Ontologies for Neuroscience and Neurology

The Neuroscience Information FrameworkFahim Imam, Stephen Larson, Georgio Ascoli, Gordon Shepherd,

Anita Bandrowski, Jeffery S. Grethe, Amarnath Gupta, Maryann E. MartoneUniversity of California, San Diego, George Mason University, Yale University

Alexander D. DiehlAlexander P. Cox, Mark P. Jensen, Alan Ruttenberg, Bianca Weinstock-Guttman, Kinga

Szigiti, and Barry SmithUniversity at Buffalo

NIF STANDARD ONTOLOGIES (NIFSTD)

• Set of modular ontologies – Covering neuroscience relevant

terminologies– Comprehensive ~60, 000 distinct concepts +

synonyms

• Expressed in OWL-DL language– Supported by common DL Resoners

• Closely follows OBO community best practices

• Avoids duplication of efforts – Standardized to the same upper level

ontologies • e.g., Basic Formal Ontology (BFO), OBO

Relations Ontology (OBO-RO), Phonotypical Qualities Ontology (PATO)

– Relies on existing community ontologies e.g., CHEBI, GO, PRO, OBI etc.

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• Modules cover orthogonal domain e.g. , Brain Regions, Cells, Molecules,

Subcellular parts, Diseases, Nervous system functions, etc.

Bill Bug et al.

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NIFSTD EXTERNAL COMMUNITY SOURCESDomain External Source Import/ Adapt Module Organism taxonomy NCBI Taxonomy, GBIF, ITIS, IMSR, Jackson Labs mouse catalog Adapt NIF-Organism

Molecules IUPHAR ion channels and receptors, Sequence Ontology (SO), ChEBI, and Protein Ontology (PRO); pending: NCBI Entrez Protein, NCBI RefSeq, NCBI Homologene, NIDA drug lists

Adapt IUPHAR, ChEBI;Import PRO, SO

NIF-MoleculeNIF-Chemical

Sub-cellular Sub-cellular Anatomy Ontology (SAO). Extracted cell parts and subcellular structures. Imported GO Cellular Component

Import NIF-Subcellular

Cell CCDB, NeuronDB, NeuroMorpho.org. Terminologies; pending: OBO Cell Ontology

Adapt NIF-Cell

Gross Anatomy NeuroNames extended by including terms from BIRN, SumsDB, BrainMap.org, etc; multi-scale representation of Nervous System Macroscopic anatomy

Adapt NIF-GrossAnatomy

Nervous system function

Sensory, Behavior, Cognition terms from NIF, BIRN, BrainMap.org, MeSH, and UMLS

Adapt NIF-Function

Nervous system dysfunction

Nervous system disease from MeSH, NINDS terminology; Disease Ontology (DO)

Adapt/Import NIF- Dysfunction

Phenotypic qualities PATO is Imported as part of the OBO foundry core Import NIF-Quality Investigation: reagents Overlaps with molecules above, especially RefSeq for mRNA Import NIF-InvestigationInvestigation: instruments, protocols

Based on Ontology for Biomedical Investigation (OBI) to include entities for biomaterial transformations, assays, data transformations

Adapt NIF-Investigation

Investigation: Resource NIF, OBI, NITRC, Biomedical Resource Ontology (BRO) Adapt NIF-Resource Biological Process Gene Ontology’s (GO) biological process in whole Import NIF-BioProcess Cognitive Paradigm Cognitive Paradigm Ontology (CogPO) Import NIF-Investigation

Mental Functioning, Mental Disease, Neurological Disease and Related Ontologies

Neurological Disease Ontology (ND)

– Based on the Ontology for General Medical Sciences

– Incorporates parts of NIF-Dysfunction– Three initial areas of focus• Dementia, in particular Alzheimer’s Disease• Multiple Sclerosis• Stroke, Cerebrovascular events

Goals• To provide a comprehensive representation of neurological diseases to support

clinicians and researchers in the diagnosis, treatment, and study of these diseases.

• To facilitate querying of medical databases for such purposes as performing quality analysis checks on diagnostic criteria at various stages of a disease’s progression.

• To allow physicians and researchers to provide a comprehensive clinical picture of a patient using a standardized language, and to connect and leverage structured descriptions in clinical and translational medicine, in EHRs and published research.

• To develop best practices for the development of other clinically oriented ontologies by identifying a robust set of relations for use with diseases and by providing an applied template for representing temporal entities within a domain.

BFO-OGMS-ND

BFO-OGMS-ND

Diseases

Alzheimer’sDisease

Alzheimer’sDisease

Referenced Ontologies

Status

ND currently contains 335 classes 199 classes have textual definitions 52 classes have logical definitions 157 classes have external references There are 190 children of disease

• First Public release planned by September 2012.

NeuroPsychological Testing Ontology