NEMO Technical Document 2010-006 Gwen FrishkoffSnezana NikolicPaea LePendu

THE STRUCTURE OF NEMO ONOLOGYCreated: 05/16/2010 (GF)

Last Updated: 11/15/2010 (GF,SN)

1. INTRODUCTION

Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).

This document provides a brief description of NEMO ontology "modules", i.e. sub-ontologies (formally encoded in *.owl files as NEMO namespace annotation) and how they are related.

The NEMO ontology file is called "NEMO.owl" and directly imports (via <owl:imports>) two files: NEMO_annotation_properties file and BFO ontology file.

The latest release of NEMO.owl can be browsed and downloaded from the BioPortal website

http://bioportal.bioontology.org/ontologies/40522

Latest release version, working version and old (legacy) versions of NEMO.owl, and all other NEMO*.owl files, can be downloaded from the NEMO SVN repository:

http://purl.bioontology.org/NEMO/ontology/

2. OVERVIEW OF NEMO "FACTORIAL" STRUCTURE

A common recommendation (e.g., see OBO Foundary "best practices") is to separate (or "factor," "normalize") the domain of interest into nonoverlapping ("orthogonal," "normalized") subdomains. This recommendation appears motivated by similar practices in database design (Rector, 2003). Distinct subdomains or modules (aka "branches," in reference to concept hierarchies) may then be stored in separate ontologies (files coded in xml/rdf or owl/rdf, etc.). Unfortunately, there appears to be no standard method of "factoring" ontologies, or at least none that has been widely adopted in the bio-ontology community (Rector, 2003). For this reason, groups such as OBO, which comprise many modules (OBI, IAO, PATO, UO, etc.), periodically restructure their work (and files). It seems likely that NEMO will periodically undergo restructuring, as well. However, most of these changes should not affect the end user, since they will typically be viewing NEMO.owl, rather than individual modules.

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Currently, NEMO contains 9 ontology modules each of which is formally represented as a NEMO namespace which is in turn encoded in <NEMO_annot:namespace> annotation properties associated with each term in the ontology. Five of these modules are the "core five" sub-ontologies and they are the focus of NEMO ontology development efforts:

1. NEMO_spatial module Contains spatial regions and qualities, as well as anatomical entities (which may be moved to another ontology module; See Section 3 for discussion)

2. NEMO_temporal module Contains temporal intervals and qualities, as well as some physiological concepts (which may be moved to another ontology module; See Section 4 for discussion)

3. NEMO_functional module Contains entities and qualities that are related to cognitive and behavioral paradigms (see Section 5 for discussion)

4. NEMO_ERP module Contains ERP spatiotemporal patterns as well as some electrophysiological entities (which may be moved to another ontology module; See Section 6 for discussion)

5. NEMO_data module Contains data_set, measurement, statistical concepts (mostly subclasses of IAO:information_content_entity"; See Section 7 for discussion).

Figure 1. Overview of five "core" NEMO ontologies. See Sections 3-7 for details.[update with correct relations...]

The other four sub-ontologies can be viewed as support modules to the five core modules listed above.

1. NEMO_annotation_properties module Contains specifications (and processing instructions) for NEMO concepts’ annotation properties.

2. NEMO_relations module - Contains all (both NEMO-native and imported) the relational properties used in NEMO.

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3. NEMO_imported_classes module - Contains all information about all classes that have been imported into NEMO from other ontologies (mostly from OBI, IAO, UO, PATO).

4. NEMO_deprecated module - Contains information about all concepts that are no longer used in any of NEMO modules.

Figure 2. Screenshot of NEMO.owl ontology file, as displayed in Protégé ontology editor.

Sections 3 ff. briefly describe each ontology module, and the final section discusses some open issues that we would like to resolve before the next release.

3. NEMO SPATIAL ONTOLOGY MODULE

NEMO_spatial represents anatomical entities, including the scalp and subdivisions of the scalp. It also includes concepts related to the spatial distribution of neural signals (EEG and MEG) across the scalp surface, where electromagnetic signals are typically measured. In future versions, NEMO_spatial will be expanded to include concepts related to the spatial distribution of neural activity within the brain (for EEG and MEG patterns that have been source modeled).

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Figure 3. Three views of NEMO_spatial module. Top left, ITT_electrode_locations defined as zero_dimensional_spatial_regions. Top right, types of spatial_anatomical_quality. Bottom, regions of the

scalp_surface.

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Figure 4. Overview of NEMO spatial ontology module

4. NEMO TEMPORAL ONTOLOGY MODULE

NEMO_temporal is one of “core five” modules in NEMO. It includes concepts related to neuroelectric (EEG) and neuromagnetic (MEG) activity and the temporal properties that are associated with different patterns of EEG and MEG activity that are observed in different experiment contexts.

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Figure 5. Four views of NEMO_temporal module. Top, temporal intervals and temporal instants. Middle left, types of event_boundary. Middle right, types of physiological_process.

Bottom, event_related temporal qualities.

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Figure 6. Overview of NEMO temporal ontology.

5. NEMO FUNCTIONAL ONTOLOGY MODULE

NEMO_functional describes concepts related to cognitive and behavioral experiments, especially elements of cognitive protocols that are relevant for analysis and interpretation of EEG and MEG experiment results.

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Figure 7. Three views of NEMO_functional module. Top, stimulus_presentation, response, and task qualities. Middle, types of plan_specification. Bottom, subject, subject_group, and stimulus qualities.

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6. NEMO ERP ONTOLOGY MODULE

NEMO_ERP includes a taxonomy of patterns that are commonly seen in ERP experiments on human perception, language, and cognitive processing. The working definition of ERP_spatiotemporal_pattern is a BFO:generically_dependent_continuant that "inheres_in an aggregate of event-related potentials," where "event-related_potential" (ERP) is defined as a type of PATO:physical_quality that inheres_in an electrodynamic_field. Each ERP_spatiotemporal_pattern is located_in some NEMO_spatial: scalp_surface_region (actually, multiple regions) and occurs within some NEMO_temporal:event-related_temporal_interval in response to an ERP_event (stimulus_onset, response_offset, etc.). The precise relationships between these concepts are being sorted out.

Meanwhile, we are combing the literature for consistent definitions of ERP_spatiotemporal_patterns and are documenting these, along with their definition source(s), in a separate FileMakerPro database. We are still adopting the perspective that ERP patterns in actual datasets should not be explicitly labeled with any of these traditional pattern names. Rather, data will be annotated using NEMO_data ontology concepts (representation of peak_latency, positive and negative centroid locations, and so forth). Since NEMO_data concepts are linked to NEMO_spatial, NEMO_temporal, and NEMO_functional (Fig. 1), they can therefore be linked to pattern classes by inference. This means that the results of forward inferences (i.e., "inference engines" or "reaoners")

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Figure 8. Most recent working list of ERP_spatiotemporal_patterns. See FileMakerPro database for more extensive list.

7. NEMO DATA ONTOLOGY MODULE

NEMO_data.owl includes concepts related to EEG and MEG experiment data, their acquisition, analysis, statistical (numeric) representation and terms that occur as input or output metrics in one of the NEMO_ERP_Analysis toolkit MATLAB scripts.

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Figure 9. Three views of NEMO_data module. Top, types of information_content_entity. Middle, types of information_entity_quality. Bottom, types of instrument

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8. NEMO ANNOTATION PROPERTIES ONTOLOGY MODULE

Please see NEMO-TR2010-002 for details.

9. NEMO IMPORTED CLASSES ONTOLOGY MODULE

Please see NEMO-TR2010-004 for details.

10. NEMO DEPRECATED ONTOLOGY

Please see NEMO-TR2010-001 for details.

11. THE STRUCTURE OF NEMO ONTOLOGY FILES

The “core five” NEMO modules (NEMO_data, NEMO_ERP, NEMO_functional, NEMO_spatial, NEMO_temporal) and the two of three “supporting” modules (NEMO_imported_classes, NEMO_relations) are all included into NEMO.owl file. NEMO_annotation_properties module is has not included into NEMO.owl for the easiness of file editing purposes,. Similarly, since NEMO_deprecated serves as global storage house for all terms that have been removed from the ontology, this file has also been excluded from NEMO.owl.

During every loading of NEMO.owl by Protege ontology editor the following two files are directly loaded: NEMO_annotation_properties and BFO (bfo-1.1.owl). NEMO_deprecated.owl can be loaded manually by using Protege import tool. Note: If NEMO.owl is edited by using a text editor, no file is automatically loaded.

NEMO_deprecated.owl, if needed, can be loaded manually by using Protege import tool, but no NEMO_deprecated.owl file editing can be made during that time.

Note: Since NEMO_deprecated.owl is not automatically loaded with NEMO.owl (unlike NEMO_annotation_properties.owl and bfo-1.1.owl), when a term needs to be deprecated, the code describing the term must be manually moved to NEMO_deprecated.owl in a separate step (see TR2010-001 for details).

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