Unstable output for owltools --save-closure-for-chado

This is a follow on from https://github.com/pombase/pombase-chado/issues/678

We're using owltools --save-closure-for-chado to generate the closure we load into Chado.

@ValWood noticed that the output changes regularly for parts of the ontology that aren't changing.

We have been using these two files for testing because they are very similar:
https://curation.pombase.org/kmr44/go-basic-2018-05-07.obo
https://curation.pombase.org/kmr44/go-basic-2018-05-08.obo

We ran these commands:

owltools ./go-basic-2018-05-07.obo --save-closure-for-chado 2018-05-07.out
owltools ./go-basic-2018-05-08.obo --save-closure-for-chado 2018-05-08.out

Using owltools from the master branch, the output from go-basic-2018-05-08.obo go-basic-2018-05-07.obo includes these lines:

GO:1904788    RO:0002213    4    GO:0000747
GO:1904788    RO:0002211    5    GO:0000747

but the output from go-basic-2018-05-07.obo go-basic-2018-05-08.obo doesn't have any lines that mention those two GO terms. We can't see any ontology changes that could cause this difference.

With the owltools from May 2017 (version 447e4156287) that we have been using to load Canto, the output is quite different. For go-basic-2018-05-07.obo, the output is:

GO:1904788   regulates   5       GO:0000747
GO:1904788   positively_regulates        4       GO:0000747

and for go-basic-2018-05-08.obo the output is:

GO:1904788   regulates   4       GO:0000747

In case it's useful here are the four output files:
https://curation.pombase.org/kmr44/owltools-chado-closure.tar.xz

(Also the recent version of owltools uses "RO:..." IDs for the relations but the older owltools uses term names like "positively_regulates". Is that a bug or should we upload our Chado loading code?)

@cmungall

Start with the owltools --save-closure-for-chado command and compare the outputs for go-basic-2018-05-07.obo and go-basic-2018-05-08.obo, using the linked owltools-chado-closure.tar.xz files. Investigate why unchanged ontology portions produce different closure lines and whether relation IDs versus term names are expected; done means the output is stable or the behavior is documented and corrected.