2020
DOI: 10.1101/2020.06.08.140533
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DotMotif: An open-source tool for connectome subgraph isomorphism search and graph queries

Abstract: As connectomics datasets continue to grow in size and complexity, methods to search for and identify interesting graph patterns offer a promising approach to quickly reduce data dimensionality and enable discovery. Recent advances in neuroscience have enabled brain structure exploration at the level of individual synaptic connections. These graphs are often too large to be analyzed manually, presenting significant barriers to searching for structure and testing hypotheses. We combine graph database and analysi… Show more

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Cited by 4 publications
(4 citation statements)
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“…The field of neuroscience has long sought a complete "wiring diagram" of the brain. One representation that has grown in popularity is a graph representation, where neurons are represented by nodes, and synapses are represented as directed edges [12], [13]. A dense reconstruction of even a modestly sized 3D volume of neural tissue comprises an enormous amount of manual labor if segmented exclusively by humans [14], [15], and so connectomics researchers generally leverage automated (often machine-learning based) tools to perform many of the key steps of connectome generation [1], [7], [16], [17].…”
Section: A Backgroundmentioning
confidence: 99%
“…The field of neuroscience has long sought a complete "wiring diagram" of the brain. One representation that has grown in popularity is a graph representation, where neurons are represented by nodes, and synapses are represented as directed edges [12], [13]. A dense reconstruction of even a modestly sized 3D volume of neural tissue comprises an enormous amount of manual labor if segmented exclusively by humans [14], [15], and so connectomics researchers generally leverage automated (often machine-learning based) tools to perform many of the key steps of connectome generation [1], [7], [16], [17].…”
Section: A Backgroundmentioning
confidence: 99%
“…We replicated the motif atlas-scan methods previously applied to partial mouse and invertebrate connectomes (7). This atlas-scan procedure involves searching for and counting all undirected subgraphs up to a certain size (here, subgraphs with six vertices or fewer).…”
Section: Undirected Motif Atlas Scans Of the Growing C Elegans Connectome Reveal A Changing Local Structurementioning
confidence: 99%
“…DrosoBOT is built to be modular and enables different types of feedback loops to be integrated for such queries. Other types of circuit motifs [20] can also be added to our programmable ontology to facilitate the construction of brain circuits that have functional significance.…”
Section: Exploration Of the Feedback Circuits Of The Fruit Fly Early Olfactory System With Neuronlp++mentioning
confidence: 99%
“…Concluding, DrosoBOT is built to be modular and enables different types of feedback loops to be added to our programmable ontology to facilitate the construction and visualization of circuit motifs [20]. NeuroNLP++ represents a step towards a more intuitive and natural way of extracting information from large connectome/synaptome datasets that are relevant for the in-depth study of the functional logic of brain circuits.…”
Section: Exploring the Morphology Of Cell-types And Feedback Circuitsmentioning
confidence: 99%