Too many prefixes in converted output

[jamesaoverton]

Fixing #26 raised some new problems. We set a lot of prefixes by default in obo_context.jsonld. With commit 493a8a1 we use the current prefixes when converting to OWL formats that support prefixes. But the resulting files include all the prefixes, even the ones that aren't used. While it doesn't break anything, it looks bad.

Possibilities:

1. Specify fewer prefixes, at least for output
2. Make OWLAPI serialization smarter

[jamesaoverton]

This is now just a problem for Turtle format. The RDFXML writer picks its own prefixes with some intelligence, and OBO format doesn't use a prefix manager.

My best idea is to add --write-prefix options and a separate prefix manager for them. I'm still hoping to come up with something better.

[beckyjackson]

Turtle only includes for all ontologies:

@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

Plus @prefix : and @base. Do we want to try and add additional prefixes to this, based on what is in the prefix manager?

[jamesaoverton]

I think this was addressed some time ago. If not, we'll open a new issue. Thanks!