Neuroscience Information Framework: Increasing Access to Neuroscience Resources on the Web

1. Neuroscience Information Framework: Increasing Access to Neuroscience Resources on the Web Maryann E.Martone, Ph. D. University of California, San Diego

2. Neuroscience Information Framework • Catalog of Neuroscience Resources, annotated with controlled vocabulary • Annotated archive of Neuroscience literature with tools for mining • Means to query “hidden” web content in databases • Interface for searching across multiple types of resources • Tools for creating discoverable resources • Strong foundation for data integration http://nif.nih.gov

3. NIF Collaborators Amarnath Gupta, UCSD, Co Investigator Jeff Grethe, UCSD, Co Investigator Gordon Shepherd, Yale University Perry Miller Luis Marenco David Van Essen, Washington University Erin Reid Paul Sternberg, Cal Tech Arun Rangarajan Hans Michael Muller Giorgio Ascoli, George Mason University Sridevi Polavarum

4. Integrated Search • NIF Registry • ~400 web resources annotated by humans with NIF vocabularies • NIF Neuroscience Web • Custom web index built using open source web tools (Nutch) from the NIF registry • Neuroscience literature • ~70,000 articles, full text indexed using Textpresso tool • NIF Data Federation • Web accessible databases registered to NIF mediator for deep content query • Limited number proof of concept • Other portals • Existing web resources that are themselves portals to resources • Science.gov

5. Registering a Resource to NIF • Level 1 • NIF Registry: high level descriptions from NIF vocabularies supplied by human curators • Level 2 • Access to deeper content; mechanisms for query and discovery • Level 3 • Direct query of web accessible database • Automated registration • Mapping of database content to NIF vocabulary by human

6. Comprehensive Ontology NIFSTD • Underlying the NIF is a rich ontology of neuroscience concepts, created from existing community resources • Built as separate modules covering domains such as anatomy, function, dysfunction, with minimum cross domain properties • Includes synonyms, lexical variants, UMLS mappings Organism Macroscopic Anatomy Cell NS Dysfunction Quality Molecule Subcellular Anatomy NS Function Investigation Gene Techniques Resource Instruments Macromolecule Molecule Descriptors Reagent Protocols

7. Building the NIF Vocabularies • NIF Basic: • Daniel Gardner held a series of workshops with neuroscientists to obtain sets of terms that are useful for neuroscientists • NIFSTD (NIF Standardized) (http://purl.org/nif/ontology/nif.owl) • Bill Bug built a set of expanded vocabularies using the structure of the BIRNLex and the import of existing terminological resources • Built from existing resources when possible • Standardized to same upper ontology • Provides enhanced coverage of domains in NIF Basic • Provides coverage of domains not included in NIF but covered by existing resources, e.g., molecules • Encoded in OWL/RDF • Provides mapping to source terminologies, including NIF Basic • Provides synonyms, lexical variants, abbreviations

8. Makes use of relations in the NIF ontology to broaden search Supports “AND” and “OR” searches

9. Moving Forward NIF is redesigning the initial registry to provide better support for level 1, 2 and 3 Population of resources Services to access resources Expanding the ontologies Exploring new interfaces and new ways of query

10. Cellular Component Small Molecule Anatomy Cell Type CNS Neuron Neuro- transmitter Transmembrane Receptor Purkinje Cell Dentate Nucleus Neuron Expressed in GABA GABA-R Cytoarchitectural Part of Cerebellar Cortex Cpllection of Deep Cerebellar Nuclei Presynaptic density Terminal Axon Bouton Dentate Nucleus Purkinje Cell Layer Transmitter Vesicle Located in

11. NIFLex Wiki