Add cell lineage info to PyOpenWorm

[slarson]

Cell lineage refers to the tree of cell divisions that occurs when an organism is growing from an embryo. We'd like to have a data structure that captures this for c. elegans. The data are out there -- now we'd like to put them into PyOpenWorm.

This is the first step in a greater project to be able to render lineage trees as "differentiation trees" for exploration and potentially simulation down the road.

• Identify best data source to begin working with
• Write a simple python script that pulls out the names of the cells and the cell division relationships and displays to console
• Augment the script to dump the data into the PyOpenWorm SQLite3 DB.
• Augment PyOpenWorm to pull this data out from the SQLite3 DB and construct an RDF graph out of it
• Build accessor functions in PyOpenWorm that can pull the whole lineage into a networkX graph, and also can report lineage information when asked for a specific cell.

Original issue: openworm/OpenWorm#179

[balicea]

UPDATE (5/13):

I have established my own Github repository for the DevoWorm project here (nuts and bolts issues, Python code, etc:
https://github.com/balicea/DevoWorm

I also have an extracted dataset that I have been playing with:
https://drive.google.com/file/d/0B7RsqJbITXXAM0RJQmkzb1o4U1E/edit?usp=sharing

[DickGordonCan]

For background on differentiation trees see:
Gordon, R. (1999). The Hierarchical Genome and Differentiation Waves: Novel Unification of Development, Genetics and Evolution. Singapore & London, World Scientific & Imperial College Press. http://www.worldscientific.com/worldscibooks/10.1142/2755
For C. elegans, we have the cell lineage tree:
Sulston, J.E., E. Schierenberg, J.G. White & J.N. Thomson (1983). The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100(1), 64-119.
The left/right organization of this tree is according to which cell was the anterior/posterior cell after a cell division. For the asymmetric divisions, which are the majority in C. elegans, we need to reorder the tree per small/large cell to create the C.elegans differentiation tree.

[DickGordonCan]

Note:
Karabey, Y. (2003). Corrections to: The embryonic cell lineage of the nematode Caenorhabditis elegans. http://www.wormatlas.org/ver1/Sulstonemblin_1983/toc.html

[balicea]

An update on the white paper and dataset. I have posted version 2.0 of both:

White Paper, 2.0 (added more detail, especially reflecting our last meeting):
http://figshare.com/articles/From_Differentiation_Waves_to_Wriggling_new_views_on_C_elegans_development/1015760

Dataset, 2.0 (cleaned up tabbed pages and extracted lineage information from the cell names):
http://figshare.com/articles/DevoWorm_Dataset/1040317

Any questions, let me know. Bradly Alicea

[balicea]

I posted a project announcement/advertisement to my blog Synthetic Daisies (Now Announcing the DevoWorm Project). The blog has a modest biology/computational readership. Check it out:

http://syntheticdaisies.blogspot.com/2014/06/now-announcing-devoworm-project.html

[mwatts15]

This is a list of names which I wasn't able to resolve immediately: http://pastebin.com/biQ8dZuQ
I'll be looking at the associate wormbase entries to try to resolve them.

[balicea]

Mark,

  Thanks. I'll make a record of them (store them in my data files). 

I do not know what their identity is.

Bradly Alicea

On 6/6/2014 9:19 AM, mwatts15 wrote:

This is a list of names which I wasn't able to resolve immediately:
http://pastebin.com/biQ8dZuQ
I'll be looking at the associate wormbase entries to try to resolve them.

—
Reply to this email directly or view it on GitHub
#7 (comment).

[mwatts15]

Recovered what looks like the source from wormatlas. Explains to me the '.' versus ' '.

[mwatts15]

I'm still fuzzy on where the P cells originate from. The 'cytoscape' spreadsheet has slashes in the names of P cells:
ABplapaapp (P1/2 L) P1/2 L
ABplapapaa
ABplapapap (P9/10 L) P9/10 L
ABplapappa (P11/12 L) P11/12 L
ABplapappp
ABplappaaa (P3/4 L) P3/4 L
ABplappaap (P5/6 L) P5/6 L

In wormbase, these relationships are shown by Equivalence_fate and its inverse Equivalence_origin, but the semantics on this are unclear to me.

[balicea]

Steve McGrew's ALFRED proposal and Bradly Alicea's literature search on developmental evolutionary algorithms:

https://www.dropbox.com/sh/iir0h6l8l4f6tbw/AACbWTivw62AyRcSK5UPXvYia

[slarson]

@mwatts15 for names like "ABplapapap (P9/10 L) P9/10 L", the first string with no spaces is the developmental name and the name in parens with slashes are the non "lineage" naming scheme. You can see an example of cell P9/10 L in the master cell list (row 273).

[slarson]

Is this one done in the alpha0.5 branch?

[mwatts15]

You can query through Cell() for all of the cells listed here:
https://github.com/openworm/PyOpenWorm/blob/alpha0.5/C.%20elegans%20Cell%20List%20-%20WormAtlas.tsv

Querying through Neuron does not work.

On Tue, Jul 29, 2014 at 9:51 PM, Stephen Larson notifications@github.com
wrote:

Is this one done in the alpha0.5 branch?

—
Reply to this email directly or view it on GitHub
#7 (comment).

Cheers,
Mark Watts
Department of Computer Science
University of Texas at Austin

[slarson]

Pretty sure this got done