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September 16, 2009

http://nemo.nic.uoregon.edu. September 16, 2009. NEMO OWL ontologies: Viewing & editing OWL/RDF files, part II. Overview Agenda. Short-term goals & methods [10 mins] Divide & conquer strategy [10 mins] Hands-on part [30-40 mins]. Overview Agenda. Short-term goals & methods [10 mins]

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September 16, 2009

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  1. http://nemo.nic.uoregon.edu September 16, 2009 NEMO OWL ontologies: Viewing & editing OWL/RDF files, part II

  2. Overview Agenda • Short-term goals & methods [10 mins] • Divide & conquer strategy [10 mins] • Hands-on part [30-40 mins]

  3. Overview Agenda • Short-term goals & methods [10 mins] • Divide & conquer strategy [10 mins] • Hands-on part [30-40 mins]

  4. Reminder: Top-Down + Bottom-Up in NEMO BOTTOM- UP TOP- DOWN NEMO Ontologies & Ontology-Based Tools for Data Mark-up and Analysis

  5.  Encode concepts (classes, relations) & their definitions in NEMO owl/rdf files

  6. Short-term goals for Top-Down • Viewing ontologies (owl/rdf files) • Discussing specific issues in NEMO • Revising ontologies Main objectives: • Get familiar with structure & contents of current versions of NEMO • Put in place protocols for collaborative work on ontologies (*) Please refer to “Instructions_NEMOontology_EditingLite” (*)

  7. Viewing ontologies • BioPortal — view latest NCBO submission on web • http://bioportal.bioontology.org/visualize/40522 • Note that we only upload full ontology (NEMO.owl) to NCBO, not modules (NEMO_spatial, _data, etc.) • Protégé — view any NEMO owl file using software installed on your machine • http://protege.stanford.edu/download/download.html • You can view any version of any file (not just latest release) • free, flexible, good graphics, easy to learn basics, but quirky & unstable, constantly updated ( new goodies, but also new bugs!) • BBEdit (or any text or syntax editor) • For viewing & editing raw rdf files

  8. Discussing specific issues • Soureforge listserve • nemoontologies-consortium@lists.sourceforge.net • Please make sure you are receiving and responding to individual postings, not just digests • Issues we’re looking into: attachments, threading of posts • PIs —your point person may contact Jason to set up account • Issues for discussion [some examples] • Classes • BFO — distinctions between types of realizable_entities (dispositions, functions, & roles) • NEMO —fiat boundaries between ERP temporal_intervals; plus more abstract (super-) classes “early,” “mid-latency,” and “late” • Distinguishing scalp_surface vs. scalp

  9. Discussing specific issues (II) • Issues for discussion (cont) • Class structure • ERP_topography is_a quality? Or is_a generically_dependent_continuant? • scalp_surface is_a object_boundary? Or is_a spatial_region? • Class annotations • See NEMO-PropertyAnnotations-09012009-gf-v9.pdf for a full list of NEMO annotation properties, their definitions and range restrictions. • Class restrictions • Disjoint classes; closed class (specification of all possible members); etc. • Relations • CARO surface_of vs RO location_of • Relations linking concepts across different modules! • E.g., ERP_pattern RO:bearer_of {spatial, temporal qualities} • E.g., electrical_field participates_in electromagnetic_polarization

  10. Revising ontologies • Correction of obvious errors &gaps • Post Ontology revision requests to Sourceforge Tracker: https://sourceforge.net/tracker/?group_id=263320&atid=1168891 • See “Instructions_NEMOontology_EditingLite” for details (incentive for students/point people: get name added as curator to each item that you help to add/revise) • PIs —your point person may contact Jason to set up account • More complex issues • Discuss first as a consortium (e.g., scalp vs. scalp_surface …) • Then make a group decision, post item to Tracker, & add NEMO_consortium as curator + change note in class annotation

  11. Overview Agenda • Short-term goals & methods [10 mins] • Divide & conquer strategy [10 mins] • Hands-on part [30-40 mins]

  12. Divide & Conquer Strategy • September — mid October, 2009 • NEMO_spatial -- Dennis & Krista • NEMO_temporal -- John & Alex • NEMO_functional -- Kerry & Stephanie • NEMO_data -- Tim & Chris • Then play musical modules…? • Leave NEMO_erp for later phase (Spring)? • Listing labels for ERP patterns that are floating around in the literature….

  13. NEMO_spatial • Review & discuss proposed scalp_surface regions (ROI) & assignment of 10-10 and EGI 128-, 256-channel e_loc to ROI • https://trac.nic.uoregon.edu/ntk/attachment/wiki/NEMOtechnicalreports/GSNtoITTtoROImappings.zip • Resolve issues with scalp, scalp_surface, scalp_region, located_in vs. surface_of etc.

  14. NEMO_spatial schematic

  15. NEMO_temporal • Review & discuss issues raises on list serve: • Fiat temporal_interval concepts: right granularity? • Validity of abstract temporal categories (early, mid, & late – per Tim’s posting)? • physiological_process concepts need lots of work; see also OPB v2.0 (not yet released…) • See email from Dan Cook (9/10/2009)

  16. NEMO_temporal schematic

  17. NEMO_functional • Study OBI & IAO (Alan Ruttenberg et al.) • Coordinate with CogPO (Jess Turner & Angie Laird); see Figure from Jess (CogPO schematic, adopted from NIH) • Study BrainMapLex.xls doc (download from brainmap website or ask us for copy)

  18. NEMO_data • Study OBI & IAO (Alan Ruttenberg et al.) • Look at draft version of NEMO autolabel spreadsheet, which has spatial, temporal, & derived metrics for data mark-up • https://trac.nic.uoregon.edu/ntk/attachment/wiki/NEMOtechnicalreports/NEMOautolabel-gf-04272009_annotated11-rf-05122009.xls

  19. Some Reference Ontologies • General (upper level) • BFO (Basic Formal Ontology) • RO (Relations Ontology) • Spatial/Anatomical • FMA/CARO (Foundational Model of Anatomy) • Temporal/Physiological • OPB (Ontology of Physics for Biology) • ECG (Cardiac Electrophysiology Ontology) • Functional (protocols, assays), Data • PATO (Phenotypic Attributes Ontology) • OBI (Ontology of Biological Investigation) • IAO (Informational Artifact Ontology) — recent extension of OBI • CogPO (Cognitive Protocols Ontology) — brand new (not yet available)

  20. Overview Agenda • Short-term goals & methods [10 mins] • Divide & conquer strategy [10 mins] • Hands-on part [30-40 mins]

  21. NEMO_spatial classes NOTE (figure underspecified here): Scalp = three_dimensional object Scalp_surface = two_dimensional object_boundary Scalp_surface_region = two_dimensional spatial_region

  22. NEMO_spatial issues (cont) • Relationship between scalp_surface & scalp_surface_region • RO: located_in (inverse = location_of) • CARO: surface_of • Relationship between ITT_electrode_location’s & scalp_surface_region’s (Larger question: how is a 0D point related to a 2D region?) • Is_a • Part_of • Located_in

  23. International 10-10 EEG Electrode Locations ITT electrode location Fz (frontocentral_scalp_region)

  24. Scalp surface “regions of interest”

  25. NEMO Temporal Ontology

  26. Early (“exogenous”) vs. Late(“endogenous”) ERP processes EARLY ~0-150 ms after event (e.g., stimulus onset) MID-LATENCY ~151-500 after event (e.g., stimulus onset) LATE 501 ms or more after event (e.g., stimulus onset)

  27. NEMO Functional Ontology Jessica Turner BIRNlex (now part of Neurolex) http://brainmap.org/scribe/index.html CogPO Angela Laird BrainMap

  28. NEMO Data Ontology:Where ontology meets epistemology Ontology for Biological Investigations (OBI) & Information Artifact Ontology (IAO)

  29. Automated ontology-based labeling of ERP data Pattern Labels Functional attributes Temporal attributes Spatial attributes = + + Concepts encoded in NEMO_Data.owl Robert M. Frank

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