1. N IF S TD : A C OMPREHENSIVE O NTOLOGY FOR N EUROSCIENCE Fahim IMAM 1, Stephen LARSON 1, Sridevi POLAVARAM 2, Georgio ASCOLI 2, Gordon SHEPHERD 3, Jeffery S. GRETHE 1, Amarnath GUPTA 1, Maryann E. MARTONE 1 ; 1 Univ. of California, San Diego, CA; 2 George Mason Univ., Fairfax, VA; 3 Yale 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

2. NIF: D ISCOVER AND UTILIZE WEB - BASED N EUROSCIENCE 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

3. 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

4. A BOUT O NTOLOGY “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 4NIF Standard Ontologies NIFSTD Ontologies neuinfo.org 4

5. Class nameAsserted necessary conditions Cerebellum Purkinje cell1.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 neurotransmitter 5.It has ‘Spiny dendrite quality’ Class nameAsserted defining (necessary & sufficient) expression Cerebellum neuronIs a ‘Neuron’ whose soma lies in any part of the ‘Cerebellum’ or ‘Cerebellar cortex’ Principal neuronIs 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 neuronIs a ‘Neuron’ that uses ‘GABA’ as a neurotransmitter O NTOLOGY – A SSERTED K NOWLEDGE 5NIF Standard Ontologies NIFSTD Ontologies neuinfo.org 5

6. N IF S TD C URRENT V ERSION 6NIF Standard Ontologies Key feature: Includes a set useful defined concepts to have inferred classifications of asserted concepts NIFSTD Ontologies neuinfo.org 6

7. C ONCEPT -B ASED S EARCH 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

8. N IF S TD AND N EURO L EX W IKI 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 NIF Standard Ontologies 8 Stephen D. Larson et al. NIFSTD Ontologies neuinfo.org 8

9. 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 Is part of S HARED BUILDING BLOCKS GABA IP3 (CHEBI:16595) IP3 (CHEBI:16595) Cerebellum Purkinje neuron Cerebellar cortex Has part NIFSTD Ontologies neuinfo.org 9

10. A CCESS TO S HARED O NTOLOGIES NIFSTD is available as – OWL Format http://ontology.neuinfo.orghttp://ontology.neuinfo.org – RDF and SPARQL Endpoint Specific contents through web services – http://ontology.neuinfo.org/ontoquest.html 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/ 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 NIF Standard Ontologies10 NIFSTD Ontologies neuinfo.org 10

11. W ORKING TO I NCORPORATE C OMMUNITY NeuroPsyGrid – http://www.neuropsygrid.org http://www.neuropsygrid.org NDAR Autism Ontology – http://ndar.nih.gov http://ndar.nih.gov Disease Phenotype Ontology – http://openccdb.org/wiki/index.php/Disease_Ontology http://openccdb.org/wiki/index.php/Disease_Ontology Cognitive Paradigm Ontology (CogPO) – http://wiki.cogpo.org http://wiki.cogpo.org Neural ElectroMagnetic Ontologies (NEMO) – http://nemo.nic.uoregon.eduhttp://nemo.nic.uoregon.edu 11NIF Standard Ontologies NIFSTD Ontologies neuinfo.org 11

12. S UMMARY AND C ONCLUSIONS 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 12NIF Standard Ontologies NIFSTD Ontologies neuinfo.org 12

13. Q UESTIONS ? NIFSTD Ontologies http://ontology.neuinfo.org NeuroLex Wiki http://neurolex.org Neuroscience Information Framework (NIF) http://neuinfo.org Visit NIF at booth # 4024 13NIF Standard Ontologies NIFSTD Ontologies neuinfo.org 13