What is in the graph

connkg build reads one connectome release and writes a typed graph to SQLite. Every neuron is a node, and every connected pair of neurons is one SYNAPSES_TO edge carrying its synapse count and a transmitter sign. Cell types, taxonomy, neuropils and annotations sit on top.

The synapse counts come from the electron microscope, and the labels on top are a thin semantic layer. A vector index over the labels (cell type names, neuropils, community labels, taxa) lets connkg query find a place to start; the graph answers everything after that. Neurons are not embedded by default, because there are 139,255 of them in FAFB v783 and their names carry little meaning. connkg build --embed-neurons embeds them anyway.

Node kinds

node kind	what it is
dataset	One connectome release, with its provenance
taxon	Super class, class and sub class, and the visual subsystems and families
hemilineage	The developmental lineage a cell type belongs to
nerve	A nerve that neurons enter or leave the brain by
neuropil	A brain region, split by side
column	A visual column in one optic lobe
connectivity_tag	A Codex connectivity tag selective enough to say something about a neuron: broadcaster, highly_reciprocal_neuron, integrator, nsrn
ontology_term	A Drosophila Anatomy Ontology (FBbt) term
cell_type	A named type, with its transmitter and sign
neuron	One reconstructed cell, keyed by root id, with position and synapse totals
label	A community annotation, with attribution

The other Codex connectivity tags (feedforward_loop_participant, reciprocal, 3_cycle_participant, rich_club) are on 44% to 95% of v783 neurons, so they stay in neuron metadata and get no node.

Edge kinds

edge kind	from	to	meaning
SYNAPSES_TO	neuron	neuron	Synapse count, transmitter and sign, and the per-neuropil breakdown
TYPE_SYNAPSES_TO	cell type	cell type	The same wiring summed over the two types
INSTANCE_OF	neuron	cell type	The neuron's type
MEMBER_OF	cell type	hemilineage	The type's lineage
CONTAINS	taxon	taxon or cell type	Super class to class to sub class, visual subsystem to family, and taxon to cell type
IN_NEUROPIL	neuron	neuropil	Pre- and postsynaptic counts in that neuropil
INNERVATES	cell type	neuropil	The type's main neuropils, by synapse count
LABELED	neuron	label	Who labeled it and when
MIRROR_OF	neuron	neuron	Left to right, for types with exactly one neuron per side
VIA_NERVE	neuron	nerve	The nerve the neuron runs through
IN_COLUMN	neuron	column	The visual column the neuron sits in
TAGGED	neuron	connectivity tag	A selective connectivity tag
MAPS_TO	cell type	ontology term	An FBbt term on at least half as many of the type's neurons as its best-supported term
IN_DATASET	top-level node	dataset	Super classes, cell types, neuropils, hemilineages and annotation nodes to their release

connkg stats prints the count of each kind for a built graph.

Transmitter signs

Signs follow Shiu et al. (2024):

• Acetylcholine, dopamine, octopamine and serotonin are +1.
• GABA and glutamate are -1. Glutamate is inhibitory in Drosophila through GluCl-alpha.
• Histamine is -1 in BANC and MCNS. FAFB's predictions have no histamine class.
• An unresolved transmitter is 0, and so is tyramine (209 BANC neurons), which has no settled sign.

A path's net sign is the product of its hop signs, so two inhibitory hops make an excitatory route. See Asking the graph a question for how paths and influence use the signs.

One graph per connectome

Each release is built into its own directory under --root:

<root>/connectomes/
  fafb783/.connectomekg/     graph.sqlite, vectors.sqlite, snapshots/
  banc888/.connectomekg/
  mcns1/.connectomekg/

Releases never share a graph, a vector index or a snapshot history. --dataset ID picks one, and it is a global option, so it goes before the command:

connkg --root . --dataset banc888 stats

Without --dataset, connkg build writes to fafb783 (synthetic with --source synthetic), and every other command uses the only built dataset. When a root holds several, the command stops and lists them. connkg datasets lists them too. Dataset ids are 1 to 64 lowercase letters, digits, _, . or -.

Move a graph from the old layout

A graph built before this layout sits in <root>/.connectomekg/. To move it into place as fafb783, run this from <root>:

mkdir -p connectomes/fafb783/.connectomekg
mv .connectomekg/*.sqlite* connectomes/fafb783/.connectomekg/

Query the SQLite directly

The graph is an ordinary SQLite file with nodes and edges tables. Edge details such as syn_count are JSON in edges.evidence:

sqlite3 connectomes/fafb783/.connectomekg/graph.sqlite \
  "SELECT rel, count(*) FROM edges GROUP BY rel"