Cargando…
DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries
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 re...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219732/ https://www.ncbi.nlm.nih.gov/pubmed/34158519 http://dx.doi.org/10.1038/s41598-021-91025-5 |
_version_ | 1783710999707123712 |
---|---|
author | Matelsky, Jordan K. Reilly, Elizabeth P. Johnson, Erik C. Stiso, Jennifer Bassett, Danielle S. Wester, Brock A. Gray-Roncal, William |
author_facet | Matelsky, Jordan K. Reilly, Elizabeth P. Johnson, Erik C. Stiso, Jennifer Bassett, Danielle S. Wester, Brock A. Gray-Roncal, William |
author_sort | Matelsky, Jordan K. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8219732 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-82197322021-06-24 DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries Matelsky, Jordan K. Reilly, Elizabeth P. Johnson, Erik C. Stiso, Jennifer Bassett, Danielle S. Wester, Brock A. Gray-Roncal, William Sci Rep Article 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. Nature Publishing Group UK 2021-06-22 /pmc/articles/PMC8219732/ /pubmed/34158519 http://dx.doi.org/10.1038/s41598-021-91025-5 Text en © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Matelsky, Jordan K. Reilly, Elizabeth P. Johnson, Erik C. Stiso, Jennifer Bassett, Danielle S. Wester, Brock A. Gray-Roncal, William DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
title | DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
title_full | DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
title_fullStr | DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
title_full_unstemmed | DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
title_short | DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
title_sort | dotmotif: an open-source tool for connectome subgraph isomorphism search and graph queries |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219732/ https://www.ncbi.nlm.nih.gov/pubmed/34158519 http://dx.doi.org/10.1038/s41598-021-91025-5 |
work_keys_str_mv | AT matelskyjordank dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries AT reillyelizabethp dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries AT johnsonerikc dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries AT stisojennifer dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries AT bassettdanielles dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries AT westerbrocka dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries AT grayroncalwilliam dotmotifanopensourcetoolforconnectomesubgraphisomorphismsearchandgraphqueries |