September 2, 2009 NEMO OWL ontologies: Viewing & editing NEMO ontologies (OWL/RDF files) .

September 2, 2009September 2, 2009

NEMO OWL ontologies:NEMO OWL ontologies:Viewing & editing NEMO Viewing & editing NEMO

ontologies (OWL/RDF files)ontologies (OWL/RDF files)

http://nemo.nic.uoregon.edu

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)

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

Overview Agenda





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

Recall: Why OWL/RDF?

Rich, explicit, computable semantics…. But takes time to build!

Sample RDF/OWL file from NEMO

• [show NEMO_spatial.owl in BBEdit… go through scalp_region_of_interest classes, class properties, class restrictions]

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…]

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)

Modules combined in top-level NEMO.owl file

• [show NEMO.owl in BBEdit and/or Protege…]

Overview Agenda





Viewing NEMO ontologies online

• [“browse” NEMO.owl via Bioportal…]

Overview Agenda





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

September 2, 2009 NEMO OWL ontologies: Viewing & editing NEMO ontologies (OWL/RDF files) .

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