Semantic representation of neural circuit knowledge in Caenorhabditis elegans.
Semantic representation of neural circuit knowledge in Caenorhabditis elegans.
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DOI：
10.1186/s40708-023-00208-5
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发表时间：
2023-11-10
影响因子：
--
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中科院分区：
文献类型：
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In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology–Causal Activity Modelling, or GO–CAM). In this study, we explored whether the GO–CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans [C. elegans Neural–Circuit Causal Activity Modelling (CeN–CAM)]. We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO2) avoidance behaviors could be faithfully represented with CeN–CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also discuss how semantic modelling may be used to functionally annotate the C. elegans connectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge. The online version contains supplementary material available at 10.1186/s40708-023-00208-5.
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
16.2
作者：
Brundage, L;Avery, L;Simon, MI
通讯作者：
Simon, MI
DOI：
10.1523/jneurosci.4541-12.2013
发表时间：
2013-06-05
期刊：
The Journal of neuroscience : the official journal of the Society for Neuroscience
影响因子：
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作者：
Carrillo MA;Guillermin ML;Rengarajan S;Okubo RP;Hallem EA
通讯作者：
Hallem EA
影响因子：
1.9
作者：
通讯作者：
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影响因子：
1.2
作者：
Chung, Samuel H.;Sun, Lin;Gabel, Christopher V.
通讯作者：
Gabel, Christopher V.