Improve BioPAX conversion processing and extend API #1392
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This PR adds a convenient function to the BioPAX API to allow processing gzipped OWL files directly. It also improves how conversions (e.g., biochemical reactions) are processed. Namely, it handles a corner case in which the ordering of simple entities on the left and right hand sides are inconsistent and therefore need to be combinatorially matched to find corresponding left and right hand side entities.