Dataset

Database related to: An open-source platform for analyzing and sharing worm-behavior data

Javer, A. (Creator), Currie, M. (Creator), Lee, C. W. (Creator), Hokanson, J. (Creator), Li, K. (Creator), Martineau, C. (Creator), Yemini, E. (Creator), Grundy, L. J. (Creator), Li, C. (Creator), Ch'ng, Q. (Creator), Schafer, W. R. (Creator), Nollen, E. (Creator), Kerr, R. (Creator), Brown, A. E. X. (Creator), Movement OpenWorm, 28-Mar-2018

Dataset

  • Avelino Javer (Creator)
  • Michael Currie (Creator)
  • Chee Wai Lee (Creator)
  • Jim Hokanson (Creator)
  • Kezhi Li (Creator)
  • Celine Martineau (Creator)
  • Eviatar Yemini (Creator)
  • Laura J Grundy (Creator)
  • Chris Li (Creator)
  • QueeLim Ch'ng (Creator)
  • William R. Schafer (Creator)
  • Ellen Nollen (Creator)
  • Rex Kerr (Creator)
  • André E X Brown (Creator)

Description

Animal behavior is increasingly being recorded in systematic imaging studies that generate large datasets. To maximize the usefulness of these data, there is a need for improved resources for analyzing and sharing behavioral data that will encourage reanalysis and methodological developments. However, for behavioral data, unlike genomic or protein structural data, there are no widely used standards. It is therefore desirable to make data available in a relatively raw form to enable flexibility in data analysis. For computational ethology to approach the level of maturity of other areas of bioinformatics, at least three challenges must be addressed: storing and accessing video files; defining flexible data formats to facilitate data sharing; and developing software to read, write, browse, and analyze the data. We have generated an open resource to begin addressing these challenges for Caenorhabditis elegans behavioral data.

The database currently (Spring 2018) consists of 14,874 single-worm tracking experiments representing 386 genotypes (building on 9,203 experiments and 305 genotypes in a previous publication2) and includes data from several larval stages as well as data from aging experiments consisting of more than 2,700 videos of animals tracked daily from the L4 stage to death (Nature Research Reporting Summary). Full-resolution videos are available in HDF5 containers that include gzip-compressed video frames, time stamps, worm outlines and midlines, feature data, and experimental metadata. HDF5 files are compatible with multiple languages including MATLAB, R, Python, and C. We have also developed an HDF5 video reader that allows video playback with adjustable speed and zoom (an important feature for reviewing high-resolution multiworm tracking data), as well as toggling of worm segmentation over the original video to verify segmentation accuracy during playback.
Date made available28-Mar-2018
PublisherMovement OpenWorm
Geographical coverageGlobal
Access to the dataset Open
Contact researchdata@rug.nl

    Keywords on Datasets

  • computational ethology, Caenorhabditis elegans, behavioural data, behavioural methods, Databases, High-throughput Screening, Machine learning, software, Biology of Aging, tierpsychology, Strain, Genes, Alleles
Related Publications
  1. An open-source platform for analyzing and sharing worm-behavior data

    Javer, A., Currie, M., Lee, C. W., Hokanson, J., Li, K., Martineau, C. N., Yemini, E., Grundy, L. J., Li, C., Ch'ng, Q., Schafer, W. R., Nollen, E. A. A., Kerr, R. & Brown, A. E. X., Sep-2018, In : Nature Methods. 15, 9, p. 645-646 2 p.

    Research output: Contribution to journalComment/Letter to the editorAcademicpeer-review

View all (1) »

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ID: 65498128