Ontologies for Neuroscience and Neurology The Neuroscience Information Framework Fahim Imam, Stephen Larson, Georgio Ascoli, Gordon Shepherd, Anita Bandrowski, Jeffery S. Grethe, Amarnath Gupta, Maryann E. Martone University of California, San Diego, George Mason University, Yale University Alexander D. Diehl Alexander P. Cox, Mark P. Jensen, Alan Ruttenberg, Bianca Weinstock-Guttman, Kinga Szigiti, and Barry Smith University at Buffalo
Ontologies for Neuroscience and Neurology. The Neuroscience Information Framework Fahim Imam, Stephen Larson, Georgio Ascoli, Gordon Shepherd, Anita Bandrowski , Jeffery S. Grethe , Amarnath Gupta, Maryann E. Martone - PowerPoint PPT Presentation
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
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
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
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