UriCvNamespaceProposalJune2006/Inoh

This is a worked example of having an extension ontology from INOH.

Main file

Extension file

The point is to add two properties to link pathways or pathway steps: MOLECULAR-VARIATION and HOMOLOGOUS-EVENT.

Then, as an example

MI0007326_Cleavage_of_Notch_in_Delta_complex_by_ADAMS2_cleavage_

is linked to (via HOMOLOGOUS-EVENT)

MI0007409_Cleavage_of_Notch_in_Delta_complex_by_ADAMS2_cleavage_Drosophila_0 and MI0007460_Cleavage_of_Notch1_in_DLL1_complex_by_TACES2_cleavage_Mammal_0

and

MI0007335_Cleavage_of_Notch_in_DSL_complex_by_ADAMS2_cleavage_0

is linked to (vi MOLECULAR-VARIATION)

MI0007326_Cleavage_of_Notch_in_Delta_complex_by_ADAMS2_cleavage_0 MI0007321_Cleavage_of_Notch_in_Serrate_Jagged_complex_by_ADAMS2_cleavage_0

Here's are the important bits.

The part of the main file that imports the extension file is this:

• <owl:Ontology rdf:about="">

  • <owl:imports rdf:resource=" http://www.biopax.org/release/biopax-level2.owl"/> <owl:imports>

    • <owl:Ontology rdf:about=" file:///Users/alanr/Desktop/BioPAX:OBO/MV_HE_AlanProposal/inoh-MV-HE-fixed.owl">

      • <bp:IMPORT-TYPE rdf:datatype="&xsd;string">Extension</bp:IMPORT-TYPE>

      </owl:Ontology>

    </owl:imports>

  </owl:Ontology>

This is also in the main file, but should be in the biopax specification. Though it doesn't hurt to be there.

• <owl:AnnotationProperty rdf:about=" http://www.biopax.org/release/biopax-level2.owl#IMPORT-TYPE"/>

Documentation from Ken

attachment:INOH_MV_HE.doc

attachment:meetingINOH_BioPAX_StatesAndGenerics_061106.doc