PyOpenWorm feature freeze

I have declared a feature freeze for PyOpenWorm. For this week we're just writing code to pass the tests we've already written and those obviously derived from the API.

I am trying to figure out how ReadTheDocs can bring in documentation from the python source files.

• update (10:33): Sphinx installed
• update (10:44): Got Network's documentation printing out. Let's see about the others.
• update (10:57): aaand, now the docs don't update from the source files. Not even deleting the build directory changes it.
• update (11:19): Started using sphinx-apidoc. Has really noisy output.

Citations, DOIs, Pubmed IDs

Since we've started discussing the API for PyOpenWorm, we've started talking about putting up citations of data sources. What we're looking at doing is making a declarative API that allows us to write things like:

n1 = Neuron('AVAL')
n2 = Neuron('ADER')
r1 = n1.connectsWith(n2) # r1 is now a representation of this 'connectsWith' relationship
s = Chemical('X')
r2 = s.modulates(r) # r2 is the representation of the 'modulates' relationship
e = Evidence(doi="http://dx.doi.org/10.1007%2Fs00454-010-9273-0")
e.asserts(r2)

In English, "10.1007%2Fs00454-010-9273-0 suggests that chemical X modulates the connection between AVAL and ADER". This 'relationship' API (a sub-API to the PyOpenWorm API), has the primary feature of allowing statements made as to be part of higher order statements.

Lineage data

I finally dug into the daughter_of tree (unfortunately, a forest. see below) cell division data.

After cleaning it up a little I put it into OpenRDF: http://107.170.133.175:8080/openrdf-workbench/repositories/OpenWorm2

There are some discontinuities which make the graph unconnected. The roots in our forest of division trees can be shown with this query:

PREFIX ns1:<http://openworm.org/entities/>

select distinct ?z where { ?y ns1:daughter_of ?z . filter(not exists { ?z ns1:daughter_of ?p }) }

These discontinuities have nothing to do with the input errors mentioned in the github issue as all of those in the daughter_of table were easily fixed.
To look at the path-to-root for 'AB plppaaaapa' :

PREFIX ns1:<http://openworm.org/entities/>

select distinct ?z where { ns1:AB_plppaaaapa ns1:daughter_of+ ?z }

The code I used to extract and upload: http://pastebin.com/NVnAfD8D

It's just the cell divisions that we've had for some time. We've discussed bringing in volume data for each of the cells in development in order to model differentiation waves discussed by Richard Gordon and colleagues. As of yet, we don't have this data readily available.

OpenRDF problems

I was having difficulty with setting up OpenRDF on a Digital Ocean machine, but figured it out. A permissions problem was preventing sesame from creating its log files. Changing the ownership of /usr/share/tomcat7 to user tomcat7 fixed it.

I've switched from using a local SQLite database to an OpenRDF SPARQL service which supports SPARQL 1.1 updates. The update statements should include mandatory information about the updater as well as other checks specific to the kind of data being modified. I'm looking into an inference engine that stands between the DB and PyOpenWorm, but in the meantime I'll be encoding the rules in PyOpenWorm itself.

I have an OWL file with WormBase data in it. And a sparql endpoint that has the same data.

Wormbase has it going on (with respect to anatomical tree displays).

Also:

• WormBase data modeling.
• The database for WormBase
• REST interface for WormBase entities

Work has started on the requirements writeup.