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

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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

NIF Standard Ontologies 13

QUESTIONS?

• NIFSTD Ontologieshttp://ontology.neuinfo.org

• NeuroLex Wikihttp://neurolex.org

• Neuroscience Information Framework(NIF)

http://neuinfo.org• Visit NIF at booth # 4024

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