September 2, 2009 NEMO OWL ontologies: Viewing & editing NEMO ontologies (OWL/RDF files) .
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Transcript of 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)
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
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)
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
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)
Viewing NEMO ontologies online
• [“browse” NEMO.owl via Bioportal…]
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)
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