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README.md

Anterior Herm. C. Elegans Connectome

The database is celegans_herm.db.gz

The connectome of the anterior section of the hermaphrodite c. elegans. The source of this data is from the second listed dataset at wormatlas. Quoting from them:

This data was first discussed by Chen, Hall, and Chklovskii, in "Wiring optimization can relate neuronal structrure and function", PNAS, March 21, 2006 103: 4723-4728 doi:10.1073/pnas.0506806103. More recently, full analysis of the data can be found by Varshney, Chen, Paniaqua, Hall and Chklovskii in "Structural properties of the C. elegans neuronal network" PLoS Comput. Biol. Feb 3, 2011 3:7:e1001066 doi:10.1371/journal.pcbi.1001067. Any publication made utilizing the following data should make a reference to this paper.

I am not incredibly thrilled with the quality of the role and neurotransmitter metadata for this model. With as much research as has been put into this system over the years, it's frustrating that bits of the worm atlas aren't even consistent. Nonetheless, this is a reasonable first attempt, especilaly for multi-cell classes.

Cells

  • cell_id : auto-inc cell ID
  • cell_name : official cell name, from original brenner paper
  • cell_class : an attempt at determining the cell class
  • soma_pos : position along the body axis, range : [0, 1]
  • role: text string of Motor, sensory, interneuron
  • neurotransmitter: text string of type of neurotransmitter

Synapses

Synapses; note that the electrical synapses are undirected, the chemical synapses directed.

  • from_id : from cell id
  • to_id : to cell id
  • synapse_type: 'E' for electrical, 'C' for chemical
  • count : # of this kind of synapse

TODO

  • Add "gross types"/ role from metadata
  • more Diagnostic plots