Re: [Mged-mage] [Mged-ontologies] ontology annotation properties

[Trish W. <wh...@pc...>]

hi michael,

apols for the delay. for background, what is the need to represent 
annotation properties in MAGE?

> i've been thinking about how ontology annotation properties can be
> handled in MAGE and wanted to run some ideas past you all.
>
> in looking at the w3c owl documentation i found
> (http://www.w3.org/TR/owl-ref/#Annotations):
>
> 	"Five annotation pes are predefined by OWL, namely:
> *	owl:versionInfo
> *	rdfs:label
> *	rdfs:comment
> *	rdfs:seeAlso
> *	rdfs:isDefinedBy"
> plus how addition annotation properties can be defined per ontology.  so
> for any arbitrary ontology, it seems there can be a set of annotation
> properties distinct to that ontology and they can be on classes, and
> object and datatype properties.  so the question becomes how that can be
> encoded in MAGE.
yes, this is true, owl/rdf/rdfs specifies the above set (and more) as well 
as protege itself specifies a few (mainly administrative types), the 
Dublin Core Metadata Initiative (mainly adminsitrative) and also SKOS and 
a newly developed resource to add to the mix, RA/RU. oh, i forgot that the 
conversion of OBO to OWL also uses a self-contained, but not necessarily 
shared set of annotation properties.

as for annotation properties as either object or datatype annotation 
properties this is true of OWL 1.0 (the format that MO exists in and what 
OBI is being developed in). For OWL 1.1, this distinction does not exist 
for annotation property 'types'. I'm not sure when OWL 1.1 will be 
released (I think that it is at least a few months away), but wanted to 
mention this since presumably it will have at least a small impact on 
coding.

> to keep with the current best practice does this seem appropriate?
haven't been following mage so closely lately, but will take a stab at 
this.


>              <OntologyEntry category = "classname" value = "classname">
for clarification, i would say class identifier. for OBI and those 
ontologies converted from OBO to OWL the class identifier will be 
something like OBI_1234, for MO it is the classname itself since that is 
the value of the rdf:ID field, therefore the class identifier.

>                <OntologyReference_assn>
>                  <DatabaseEntry accession="@classname">
>                    <Database_assnref>
>                       <Database_ref
> identifier="www.ontology.com:Database:ontology name" name="ontology
> name"/>
>                    </Database_assnref>
>                  </DatabaseEntry>
>                </OntologyReference_assn>
>                <Associations_assnlist>
>                  <!-- annotation properties for a class -->
>                  <OntologyEntry category = "annotation_properties"
> value = "annotation_properties" >
>                    <Associations_assnlist>
>                      <OntologyEntry category = "label" value = "Class
> Name" />
>                      <OntologyEntry category = "arbitrary property"
> value = "arbitrary value" />
>                    </Associations_assnlist>
>                  </OntologyEntry>
>                  <OntologyEntry category = "datatypepropertyname" value
> = "datatypepropertyname" >
>                    <Associations_assnlist>
>                      <OntologyEntry category = "datatypeproperty" value
> = "value" />
>                      <!-- annotation properties for a datatype property
> -->
>                      <OntologyEntry category = "annotation_properties"
> value = "annotation_properties" >
>                        <Associations_assnlist>
>                          <OntologyEntry category = "label" value =
> "Datatype Property Name" />
>                        </Associations_assnlist>
>                      </OntologyEntry>
>                    </Associations_assnlist>
>                  </OntologyEntry>
>                </Associations_assnlist>
>              </OntologyEntry>

Are you separating out the owl annotation properties from object or 
datatype annotation properties, not sure I follow the comments? As for 
other questions, it prob would be easier to discuss via phone if that is 
ok.

Trish