content.
  • The only valid values for this property are DC or SKOS (core) AnnotationProperty URIs.
  • example:    <owl:AnnotationProperty rdf:ID="synonym">     <annotationType>&core;altLabel</annotationType> </owl:AnnotationProperty>

EnumerationClass -- A parent class for all enumerations used for class annotation.  An enumeration class provides a strict set of possible values for a given property range.

  • When creating or subclassing a new EnumerationClass, we recommend also specifying that all enumerations are mutually distinct.
  • example:  NEMO_curator and NEMO_namespace are enumeration classes.
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