Transcript 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)
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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) *
* Current foundry ontologies
• Target for expressed proteins/ receptors/neurotransmitters
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.
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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
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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/Q4 2010
• Incorportion of Neuron types from Ascoli effort as collection emerges –
est. Q3/Q4 2010
• 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
Alan Ruttenberg