Glossary
Neuroscience Terms
Axon — The elongated projection of a neuron that conducts electrical impulses away from the cell body. GO:0030424
Brain region — An anatomically or functionally defined subdivision of the brain. SynDB uses terms from the UBERON multi-species anatomy ontology.
Cable length — The total path length of a neuron’s skeletal reconstruction, measured in nanometers.
Cell type — A classification of neurons by morphology, connectivity pattern, molecular markers, or electrophysiology.
Connectome — A comprehensive map of neural connections in a nervous system. Wikipedia
Degree (in/out) — The number of incoming (in-degree) or outgoing (out-degree) synaptic connections of a neuron.
Dendrite — A branched projection of a neuron that receives synaptic input. GO:0030425
Dendritic spine — A small membranous protrusion on a dendrite that forms the postsynaptic side of most excitatory synapses. GO:0043197
Mitochondria — Organelles responsible for ATP production; their density in neurons correlates with synaptic activity. GO:0005739
Neuron — The fundamental unit of the nervous system; an electrically excitable cell that communicates via synapses. CL:0000540
Neurotransmitter — A chemical substance released at a synapse to transmit signals. Common types in SynDB: GABA, glutamate, acetylcholine, dopamine, octopamine, serine.
Pre-synaptic terminal — The axon terminal from which neurotransmitter is released into the synaptic cleft. GO:0098793
Reciprocity — The fraction of synaptic connections in a network that are bidirectional.
Sphericity — A measure of how closely a shape approximates a sphere (1.0 = perfect sphere).
Synapse — A junction between two neurons where signals are transmitted chemically or electrically. GO:0045202
Triadic census — An enumeration of all 16 possible three-node directed subgraph patterns in a network, used to characterize network motifs.
Vesicle — A small membrane-bound compartment in the pre-synaptic terminal that stores neurotransmitter molecules. GO:0099503
Platform Terms
Academic verification — Identity verification via CILogon institutional login, required for compute-intensive operations.
Arrow Flight — A high-performance gRPC protocol from Apache Arrow used for streaming data transfer between SynDB components.
Collection — A curated grouping of datasets for organizational or meta-analysis purposes. See Collections & Tags.
Compartment — A structural subdivision of a neuron (axon, dendrite, spine, terminal, vesicle, mitochondria) that maps to a SynDB table.
Dataset — A collection of neuroanatomical measurements sharing common metadata (species, brain region, microscopy method). The fundamental unit of organization in SynDB.
ETL — Extract, Transform, Load. The pipeline that imports external connectomics datasets into SynDB’s schema. See External sources.
Federation — A decentralized architecture where multiple institutions run independent SynDB nodes while participating in cross-institutional queries. See Federation overview.
Hub — The central coordinating instance in a federation. Runs the full SynDB stack and routes cross-cluster queries.
Job — An asynchronous unit of work (query execution, graph analysis) managed by the job queue. See Jobs system.
Materialized view (MV) — A pre-aggregated ClickHouse table that stores intermediate results for fast analytics. SyQL automatically rewrites eligible queries to use MVs.
Node — A lightweight federation participant running ClickHouse and the syndb-node binary. Data stays on the node’s infrastructure.
Provenance — The audit trail tracking who created, modified, or derived from a dataset. See Provenance & Citations.
SyQL — SynDB Query Language. A declarative SQL-like language that resolves dataset metadata into optimized ClickHouse queries. See SyQL documentation.
Table — A typed schema within SynDB corresponding to a neuronal compartment (e.g., neurons, synapses, axons, dendrites). Each table has its own column definitions.