Alan Ruttenberg PONS R&D Task force Alan Ruttenberg Science Commons

Alan Ruttenberg Program on Ontologies of Neural Structures Three task forces – Structural Lexicon Task Force – Neuron Registry Task Force – Representation and Deployment Task Force Goals – Concensus terms and definitions for top level brain structures – Representation and collection of Neuron types – Enable community engagement in curation effort Strategy – Representation to OBO Foundry standards – Get consensus on representation then work towards user interface

Alan Ruttenberg Target OBO Ontologies for PONS Work Gene Ontology (GO) * Subcellular structures added to GO CC Cell Ontology (CL) Target for neuron types Foundational Model of Anatomy (FMA) Target for cross-species Anatomical Structures Relation Ontology (RO) Target for connectivity and spatial relations Chemical Entities of Biological Interest (CheBI) * Target for some (non-gene-product/small molecule) neurotransmitters Phenotype Ontology (PATO) * Target for morphology description Ontology for Biomedical Investigations (OBI) Target for methods Protein Ontology (PRO) * Target for expressed proteins/ receptors/neurotransmitters * Current foundry ontologies

Alan Ruttenberg Accomplishments Subcellular components used in Neurolex incorporated into GO Two workshops – First focused on establishing group/synchronizing – Second focused on making progress on representation of Neurons/Anatomical Structures Enumeration of potential connectivity and spatial relations, with relevance from fly to human Enumeration of primary methods for obtaining evidence of connectivity Exploratory conversions of BAMS to OWL Smaller meetings around coordination of BAMS/CL cell types.

Alan Ruttenberg Challenges Tension between allocating work to user-interface tools versus representation Namefights – X should be called “basket cell”. Y should be called “basket cell” – X should be called “Hippocampus”. X should be called “Hippocampal region” Focus on relations, definitions. Particularly difficult in brain structures, where emphasis has been on atlases as reference Huge range of existing and overlapping nomenclatures Large number of characterization methods for neurons

Alan Ruttenberg Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex

Alan Ruttenberg Next steps Cell ontology meeting mid May, leading to curation of priority neuron types to CL summer 2010, initially BAMS cell types. Summer 2010 workshop focused on curating subset of priority cross species brain structures into FMA Review and condensation of proposed set of relations to core set – Q3/Q Incorportion of Neuron types from Ascoli effort as collection emerges – est. Q3/Q Semantic web accessible versions of above – Q4/2010 Synchronization between Neurolex/Semweb versions – ongoing Q2-Q1 2010: Q4 Assessement of curation needs – do we need to contract for curation or will community participation suffice? Goal: Main issues addressed in 2010 with prototypes, with 2011 focused on growing set of neuron and structure types