Use functional syntax instead of OBO #121
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@balhoff I want to clarify what's going on here. Is this that the intermediate is ofn, then gets converted to obo or owl at the end. This seems to be true, as I still see the "neo.obo neo.owl" targets, but want to confirm. |
cmungall
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Oct 11, 2024
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@kltm that is correct. I ran it locally works like a charm (or as much as perl can ever be charming) |
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This PR is an alternative to #119, and would fix geneontology/noctua#902.
In this repo we have had a few different hacks related to prefixes and OBO format. In #119 I updated things to use the new OBO support for prefixes, but still ran into a few corner cases. Here I just updated the text output from the perl scripts to write OFN instead of OBO. This gives us much more control over the exact OWL we end up with, and has reliable handling of prefixes. Also, now the OBO file is a terminal output and doesn't need to round-tripped within this build.
I think the only remaining issues are those with TAIR IDs mentioned in #119. But I do still need to do a careful diff. @cmungall suggests taking a simple prefix-based approach to the TAIR IDs (as done here) since the IRIs aren't used currently in Noctua models anyway.