External access to NMO via URL

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NeuroMorpho.Org Giorgio A. Ascoli Center for
Neural Informatics, Structures, and Plasticity
Molecular Neuroscience Department, Krasnow
Institute for Advanced Study, George Mason
University Fairfax, Virginia (USA)
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Sneak preview of the hands-on demo

• First things first What are we talking about?
• The data digital reconstructions of neuronal
  morphology
• NeuroMorpho.Org by the numbers relationship
  with NIF the bird view
• Browsing each and all neurons
• The main axes by lab, brain region, cell type
• The raw files original, curated, and everything
  in between
• The visuals images, movies, and virtual reality
• The individual objects attributes, references,
  and links (out and in)
• Searching NeuroMorpho.Org
• By metadata organization, retrieval, and display
• By morphometry (i.e., content-based queries)
• By keywords (also direct external access via URL)
• Through the NIF
• How things work
• Help and usage statistics
• Level III Registration with NIF

The brains behind the neurons Ken
Smith Jeffrey Hoyt Gail Hamilton
Maryam Halavi Sridevi Polavaram Duncan Donohue
and the NIF Team!
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Single Cell Arborizations Dendrites Axons
In vivo, slice, culture
Cell excitability Synaptic integration Signal
delay failure Network connectivity Molecular
segregation

• Golgi
• Intracellular
• GFP
• diI

Visualization Imaging
Image Stack (or microscopy feed)
Camera lucida

• ImageJ Plugin N_M
• MBF Neurolucida
• Imaris Bitplane

Surface rendering
3D Vector Tracing
Digital Morphologies
Jacobs Theunissen, J Neurosci. 96 Chklovskii,
Neuron 04 Shepherd et al, Nat Neurosci
05 Kalisman et al, PNAS 05 Stepanyants et al,
Cereb Cx 07 Jefferis et al, Cell 07
Growth Sims
L-Neuron
NEURON, Genesis
NeuroMorpho.Org
Compartmental Models (SenseLab ModelDB!)
Potential synaptic contacts
L-Measure MBF NeuroExplorer
Archiving, Data mining DB storage retrieval
CRCNS (NIA, NSF) HBP (NINDS, NIMH, NSF) NIF
(NIDA/BP)
Morphometric Analysis Classification
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NeuroMorpho.Org

• Current Status
• 1826 cell reconstructions
• Across 25 different laboratories
• Available in 10 different formats
• Approximately 50 cell types
• And 92 brain regions
• Across 20 different species
• Statistics
• Since August 1, 2006
• Total site hits 6171
• Total downloads 54517

• Relationship to NIF
• Focused data type
• Well defined subcommunity
• Goal of dense coverage
• Time line
• Active stand-alone for 1yr
• Registration started
• Progress ahead of schedule

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External access to NeuroMorpho.Org via URL

• NMO could be directly accessed by a URL to
  retrieve a summary detail page on specific search
  criteria.
• URL e.g
• http//neuromorpho.org/neuroMorpho/FormSubmit.jsp
  ?Format..
• URL syntax takes 6 name-value pairs
• Format NeuronSummary default
• Datasource main default
• outputSize none default
• Workflow Direct SQL default
• Form name of URL originator optional
• Query appropriate SQL query required

http//neuromorpho.org/neuroMorpho/FormSubmit.jsp?
FormatNeuronSummaryDatasourcemainoutputSizeno
neworkflowDirect20SQLformSearchPage2.jspquer
ySELECT20DISTINCT20neuron.neuron_name,20archiv
e.archive_name,20species.species,20neuron_region
1.region1,20neuron_region2.region2,20neuron_clas
s1.class120AS20'Main20Cell20Type',20neuron_cl
ass2.class2,20file.filename20From20neuron,20ar
chive,20species,20neuron_class1,20reconstructio
n,20neuron_class2,20file,20neuron_region1,20ne
uron_region220where20(neuron.region1_id'8')20A
ND20(neuron.species_id'2')20AND20(neuron.class
2_id'3')20AND20neuron_region1.region1_idneuron
.region1_id20AND20file.neuron_idneuron.neuron_i
d20AND20neuron_region2.region2_idneuron.region2
_id20AND20reconstruction.reconstruction_idneuro
n.reconstruction_id20AND20neuron_class1.class1_i
dneuron.class1_id20AND20species.species_idneur
on.species_id20AND20neuron_class2.class2_idneur
on.class2_id20AND20archive.archive_idneuron.arc
hive_id20ORDER20BY20species.species20ASC,20ar
chive.archive_name20ASC,20neuron_region1.region1
20ASC,20neuron_class2.class220ASC
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SQL query

• SQL query for brainstem, motoneuron and rat
  
• SELECT DISTINCT neuron.neuron_name,
  archive.archive_name, species.species,
  neuron_region1.region1, neuron_region2.region2,
  neuron_class1.class1 AS 'Main Cell Type',
  neuron_class2.class2, file.filename From neuron,
  archive, species, neuron_class1, reconstruction,
  neuron_class2, file, neuron_region1,
  neuron_region2 where (neuron.region1_id'8') AND
  (neuron.species_id'2') AND (neuron.class2_id'3')
  AND neuron_region1.region1_idneuron.region1_id
  AND file.neuron_idneuron.neuron_id AND
  neuron_region2.region2_idneuron.region2_id AND
  reconstruction.reconstruction_idneuron.reconstruc
  tion_id AND neuron_class1.class1_idneuron.class1_
  id AND species.species_idneuron.species_id AND
  neuron_class2.class2_idneuron.class2_id AND
  archive.archive_idneuron.archive_id ORDER BY
  species.species ASC, archive.archive_name ASC,
  neuron_region1.region1 ASC, neuron_class2.class2
  ASC

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NeuroMorpho.Org database attributes

• Diverse in many respects
• Many species (human, macaque, rodents, reptiles,
  insects)
• Many cell_types (interneurons, principal_cells,
  Axonal_terminals)
• Many reconstruction methods (Neurolucida,
  Eutectic, Neuron_Morpho, amira, etc.,)
• Many morphometrics (Volume, no.of bifurcations,
  surface area, fractal_dim, etc.,)
• Published, unpublished datasets
• Data access online visualization (cvapp)
  download
• Search options coordinates regional labels
  functional attributes

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NeuroMorpho.Org database schema
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NIF accessible NeuroMorpho.Org view definition

• View definition
• create view NIF_neuron2 as select distinct
  n.neuron_id, n.neuron_name, n.max_age,
  n.age_scale,n.min_age, n.min_weight,
  n.max_weight,    n.gender, n.URL_reference,
  n.note, ag.age_classneuron_class, nc.class2,
  nc3.class3, sp.species, an.strain_name,   
  an.scientific_name, nr.region1 neuron_region,
  st.stain,

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NeuroMorpho.Org registration with NIF
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NeuroMorpho.Org term mapping to NIF concepts
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Sample NIF query
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Search Yale interface view NeuroMorpho.Org
http//nif.sdsc.edu8080/edu.sdsc.daks.nif.nifgwt/
nifgwt.html
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Mind the Acronyms (join the AAAAA)

• A Principal Component analysis of the PC word.
• To be Politically Correct, I should report that
  in the Parietal Cortex (and in my Personal
  Computer) the Principal Cell associated with the
  term PC corresponds to the concept of Pyramidal
  Cell rather than of Purkinje Cell!

American Association Against Acronym Abuse