Bentley et al. 2016 expression data #285
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Add neurotransmitter and receptor expression pattern data, receptor-ligand mappings, and neurotransmitter types (monoamine vs. neuropeptide) as used in Bentley et al. 2016. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005283
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I haven't been able to test this because I can't install pyopenworm through pip in either py2 or py3. py2: I think FuXi is the problem: it requires rdflib < 3a and the the setup.py requires rdflib==4.1.2. FuXi also doesn't install its own dependencies properly (specifically ez_setup). py3: wsgiref==0.1.2 has a py2 print statement in it. |
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Build failures are just due to the doctests having the wrong expectations for the new data. |
| @@ -158,9 +161,11 @@ def upload_neurons(): | |||
| def get_altun_evidence(): | |||
| return parse_bibtex_into_evidence('../aux_data/bibtex_files/altun2009.bib') | |||
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Changes for pep8 compliance are fine, but please don't introduce newlines unnecessarily.
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To be consistent with other spacing between other methods is fine. Nevermind.
OpenWormData/scripts/insert_worm.py
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| for neur in neurons: | ||
| n = NETWORK.neuron(neur) | ||
| print ("uploaded " + str(i) + " statements about types, receptors, innexins, neurotransmitters and neuropeptides") | ||
| _ = NETWORK.neuron(neur) |
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n really is unused. It's okay to just remove the assignment.
Resolves openworm#284 Searches OpenWormData/aux_data/expression_data for innexin, neuropeptide, neurotransmitter and receptor expression data not already added.
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Build should be green, now, forgot a dash in a receptor name... Paradoxically, I can't do the URLs for the docs page until the PR is merged but I've got the changes except the URLs in a local branch (accidentally pushed it but then --force undid it, which is why this history might look a bit squiffy) so they can go up as soon as this PR is merged and OpenWorm has taken ownership of the spreadsheet https://docs.google.com/spreadsheets/d/1kCxOOKu1wAREa9VbBiWVVHh-GEC3kJk0A3YVEipPKcc/edit#gid=0 |
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lgtm |
Resolves #284
Data spreadsheet: https://docs.google.com/spreadsheets/d/1kCxOOKu1wAREa9VbBiWVVHh-GEC3kJk0A3YVEipPKcc/edit#gid=0
Modified celegans db dump.csvinsert_worm.upload_additional_receptors_neurotransmitters_neuropeptides_innexins(), which recursively searches the expression_data in lexicographic sort order for.csvfiles and adds any novel data to the networkupload_receptors_types_neurotransmitters_neuropeptides_innexinsandupload_additional_receptors_neurotransmitters_neuropeptides_innexinsStill todo: