Abstract

NeuroML is an extensible markup language for describing complex mathematical models of neurons and neuronal networks. NeuroML is unique in its modular, multi-scale structure-not only can entire NeuroML models be exchanged, but subcomponents of these models that correspond to neuroscience objects, like channels or synapses, also can be shared and reimplemented in a different model. This paper presents the design, implementation, and evaluation of an ontology-Assisted search for NeuroML models. Specifically, the paper describes the design of the system, including the database that stores the modular NeuroML models and the architecture of the Web-based search (neuroml-db.org). The implementation takes advantage of the nested structure of NeuroML models and the NeuroLex ontology for neuroscience to provide additional semantic information to enhance the search. In addition to NeuroLex terms that may exist in model metadata, this initial implementation takes advantage of several semantic relationships provided by the NeuroLex ontology: Is-part-of, Located-in, and Neurotransmitter. An evaluation of the system illustrates its effectiveness both for functionality and performance, covering various types of searches broken down by keyword searches over the database and ontology searches using the semantic relationships.

Original languageEnglish (US)
Title of host publicationACM International Conference Proceeding Series
PublisherAssociation for Computing Machinery
Volume29-June-2015
ISBN (Print)9781450337090
DOIs
StatePublished - Jun 29 2015
Event27th International Conference on Scientific and Statistical Database Management, SSDBM 2015 - San Diego, United States
Duration: Jun 29 2015Jul 1 2015

Other

Other27th International Conference on Scientific and Statistical Database Management, SSDBM 2015
CountryUnited States
CitySan Diego
Period6/29/157/1/15

Fingerprint

Ontology
Semantics
Metadata
XML
Neurons
Mathematical models

Keywords

  • Model Description Languages
  • NeuroLex
  • NeuroML Database
  • Ontology Based Search
  • Scientific Database Search

ASJC Scopus subject areas

  • Human-Computer Interaction
  • Computer Networks and Communications
  • Computer Vision and Pattern Recognition
  • Software

Cite this

Birgiolas, J., Dietrich, S., Crook, S., Rajadesingan, A., Zhang, C., Penchala, S. V., & Addepalli, V. (2015). Ontology-Assisted keyword search for NeuroML models. In ACM International Conference Proceeding Series (Vol. 29-June-2015). [a37] Association for Computing Machinery. https://doi.org/10.1145/2791347.2791360

Ontology-Assisted keyword search for NeuroML models. / Birgiolas, Justas; Dietrich, Suzanne; Crook, Sharon; Rajadesingan, Ashwin; Zhang, Chao; Penchala, Shriharsha Velugoti; Addepalli, Veerasekhar.

ACM International Conference Proceeding Series. Vol. 29-June-2015 Association for Computing Machinery, 2015. a37.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Birgiolas, J, Dietrich, S, Crook, S, Rajadesingan, A, Zhang, C, Penchala, SV & Addepalli, V 2015, Ontology-Assisted keyword search for NeuroML models. in ACM International Conference Proceeding Series. vol. 29-June-2015, a37, Association for Computing Machinery, 27th International Conference on Scientific and Statistical Database Management, SSDBM 2015, San Diego, United States, 6/29/15. https://doi.org/10.1145/2791347.2791360
Birgiolas J, Dietrich S, Crook S, Rajadesingan A, Zhang C, Penchala SV et al. Ontology-Assisted keyword search for NeuroML models. In ACM International Conference Proceeding Series. Vol. 29-June-2015. Association for Computing Machinery. 2015. a37 https://doi.org/10.1145/2791347.2791360
Birgiolas, Justas ; Dietrich, Suzanne ; Crook, Sharon ; Rajadesingan, Ashwin ; Zhang, Chao ; Penchala, Shriharsha Velugoti ; Addepalli, Veerasekhar. / Ontology-Assisted keyword search for NeuroML models. ACM International Conference Proceeding Series. Vol. 29-June-2015 Association for Computing Machinery, 2015.
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