Download Virtual Fly Brain – under the hood.

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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
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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
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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.
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We might wish to record:
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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 ?
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Defining DL1 adPN
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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
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Live demo of VFB
- http://www.virtualflybrain.org
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queries on antennal lobe and antennal lobe glomerulus DL1
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Current status – live!
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Website now in beta testing – please visit us at:
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http://www.virtualflybrain.org
adult brain ontology - current stats
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495 neuron classes
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1147 neuronal innervation statements
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360 brain regions
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81 references
Adult brain phenotypes and transgenes – current stats
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4062 phenotype records
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2142 transgene expression records
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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
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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’
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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’
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Auto-classification
‘adPN’ EquivalentTo: ‘antennal lobe
projection neuron’ that develops_from
some 'ad AL neuroblast’ and
has_postsynaptic_terminals_in some
‘antennal lobe’
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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
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How to proceed
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Start from detailed, well referenced definitions.
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Be cautious about asserting classification
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Gradually work at formalising – checking that classification
and queries work as expected.
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This works best with feedback between ontology developers and
experts.
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What needs to be standardised?
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Upper level classification of neurons
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motor; sensory ; interneuron ; intrinsic/principal/projection ; neurosecretory/neuro-endocrine
Relations and their targets for recording neuron properties
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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
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Acknowledgements
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Virtual Fly Brain Project (funded by the BBSRC):
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FlyBase
Richard Baldock group– collaborative development of the VFB stack
browser
BrainName
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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
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Barry Smith, Chris Mungall, Alan Ruttenburg and others
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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’)
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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