PyOpenWorm Data Sources

The sources of data for PyOpenWorm are stored under the OpenWormData/aux_data directory.

These data sources are brought into PyOpenWorm by means of the insert_worm.py script, which shows exactly how a given kind of data is brought into the system. For example this method shows where data about muscles comes from, while this method shows where the connectivity data comes from. A more detailed human readable key is provided below.

A Note on PyOpenWorm Data

Below, each major element of the worm’s anatomy that PyOpenWorm stores data on is considered individually. The data being used is tagged by source in a superscript, and the decisions made during the curation process (if any) are described.

Neurons

Gene expression data below, additional to that extracted from WormAtlas concerning receptors, neuropeptides, neurotransmitters and innexins are parsed by this method:

Muscle cells

Connectome

  • Gap junctions between neurons [3]: Extracted from data personally communicated by S. Cook. Staged in this csv file. Parsed by this method.
  • Synapses between neurons [3]: Extracted from data personally communicated by S. Cook. Staged in this csv file. Parsed by this method.

Curation note

There was another source of C. elegans connectome data that was created by members of the OpenWorm project that has since been retired. The history of this spreadsheet is mostly contained in this forum post We decided to use the Emmons data set [3] as the authoritative source for connectome data, as it is the very latest version and updated version of the C. elegans connectome that we are familiar with.

Data Source References

[1](1, 2, 3, 4, 5, 6, 7, 8, 9) Altun, Z.F., Herndon, L.A., Wolkow, C.A., Crocker, C., Lints, R. and Hall, D. H. (2015). WormAtlas. Retrieved from http://www.wormatlas.org - WormAtlas Complete Cell List
[2](1, 2)
  • Harris, T. W., Antoshechkin, I., Bieri, T., Blasiar, D., Chan, J., Chen, W. J., … Sternberg, P. W. (2010). WormBase: a comprehensive resource for nematode research. Nucleic Acids Research, 38(Database issue), D463–7. http://doi.org/10.1093/nar/gkp952
  • Lee, R. Y. N., & Sternberg, P. W. (2003). Building a cell and anatomy ontology of Caenorhabditis elegans. Comparative and Functional Genomics, 4(1), 121–6. http://doi.org/10.1002/cfg.248
[3](1, 2, 3, 4) Emmons, S., Cook, S., Jarrell, T., Wang, Y., Yakolev, M., Nguyen, K., Hall, D. Whole-animal C. elegans connectomes. C. Elegans Meeting 2015 http://abstracts.genetics-gsa.org/cgi-bin/celegans15s/wsrch15.pl?author=emmons&sort=ptimes&sbutton=Detail&absno=155110844&sid=668862
[4]Bentley B., Branicky R., Barnes C. L., Chew Y. L., Yemini E., Bullmore E. T., Vertes P. E., Schafer W. R. (2016) The Multilayer Connectome of Caenorhabditis elegans. PLoS Comput Biol 12(12): e1005283. http://doi.org/10.1371/journal.pcbi.1005283