Neuroscience Information Framework Increasing Access to Neuroscience Resources

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

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

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

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

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

Comprehensive Ontology NIFSTD Macroscopic Anatomy Organism Subcellular Anatomy Molecule Macromolecule Molecule Descriptors • • • NS Dysfunction Cell Gene NS Function Techniques Resource Reagent Quality Investigation Instruments Protocols 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

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

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

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

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

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