September 16, 2009

NEMO OWL ontologies:Viewing & editing OWL/RDF files,

part II

http://nemo.nic.uoregon.edu

Overview Agenda

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

Overview Agenda

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

Reminder: Top-Down + Bottom-Up in NEMO

NEMO Ontologies & Ontology-Based Tools for Data Mark-up

and Analysis

TOP-DOWN

BOTTOM-UP

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

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”

(*)

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

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

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

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

Overview Agenda

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

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….

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.

NEMO_spatial schematic

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)

NEMO_temporal schematic

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)

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

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)

Overview Agenda

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

NEMO_spatial classes

NOTE (figure underspecified here):Scalp = three_dimensional objectScalp_surface = two_dimensional object_boundaryScalp_surface_region = two_dimensional spatial_region

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

International 10-10 EEG Electrode Locations

ITT electrode location Fz(frontocentral_scalp_region)

Scalp surface “regions of interest”

NEMO Temporal Ontology

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

NEMO Functional Ontology

Angela LairdBrainMap

Jessica TurnerBIRNlex

(now part of Neurolex)

CogPO

http://brainmap.org/scribe/index.html

NEMO Data Ontology:Where ontology meets epistemology

Ontology for Biological Investigations (OBI)

&Information Artifact

Ontology (IAO)

Automated ontology-based labeling of ERP data

Pattern Labels

Functional attributes

Temporal attributes

Spatial attributes

= + +

Robert M. Frank

Concepts encoded in NEMO_Data.owl