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+ http://www.virtualflybrain.org Virtual Fly Brain – under the hood. David Osumi-Sutherland, Simon Reeve, Nestor Milyaev, J. Douglas Armstrong, Michael Ashburner + Defining overlaps X Y part_of X Y X Z Y X overlaps Y if and only if: some Z exists and Z part_of X and Z part_of Y + DL1 adPN Lateral Horn Mushroom Body axon calyx adPN MBc cell body innervation MBc & LH glomerulus terminal arbour of dendrite fills glomerulus DL1, receives synapses LH iACT dendrite antennal lobe The Problem - an example We thank Greg Jefferies for kindly allowing us to use this image. We might wish to record: where are the neurons? the partonomy is complicated – parts of neurons are part of various structures. Where are the synapses, what is their direction ? What is the lineage of the neurons? What neurotransmitters do they release ? What functions are they implicated in ? If many neurons of some class are present per animal does what we wish to record about them apply all or just some of the class ? + Defining DL1 adPN Name: DL1 adPN Definition: "Antennal lobe projection neuron from the ad neuroblast lineage whose dendrites innervate only antennal lobe glomerulus DL1. Neurons of this class are derived from the first larval division of the antero-dorsal antennal lobe neuroblast (Yu et al., 2010)…" Jefferis et al., 2001, Nature 414(6860): 204—208; Komiyama and Luo, 2007, Curr. Biol. 17(3): 278—285; Yu et al., 2010, PLoS Biol. 8(8): Parent classes: * adult antennal lobe projection neuron adPN Relationships: * develops_from antero-dorsal AL neuroblast * has_postsynaptic_terminals_in antennal lobe glomerulus DL1 * has_presynaptic_terminals_in mushroom body calyx * has_presynaptic_terminals_in lateral horn * has_soma_location cortex of antennal lobe * releases_neurotransmitter acetylcholine * fasciculates_with iACT + Live demo of VFB - http://www.virtualflybrain.org queries on antennal lobe and antennal lobe glomerulus DL1 + + + + + + + + Current status – live! Website now in beta testing – please visit us at: http://www.virtualflybrain.org adult brain ontology - current stats 495 neuron classes 1147 neuronal innervation statements 360 brain regions 81 references Adult brain phenotypes and transgenes – current stats 4062 phenotype records 2142 transgene expression records + How does it work? Menu option: DL query: neuron that … overlaps some X … has_synaptic_terminal_in some X … has_presynaptic_terminal_in some X … has_postsynaptic_terminal_in some X + neuron that overlaps some ‘antennal lobe glomerulus DL1’ label: ‘DL1 adPN’ SubClassOf: 'antennal lobe projection neuron' SubclassOf: interneuron SubClassOf: neuron has_postsynaptic_terminal_in some ‘antennal lobe glomerulus DL1’ rule: if X has_postsynaptic_terminal_in Y then X overlaps Y ‘DL1 adPN’ neuron that overlaps some ‘antennal lobe glomerulus DL1’ + neuron that overlaps some ‘adult antennal lobe’ label: ‘DL1 adPN’ neuron that overlaps some ‘antennal lobe glomerulus DL1’ ‘antennal lobe glomerulus DL1’ part_of some ‘antennal lobe’ rule: If X overlaps Y and Y part_of Z then X overlaps Z ‘DL1 adPN’ neuron that overlaps some ‘antennal lobe’ + Auto-classification ‘adPN’ EquivalentTo: ‘antennal lobe projection neuron’ that develops_from some 'ad AL neuroblast’ and has_postsynaptic_terminals_in some ‘antennal lobe’ + Auto-classification ‘adPN’ EquivalentTo: ‘antennal lobe projection neuron’ that develops_from some 'ad AL neuroblast’ and has_postsynaptic_terminals_in some ‘antennal lobe’ ‘DL1 adPN’ has_postsynaptic_terminals_in some ‘antennal lobe glomerulus DL1’ ‘DL1 adPN’ develops_from some ‘ad AL neuroblast’ ‘antennal lobe glomerulus DL1’ part_of some ‘antennal lobe’ If X has_postsynaptic_terminals_in Y and Y part_of Z then X has_postsynaptic_terminals_in Z ‘DL1 adPN’ SubClassOf adPN + How to proceed Start from detailed, well referenced definitions. Be cautious about asserting classification Gradually work at formalising – checking that classification and queries work as expected. This works best with feedback between ontology developers and experts. + What needs to be standardised? Upper level classification of neurons motor; sensory ; interneuron ; intrinsic/principal/projection ; neurosecretory/neuro-endocrine Relations and their targets for recording neuron properties neurotransmitter location of various parts See forthcoming paper on relations used in VFB innervation and fasciculation patterns See forthcoming paper on relations used in VFB shape – of soma; branchiness function lineage + Acknowledgements Virtual Fly Brain Project (funded by the BBSRC): FlyBase Richard Baldock group– collaborative development of the VFB stack browser BrainName Douglas Armstrong, Simon Reeve, Nestor Milyaev, Michael Ashburner Kei Ito, Kazunori Shinomiya, Douglas Armstrong, George Boyan, Volker Hartenstein, Steffen Harzsch, Martin Heisenberg, Uwe Homberg, Arnim Jenett, Haig Keshishian, Linda Restifo, Wolfgang Rössler, Julie Simpson, Nicholas J. Strausfeld, Roland Strauss, Leslie B. Vosshall Greg Jefferis – consultation on olfactory system OBO Foundry Barry Smith, Chris Mungall, Alan Ruttenburg and others + Anatomy of a relation region Y neuron X has_presynaptic_terminal_in expands_to: has_part some ('presynaptic membrane ; GO_0042734' that part_of some ('synapse ; GO_0045202' that part_of some Y? ) 'neuron X' has_presynaptic_terminal_in some 'region Y' => ‘neuron X’ has_part some ('presynaptic membrane ; GO_0042734' that part_of some ('synapse ; GO_0045202' that part_of some ‘region Y’) + Defining overlaps X Y part_of X Y X Z Y X overlaps Y if and only if: some Z exists and Z part_of X and Z part_of Y