No Euphemisms Required: BIRN on the Leading Edge of Community Ontology Development

The Ontology Task Force: Cross Test Beds  Carol Bean (co-chair), NIH-NCRR  Maryann Martone (co-chair), BIRN CC  Amarnath Gupta, BIRN CC  Bill Bug, Mouse BIRN  Christine Fennema-Notestine, Morph BIRN  Jessica Turner, FBIRN Jeff Grethe, BIRN CC Daniel Rubin, NCBO David Kennedy, Morph BIRN Provide a dynamic knowledge infrastructure to support integration and analysis of BIRN federated data sets, one which is conducive to accepting novel data from researchers to include in this analysis Identify and assess existing ontologies and terminologies for summarizing, comparing, merging, and mining datasets. Relevant subject domains include clinical assessments, assays, demographics, cognitive task descriptions, neuroanatomy, imaging parameters/data provenance in general, and derived (fMRI) data Identify the resources needed to achieve the ontological objectives of individual test-beds and of the BIRN overall. May include finding other funding sources, making connections with industry and other consortia facing similar issues, and planning a strategy to acquire the necessary resources

Goals from Last Year Develop policies and procedures for utilizing and constructing ontologies in BIRN Posted on OTF Wiki Hold workshop for BIRN participants on using and extending ontologies Jan 2006 March 2006 (NCBO) Develop curation procedures and policies Cross test bed integration Neuroanatomy Animal model - human disease

Ontology Task Force Workshops Workshop in January 2006: Annotating BIRN data –Evaluated current state of terminologies (Bonfire) and tools for annotation Carol Bean arranged for OTF to attend workshop in March 2006 –National Center for Biomedical Ontologies (NCBO), NCBC, Mark Musen, P. I. Suzanna Lewis, Barry Smith, Michael Ashburner, Mark Musen, Daniel Rubin –Educated us on efforts underway at NCBO and vice versa –Provided their view on ontology “best practices” and what were examples of good ontologies –Evaluated BIRN’s current efforts

BIRNLex Major accomplishment: Version 1.0 of BIRNLexBIRNLex Grew out of BIRN Ontology Workshops –Meant to cover all domains of interest to BIRN: imaging, neuroanatomy, experimental techniques, behavior –Presented at this year’s SFN meeting; version 1.0 to be released very soon –Draft version posted on the web (see OTF Wiki) –Current domain areas: neuroanatomy, taxonomy, behavioral paradigms, mouse strain nomenclature MIND ontology –Next step: transition the BIRNLex into a fully structured ontology –“Multiscale investigation of neurological disease”

BIRNLex - General Principles OTF has adopted and refined best practices for ontology development being promoted by NCBO/OBO Foundry re-use existing community ontologies covering BIRN require domains - e.g. OBI, CARO, BFO, GO Cellular Component, NCBI taxonomy novel domains - behavioral paradigms, imaging protocols, etc. - submit to OBO Foundry or contribute to relevant community effort (e.g., imaging experiments and processing going into OBI) for all BIRNLex entities - must have Aristotelian definitions (genera & differentia) OTF and other BIRN members are holding regular curation sessions (Jyl Boline, Brett Peterson) heavy use of curatorial metadata to support automated evaluation/analysis/maintenance of ontology - match practice in field Use OWL and other supporting technologies enabling us to leverage variety of mature and emerging tools to support ontology curation, ontology-centric annotation, and ontology-driven semantic querying

Core domain: Neuroanatomy Evaluated the use of neuroanatomical terms within and across Mouse BIRN and Morph BIRN –Christine Fennema-Notestine, Maryann Martone, Jyl Boline, Allan MacKenzie-Graham Imported entities from Neuronames into BIRNLex (Bill) –Providing clear definitions for each anatomical entity –Defining a core neuroanatomy for BIRN that will cross test beds Will discuss findings and strategies at Wednesday’s session

BIRN is a valuable testbed Thanks largely to the efforts of Bill Bug, BIRN is now represented in many of the terminology and ontology efforts currently underway: –OBI –PATO (will be attending workshop in December) –Disease Ontology (meeting in November) –NIF –The Neurocommons Project (outgrowth of Science commons and W3C Semantic Web activity) We have assembled use cases for all of these groups; posted on OTF Wiki BIRN has already gone further than most groups in defining the ways in which these ontologies need to grow and adapt Complex domain (studies of CNS disease) providing attractive exemplar for community biomed. ontology projects

Community Biomedical Ontology Development (NCBO) BIRN Contributions BIRNLex is the best example of these emerging community best practices put into effect on a broad, complex domain - neuroscience at multiple time, spatial, and conceptual domains - in the critically important context of translational research still a lot more software development to be done making important progress in novel ontological domains - organism tax., neuroanatomy, microscopy & imaging methods, behavioral paradigms, etc. - remember - a terminology IS NOT an ontology providing a means by which other extremely valuable neuroinformatic knowledge resources can integrate more completely into the community of formal semantic biomed. frameworks - e.g., Brainmap.org, BAMS, NeuroNames, RadLex, etc.

BIRN is a valuable partner BrainMap –Close collaboration with Peter Fox’s group –Defining behavioral paradigms Jessica Turner, Angie Laird UK NeuroGrid and PsyGrid projects –Contacted OTF –Want to partner with BIRN on ontology development

Presenting BIRNLex Imaging Ontology workshop, March 2006 Society for Neurosciences meeting –Two posters on BIRNLex and Data Integration –Manuscripts are in preparation PATO workshop AMIA UK e-science Neuro/Psy Grid meeting

Resources for Ontology Work NIF: Neuroinformatics Framework –Maryann,Jeff, Amarnath, Bill Collaborating RO1 with NCBO to develop tools for annotation of multiscale imaging data and drive development of disease- model mapping (BIRN CC)

Summary of Activities of OTF (and friends) Developed BIRNLex –BIRN has gone farther than most of the neuroscience community in embracing standards for ontology construction utilized by other communities in the Life Sciences –Mouse BIRN is already using BIRNLex We have developed a set of ontology “best practices” and procedures for community ontology development –Next steps: tools for community contribution and utilization of BIRNLex Sessions on Wednesday will introduce the BIRNLex and provide overview of efforts on cross-test bed neuroanatomy