NeuroNLP: a natural language portal for aggregated fruit fly brain data

Ukani, N. H.; Tomkins, A.; Yeh, C.-H.; Bruning, W.; Fenichel, A. L.; Zhou, Y.; Huang, Y.-C.; Florescu, D.; Ortiz, C. L.; Richmond, P.; Lo, C.-C.; Coca, D.; Chiang, A.-S.; Lazar, A. A.

doi:10.1101/092429

bioRxiv · 10.1101/092429

NeuroNLP: a natural language portal for aggregated fruit fly brain data

Ukani, N. H.·Tomkins, A.·Yeh, C.-H.·Bruning, W.·Fenichel, A. L.·Zhou, Y.·Huang, Y.-C.·Florescu, D.·Ortiz, C. L.·Richmond, P.·Lo, C.-C.·Coca, D.·Chiang, A.-S.·Lazar, A. A.

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Abstract

NeuroNLP, is a key application on the Fruit Fly Brain Observatory platform (FFBO, http://fruitflybrain.org), that provides a modern web-based portal for navigating fruit fly brain circuit data. Increases in the availability and scale of fruit fly connectome data, demand new, scalable and accessible methods to facilitate investigation into the functions of the latest complex circuits being uncovered. NeuroNLP enables in-depth exploration and investigation of the structure of brain circuits, using intuitive natural language queries that are capable of revealing the latent structure and information, obscured due to expansive yet independent data sources. NeuroNLP is built on top of a database system call NeuroArch that codifies knowledge about the fruit fly brain circuits, spanning multiple sources. Users can probe biological circuits in the NeuroArch database with plain English queries, such as \"show glutamatergic local neurons in the left antennal lobe\" and \"show neurons with dendrites in the left mushroom body and axons in the fan-shaped body\". This simple yet powerful interface replaces the usual, cumbersome checkboxes and dropdown menus prevalent in todays neurobiological databases. Equipped with powerful 3D visualization, NeuroNLP standardizes tools and methods for graphical rendering, representation, and manipulation of brain circuits, while integrating with existing databases such as the FlyCircuit. The userfriendly graphical user interface complements the natural language queries with additional controls for exploring the connectivity of neurons and neural circuits. Designed with an open-source, modular structure, it is highly scalable/flexible/extensible to additional databases or to switch between databases and supports the creation of additional parsers for other languages. By supporting access through a web browser from any modern laptop or smartphone, NeuroNLP significantly increases the accessibility of fruit fly brain data and improves the impact of the data in both scientific and educational exploration.

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Ukani, N. H., Tomkins, A., Yeh, C.-H., Bruning, W., Fenichel, A. L., Zhou, Y., Huang, Y.-C., Florescu, D., Ortiz, C. L., Richmond, P., Lo, C.-C., Coca, D., Chiang, A.-S., Lazar, A. A.. 2016-12-14. NeuroNLP: a natural language portal for aggregated fruit fly brain data. https://doi.org/10.1101/092429

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