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NIF S TANDARD O NTOLOGIES (N IF S TD ) Set of modular ontologies – Covering neuroscience relevant terminologies – Comprehensive 50,000+ distinct concepts + synonyms Expressed in OWL-DL language Closely follows OBO community best practices – As long as they seem practical 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. 3NIF Standard Ontologies Modules cover orthogonal domain e.g., Brain Regions, Cells, Molecules, Subcellular parts, Diseases, Nervous system functions, etc. Bill Bug et al. NIFSTD Ontologies neuinfo.org 3
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NIFSTD: A COMPREHENSIVE ONTOLOGY FOR NEUROSCIENCE
Fahim IMAM1, Stephen LARSON1, Sridevi POLAVARAM2, Georgio ASCOLI2, Gordon SHEPHERD3, Jeffery S. GRETHE1, Amarnath GUPTA1,
Maryann E. MARTONE1; 1Univ. of California, San Diego, CA; 2George Mason Univ., Fairfax, VA; 3Yale Univ.,
New Haven, CT
November 14, 2010
Funded in part by the NIH Neuroscience Blueprint HHSN271200800035C via NIDA.
NEUROSCIENCE INFORMATION FRAMEWORK
NIFSTD Ontologies neuinfo.org 1
NIF: DISCOVER AND UTILIZE WEB-BASED NEUROSCIENCE RESOURCES
A portal to finding and using neuroscience resources
A consistent framework for describing resources
Provides simultaneous search of multiple types of information, organized by category
NIFSTD Ontology, a
critical component Enables concept-based search
UCSD, Yale, Cal Tech, George Mason, Harvard MGH
Supported by NIH Blueprint
NIFSTD Ontologies neuinfo.org 2
NIF STANDARD ONTOLOGIES (NIFSTD)
• Set of modular ontologies – Covering neuroscience relevant
terminologies– Comprehensive 50,000+ distinct concepts +
synonyms
• Expressed in OWL-DL language
• Closely follows OBO community best practices – As long as they seem practical
• 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.
3NIF Standard Ontologies
• Modules cover orthogonal domain e.g. , Brain Regions, Cells, Molecules,
Subcellular parts, Diseases, Nervous system functions, etc.
Bill Bug et al.
NIFSTD Ontologies neuinfo.org 3
NIF Standard Ontologies 4
ABOUT ONTOLOGY
• “Explicit specification of conceptualization” - Tom Gruber
• Organizing the concepts involved in a domain into a hierarchy and
• Precisely specifying how the concepts are ‘related’ with each other (i.e., logical axioms)
• Explicit knowledge are asserted but implicit logical consequences can be inferred – Most powerful feature of an ontology
NIFSTD Ontologies neuinfo.org 4
NIF Standard Ontologies 5
Class name Asserted necessary conditions Cerebellum Purkinje cell 1. Is a ‘Neuron’
2. Its soma lies within 'Purkinje cell layer of cerebellar cortex’3. It has ‘Projection neuron role’4. It uses ‘GABA’ as a neurotransmitter5. It has ‘Spiny dendrite quality’
Class name Asserted defining (necessary & sufficient) expressionCerebellum neuron Is a ‘Neuron’ whose soma lies in any part of the ‘Cerebellum’ or
‘Cerebellar cortex’ Principal neuron Is a ‘Neuron’ which has ‘Projection neuron role’, i.e., a neuron
whose axon projects out of the brain region in which its soma lies GABAergic neuron Is a ‘Neuron’ that uses ‘GABA’ as a neurotransmitter
ONTOLOGY – ASSERTED KNOWLEDGE
NIFSTD Ontologies neuinfo.org 5
NIF Standard Ontologies 6
NIFSTD CURRENT VERSION
• Key feature: Includes a set useful defined concepts to have inferred classifications of asserted concepts
NIFSTD Ontologies neuinfo.org 6
CONCEPT-BASED SEARCH• Search Google: GABAergic neuron• Search NIF: GABAergic neuron
– NIF automatically searches for types of GABAergic neurons
Types of GABAergic neurons
NIFSTD Ontologies neuinfo.org 7
NIF Standard Ontologies
NIFSTD AND NEUROLEX WIKI
• Semantic wiki platform• Provides simple forms for
structured knowledge• Can add concepts,
properties• Generate hierarchies
without having to learn complicated ontology tools
• Good teaching tool for principles behind ontologies
• Community can contribute– Each term gets its own unique
ID
8
Stephen D. Larson et al.NIFSTD Ontologies neuinfo.org 8
Cerebellum Purkinje cell soma
Cerebellum Purkinje cell
dendrite
Cerebellum Purkinje cell axon
Cerebellum granule cell layer
Cerebellum Purkinje cell layer
Cerebellum molecular layer
Has part
Has part
Has part
Is part of
Is part of
Is part of
SHARED BUILDING BLOCKS
GABA IP3(CHEBI:16595)
Cerebellum Purkinje neuron
Cerebellar cortex
Has partHas part
Has part
NIFSTD Ontologies neuinfo.org 9
NIF Standard Ontologies 10
ACCESS TO SHARED ONTOLOGIES
• NIFSTD is available as– OWL Format http://ontology.neuinfo.org – RDF and SPARQL Endpoint
• Specific contents through web services – http://ontology.neuinfo.org/ontoquest.html
• Available through NCBO Bioportal– Repository of biomedical ontologies– 199 ontologies including NIFSTD– Provides annotation and mapping services– http://bioportal.bioontology.org/
• INCF Program on Ontologies for Neural Structure– Neuronal Registry Task Force: Description of neural
properties– Structural Lexicon: Description of structures across
scales
NIFSTD Ontologies neuinfo.org 10
NIF Standard Ontologies 11
WORKING TO INCORPORATE COMMUNITY
• NeuroPsyGrid – http://www.neuropsygrid.org
• NDAR Autism Ontology – http://ndar.nih.gov
• Disease Phenotype Ontology– http://openccdb.org/wiki/index.php/Disease_Ontology
• Cognitive Paradigm Ontology (CogPO) – http://wiki.cogpo.org
• Neural ElectroMagnetic Ontologies (NEMO) – http://nemo.nic.uoregon.edu
NIFSTD Ontologies neuinfo.org 11
NIF Standard Ontologies 12
SUMMARY AND CONCLUSIONS
• NIF project with NIFSTD is an example of how ontologies can be used to enhance search and data integration across diverse resources
• NIFSTD continues to create an increasingly rich knowledgebase for neuroscience integrating with other life science community
• NIF encourages the use of community ontologies for resource providers
NIFSTD Ontologies neuinfo.org 12
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