source of the "C. Elegans Neuronal Network Details condensed"

[Yi Zeng]

Dear all,

The data from the downloads are cool and very useful. I am wondering where the data in the "C. Elegans Neuronal Network Details condensed" file are from. 

If I need to cite the source of the data, besides the openworm downloads page, which papers should I point to.

Thank you in advance.

Best wishes,

Yi

[Stephen Larson]

Hi Yi,

   Thanks for the question.  I think Tim Busbice can answer.  The spreadsheet in question is:

https://docs.google.com/spreadsheet/ccc?key=0Avt3mQaA-HaMdG9HX1IxVlltSk9yUklLM3htUG54RUE#gid=0

   This raises a good point -- we should as much as possible include citations in our spreadsheets: I've created an issue for this here: https://github.com/openworm/OpenWorm/issues/134

   Yi -- you should be aware that these data sheets may not represent data that are 100% experimentally confirmed -- some of the columns may represent works in progress of inferences of what some of the data elements are.  I already see that the neurotransmitters in this spreadsheet, for example, are the product of a reasoning process from section 4.3 here:

https://lirias.kuleuven.be/bitstream/123456789/316487/3/EPIA2011_p_298-312_166.pdf

   It might not hurt for us to include descriptions on the spreadsheets that say this as well.

Thanks,

  Stephen

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[InterIntelligence Research]

I am working on a new (semantic) data base that will contain all this data. Crystin has done a great job but I have taken it one step further to reduce everything down to two tables whereas one table is each entity that makes up the worm (cell = neuron, protein = neuropeptide, kinase, etc) and the other table is the properties or predicate or how the different entities link to one another. This will include all the attributes of the entities as well as the attributes of the properties (e.g. citations). I should have completed very soon so please give me a few more days.

 

Thanks

 

Tim

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