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

2. Overview Agenda 1.Milestones & timeline for next 2 mos (5 mins) 2.Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) 3.Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) 4. Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

3. Overview Agenda 1.Milestones & timeline for next 2 mos (5 mins) 2.Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) 3.Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) 4. 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 1.Milestones & timeline for next 3 mos (5 mins) 2.Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) 3.Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) 4. 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. My Homepage under construction in perpetuity XML, eXtensible Markup Language, lets users self-define new tags: Dejing Dou Assistant Professor Paea LePendu …. 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)

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

13. Overview Agenda 1.Milestones & timeline for next 3 mos (5 mins) 2.Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) 3.Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) 4. Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

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

15. Overview Agenda 1.Milestones & timeline for next 3 mos (5 mins) 2.Overview of how NEMO OWL/RDF files (NEMO.owl, NEMO_spatial.owl, etc.) are structured (10 mins) 3.Introduction to NCBO's Bioportal (for viewing the current "release" of NEMO.owl (10 mins) 4. Tutorial on using Sourceforge (nemoontologies Tracker & List) to post requests for changes & additions to NEMO ontologies (10+ mins)

16. 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