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

2. Overview Agenda 1.Short-term goals & methods [10 mins] 2.Divide & conquer strategy [10 mins] 3.Hands-on part [30-40 mins]

3. Overview Agenda 1.Short-term goals & methods [10 mins] 2.Divide & conquer strategy [10 mins] 3.Hands-on part [30-40 mins]

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

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 1.Short-term goals & methods [10 mins] 2.Divide & conquer strategy [10 mins] 3.Hands-on part [30-40 mins]

13. 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….

14. 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/NEMOt echnicalreports/GSNtoITTtoROImappings.zip Resolve issues with scalp, scalp_surface, scalp_region, located_in vs. surface_of etc.

15. NEMO_spatial schematic

16. 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)

17. NEMO_temporal schematic

18. 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)

19. 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

20. 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)

21. Overview Agenda 1.Short-term goals & methods [10 mins] 2.Divide & conquer strategy [10 mins] 3.Hands-on part [30-40 mins]

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

23. 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

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

25. Scalp surface “regions of interest”

26. NEMO Temporal Ontology

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

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

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

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