Model measurements #342
Model measurements #342
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In particular, started on some graph oriented metrics.
This cures some problems with reading owl ontologies out of RDF via the Rio library. On a small fraction of models, notably those that imported go-lego-reacto.owl , the title for the model would not make it into the OWLOntology annotations. Switching to 4.5.15 fixed this in all cases tested.
the information will just show up in the tab-delimited output file previously containing just the shex and owl result for each gocam.
This way we can compute on gpad if we want to without reading it out as a string. Just used at the moment for getting row count for stats.
fixBrokenObjectPropertiesAndAxioms alleviates problems with object properties being read in as annotation properties. It uses the RO namespace to guess what should be an object property and what should not. With the OWL-API update, this may not be useful anymore. Also added a simple test to see if a gocam has the go-lego import statement.
Also made more things just on be default to reduce parameter explosion.
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@goodb Good to go to |
leaving the gocam instance ontology alone, but replacing the term with its replacement for calculating stats.
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@kltm lets let the changes I just pushed weave through travis test before merging. Right now, the only impact of these changes should be on the command line validation routine. (Though the owl api upgrade likely cures some other unknown weirdnesses like the one that was killing me last week.) It will produce a much more detailed report about the model collection that it is fed. I'm using this to prepare information for the reactome paper but I believe it is generally useful for batch understanding of model collections. |
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@goodb Taking a quick look at all the changes, I was wondering if one of them was the proposed (#335 (comment)) fix for |
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Yes, the important change for that issue (as shown in #341 ) is in there. |
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@goodb If there is nothing more here, I'll merge. Would there be any issue with this going into |
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@kltm I think it ought to be fine. Lets cycle dev and give it a quick manual check there first though, okay ? |
upgrade to owl api 4.5.15 from 4.5.13
Add gocam stat calculation to command line validation.