Data Provenance

[jescab01]

Hello everyone!

I think it would be useful to made a readme.txt in the data folders to account about the data provenance.

Anyway, could anyone tell me where is the data coming from:

I am using neuroML2 models of neurons, herm_full_edgelist_MODIFIED, and CElegansNeuronTables.csv.

Thanks!

[mwatts15]

Hello, @jescab01 . I haven't looked at the history of herm_full_edgelist_MODIFIED, but it is a modification of the data set from

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

There are some gap junctions added in the modified version. @pgleeson should be able to explain why they were added.

The CElegansNeuronTables.csv originates from "Data acquisition and modeling for learning and reasoning in probabilistic logic environment". Shterionov, Janssens (2011) as described in this issue:

openworm/owmeta#152

and in this post

https://groups.google.com/forum/#!topic/openworm-discuss/G9wKoR8N-l0/discussion

although that has been superceded by the herm_full_edgelist.

[lungd]

Hi @jescab01, herm_full_edgelist_MODIFIED is the connectome generated by Emmons lab with some additional artificial connections, I needed for the forward crawling circuit (c302_FW.py).
Our plan is to modify the c302 script, so we can define such connections with a parameter.

[pgleeson]

@jescab01 See here for the (hopefully) central location on where the different data is coming from: https://github.com/openworm/PyOpenWorm/blob/dev/docs/data_sources.rst.

The herm_full_edgelist_MODIFIED, as @lungd says, is a manually edited version which was needed for the FW model, as described in the c302 paper: c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans Padraig Gleeson, David Lung, Radu Grosu, Ramin Hasani, Stephen D. Larson, Phil. Trans. R. Soc. B 2018 373 20170379; DOI: 10.1098/rstb.2017.0379.

Eventually we don't want to use the spreadsheets here, but get all this data from PyOpenWorm (see #10), and potentially modify it as required.

For your purposes I'd recommend trying to access the data through PyOpenWorm.

[jescab01]

Thank you all! Very helpful.

I still haven't found the source for the neuroML2 models of neurons. I am using their soma location to set a 3D representation. Does anyone know where are these data coming from?

[pgleeson]

The NeuroML2 files for the individual cells can be found here: https://github.com/openworm/c302/tree/master/c302/NeuroML2. The 3D positions of the somas (and dendrites) are all absolute, and trace out the curved worm as initially reconstructed by Christian Grove: http://canopus.caltech.edu/virtualworm/

The positions of the somas can be seen in the segment info, e.g. https://github.com/openworm/c302/blob/master/c302/NeuroML2/ADAL.cell.nml#L15

The NML (v1) was originally generated using this code: https://github.com/openworm/Blender2NeuroML and then refined (using neuroConstruct) in this: https://github.com/openworm/CElegansNeuroML