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2021

DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries


Abstract

Recent advances in neuroscience have enabled the exploration of brain structure at the level of individual synaptic connections. These 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. 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 analysis libraries with an easy-to-use neuroscience grammar suitable for rapidly constructing queries and searching for subgraphs and patterns of interest. Our approach abstracts many of the computer science and graph theory challenges associated with nanoscale brain network analysis and allows scientists to quickly conduct research at scale. We demonstrate the utility of these tools by searching for motifs on simulated data and real public connectomics datasets, and we share simple and complex structures relevant to the neuroscience community. We contextualize our findings and provide case studies and software to motivate future neuroscience exploration.


Citation

@ArticleMatelsky2021 author=Matelsky Jordan K. and Reilly Elizabeth P. and Johnson Erik C. and Stiso Jennifer and Bassett Danielle S. and Wester Brock A. and Gray-Roncal William title=DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries journal=Scientific reports year=2021 month=Jun day=22 publisher=Nature Publishing Group UK volume=11 number=1 pages=13045-13045 abstract=Recent advances in neuroscience have enabled the exploration of brain structure at the level of individual synaptic connections. These 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. 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 analysis libraries with an easy-to-use neuroscience grammar suitable for rapidly constructing queries and searching for subgraphs and patterns of interest. Our approach abstracts many of the computer science and graph theory challenges associated with nanoscale brain network analysis and allows scientists to quickly conduct research at scale. We demonstrate the utility of these tools by searching for motifs on simulated data and real public connectomics datasets and we share simple and complex structures relevant to the neuroscience community. We contextualize our findings and provide case studies and software to motivate future neuroscience exploration. note=34158519[pmid] note=PMC8219732[pmcid] issn=2045-2322 doi=10.1038/s41598-021-91025-5 url=https://pubmed.ncbi.nlm.nih.gov/34158519 url=https://doi.org/10.1038/s41598-021-91025-5 language=eng

Citation

@ArticleMatelsky2021 author=Matelsky Jordan K. and Reilly Elizabeth P. and Johnson Erik C. and Stiso Jennifer and Bassett Danielle S. and Wester Brock A. and Gray-Roncal William title=DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries journal=Scientific reports year=2021 month=Jun day=22 publisher=Nature Publishing Group UK volume=11 number=1 pages=13045-13045 abstract=Recent advances in neuroscience have enabled the exploration of brain structure at the level of individual synaptic connections. These 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. 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 analysis libraries with an easy-to-use neuroscience grammar suitable for rapidly constructing queries and searching for subgraphs and patterns of interest. Our approach abstracts many of the computer science and graph theory challenges associated with nanoscale brain network analysis and allows scientists to quickly conduct research at scale. We demonstrate the utility of these tools by searching for motifs on simulated data and real public connectomics datasets and we share simple and complex structures relevant to the neuroscience community. We contextualize our findings and provide case studies and software to motivate future neuroscience exploration. note=34158519[pmid] note=PMC8219732[pmcid] issn=2045-2322 doi=10.1038/s41598-021-91025-5 url=https://pubmed.ncbi.nlm.nih.gov/34158519 url=https://doi.org/10.1038/s41598-021-91025-5 language=eng