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September 2, 2009

http://nemo.nic.uoregon.edu. September 2, 2009. NEMO OWL ontologies: Viewing & editing NEMO ontologies (OWL/RDF files). Overview Agenda. Milestones & timeline for next 2 mos (5 mins) Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins)

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September 2, 2009

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  1. http://nemo.nic.uoregon.edu September 2, 2009 NEMO OWL ontologies: Viewing & editing NEMO ontologies (OWL/RDF files)

  2. Overview Agenda • Milestones & timeline for next 2 mos (5 mins) • Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) • Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) • Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

  3. Overview Agenda • Milestones & timeline for next 2 mos (5 mins) • Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) • Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) • Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

  4. Milestones (Sept–Oct 2009) • September 2009 goals • Edit OWL/RDF ontology files • Move concepts from hasCuratorStatus = definition_incomplete to curation_complete [see “NEMO-PropertyAnnotations…” doc for details; this will make sense after we review the owl/rdf docs…] • October 2009 goals • Continue with ontology editing • Begin testing & refinement of pattern analysis & measure-generation tools

  5. Overview Agenda • Milestones & timeline for next 3 mos (5 mins) • Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) • Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) • Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

  6. Recall: Diff between XML/RDF/OWL • HTML, HyperText Markup Language, familiar language of the WWW. <html><head><title>My Homepage</title></head> <body>under construction in perpetuity</body></html> • XML, eXtensible Markup Language, lets users self-define new tags: <?xml version="1.0" encoding='UTF-8'?> <faculty> <name>Dejing Dou</name> <ranking>Assistant Professor </ranking> <student>Paea LePendu </student> …. </faculty> In this example, we defined several tags (faculty, name, ranking…), but XML does not encode the meaning or semantics of these tags. • RDF (Resource Definition Framework) and OWL (Web Ontology Language) are a set of XML tags specifically designed to encode semantics: relations/properties to link and to annotate tags (which can then point to richly defined classes)  ontologies

  7. Recall: Why OWL/RDF? Rich, explicit, computable semantics…. But takes time to build!

  8. Sample RDF/OWL file from NEMO • [show NEMO_spatial.owl in BBEdit… go through scalp_region_of_interest classes, class properties, class restrictions]

  9. Same file can also be viewed in Ontology editing software • [show NEMO_spatial.owl in Protege… Note that for now we hide this backend implementation. Use Bioportal to view finished product online…]

  10. NEMO RDF/OWL “modules” • We currently have 8 separate RDF/OWL files: • NEMO.owl • NEMO_spatial.owl • NEMO_temporal.owl • NEMO_functional.owl • NEMO_ERP.owl • NEMO_data.owl • NEMO_backend.owl • NEMO_annotation_properties.owl • BFO, OBO_REL (RO)

  11. Modules combined in top-level NEMO.owl file • [show NEMO.owl in BBEdit and/or Protege…]

  12. Overview Agenda • Milestones & timeline for next 3 mos (5 mins) • Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) • Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) • Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

  13. Viewing NEMO ontologies online • [“browse” NEMO.owl via Bioportal…]

  14. Overview Agenda • Milestones & timeline for next 3 mos (5 mins) • Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) • Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) • Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

  15. Jason & Paea • Illustrate full workflow for a single change request & implementation • Demonstrate how to link back & forth between mailing list (nemoontologies-consortium list) and the Tracker • Show how to access mailing list Archives

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