Ontologies for Neuroscience and Neurology
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Transcript of Ontologies for Neuroscience and Neurology
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