Updates to handle Bioportal normalization #16
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| @@ -406,3 +399,48 @@ def load_sssom_maps(maps) -> tuple: | |||
| print(f"Loaded {len(cat_map)} category mappings.") | |||
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| return (id_map, cat_map) | |||
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| def obo_handle(old_id: str) -> str: | |||
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We should really be fixing the sources rather than writing such exception handling code.. is there a way we can get a report of all "exceptions" fixed this way so we can try to correct them in the ontologies?
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I'd love a way to automate fixing this across the original ~1,000 Bioportal entries (because that's mostly what this is for), but for now, all IDs are written out to one of three different reports, as needed:
- IDs of unexpected format, e.g.,
ID
OBO:ExO_0000030
OBO:ExO_0000151
OBO:ExO_0000152
- IDs with remapped categories
Old ID New Category
OBO:ExO_0000030 biolink:NamedThing
OBO:ExO_0000151 biolink:NamedThing
OBO:ExO_0000152 biolink:NamedThing
- IDs with remapped IDs
Old ID New ID
OBO:ExO_0000030 EXO:0000030
OBO:ExO_0000151 EXO:0000151
OBO:ExO_0000152 EXO:0000152
So that last report would be most useful for finding the easily-solved exceptions, but the first report may also contain some candidates for repair.
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Remind me, why are these not correctly understood to be: ExO:0000030?
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In this case, it's to align with the Bioportal ID (EXO). I'm thinking about adding a profile option to use "OBO mode" so the Bioportal prefixes can still be used for mapping but will be normalized to the preferred forms like ExO.
--contexts) to provide one or more prefix contexts to use