Add SBGN-ML importer #439
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Add SBGN-ML importer #439
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Codecov Report
@@ Coverage Diff @@
## master #439 +/- ##
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- Coverage 79.10% 76.59% -2.52%
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Files 171 176 +5
Lines 9039 8962 -77
Branches 1307 1333 +26
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- Hits 7150 6864 -286
- Misses 1608 1832 +224
+ Partials 281 266 -15
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Will time out due to pyobo though. need mocks that will be implemented with biopragmatics/pyobo#62
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Closes #423
This PR introduces the
pybel.io.sbgnmlI/O module, which first consumes SBGN-ML and converts it into a facile JSON-like data structure (which is generally reusable) then reasons over it and converts to BEL.The code also has some grounding mechanisms built in to deal with the often missing identifiers from the COVID-Pathways content, but I might remove this to make the tool more generally reusable. I'm not really sure who else generates SBGN-ML if not from CellDesigner (and more specifically, coming out of MINERVA)
DEMO NOTEBOOK
Example SBGN-ML Content
For an example, see the content posted by @cannin https://cannin.github.io/covid19-sbgn. The SBGN-ML file (disregard the SIF and SIF SVG, since those are derived resources).
He notes on his site that these SBGN-ML files were converted from CellDesigner using https://github.com/sbgn/cd2sbgnml. It's clear that there's some lost information due to
cd2sbgnml(or there are strange pockets of incredibly low quality curation), so it will be a future step to write a CellDesigner importer later (see #440).For example, this script can be run (after installing this branch in development mode) with the following code in the python REPL: