Exact synonym updates - Build 1 #601
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@matentzn @twhetzel I haven't reviewed this yet, but I believe all our outputs are here, and we can review this now if you like even though the build is failing, because it is failing on the prepare_release step at the very end.
- Update: remaps IAO:0000118 (alt label) to oboInOwl:exactSynonym - Add: exact_syn_from_label.ru: adds oboInOwl:exactSynonym for all rdfs:label on components - Update: component goals to use new query
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Massive change.. interesting to look out for in general, but no indication anything is broken in this pr
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Better leave branch builds in draft PR mode? not sure.
@twhetzel I know this is another tedious SOP detail. Do you have opinion? I like to undraft to let it be known it's ready for review. In case of accidental merge I know how to fix. I don't mind either way
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As for the changes... you're saying it's not anything to worry about in scope of this PR, so I'll stop here at the analysis. I just checked other recent PRs because I expected to see similar diffs in those ones as well, thinking that this was due to a recent change in the upstream source and nothing to do with the changes in this PR. But this PR is the only one with such large differences.
This PR: many changes
exact-syn-updates-build
git diff --stat origin/exact-syn-updates-build develop src/ontology/external/nord.robot.owl
src/ontology/external/nord.robot.owl | 7866 ++++++++++++++++++++++++++++++++++++++++++++++++++--------
1 file changed, 6873 insertions(+), 993 deletions(-)
Other recent PRs: minimal changes
dataload-subclass-sync-switch-edit
git diff --stat origin/dataload-subclass-sync-switch-edit develop src/ontology/external/nord.robot.owl
src/ontology/external/nord.robot.owl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
data-built-refactor-git-refresh
git diff --stat origin/data-built-refactor-git-refresh develop src/ontology/external/nord.robot.owl
src/ontology/external/nord.robot.owl | 60 ++++++++----------------------------------------------------
1 file changed, 8 insertions(+), 52 deletions(-)
build_2024-07-03_main
git diff --stat origin/build_2024-07-03_main develop src/ontology/external/nord.robot.owl
src/ontology/external/nord.robot.owl | 86 +++++++++++++++---------------------------------------------
1 file changed, 21 insertions(+), 65 deletions(-)
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Thanks for asking. I also prefer to have feature branch builds in Draft mode.
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huge change, maybe investigate the pattern of this change. Probably a serialiser thing with blank nodes, just guessing
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Will take a look soon.
I wonder if / how this might have resulted from the changes in this pr
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OK, so @matentzn I don't think this is worrisome at all. This is expected.
doid-unmapped.owl | 104 +-
icd10cm-unmapped.owl | 95849 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
icd10who-unmapped.owl | 12544 ++++++++++++++++-
icd11foundation-unmapped.owl | 70034 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
ncit-unmapped.owl | 2 +-
omim-unmapped.owl | 795 +-
ordo-unmapped.owl | 10925 ++++++++++++++-
With the exception of NCIT & DOID (see comment below), I think that the size of these diffs are simply roughly correlated to the amount of unmapped terms.
unmapped.md table
Note that they don't correlate quite exactly. That bugs me a little bit but I'm not going to worry about it.
Mapping progress report
| Ontology | Tot terms | Tot excluded | Tot deprecated | Tot deprecated unmapped | Tot mappable (!excluded, !deprecated) | Tot mapped (mappable) | Tot unmapped (mappable) | % unmapped (mappable) |
|---|---|---|---|---|---|---|---|---|
| ICD10WHO | 12,542 | 0 | 0 | 0 | 12,542 | 18 | 12,524 | 99.9% |
| ICD10CM | 95,847 | 15,452 | 0 | 0 | 80,395 | 1,163 | 79,232 | 98.6% |
| NCIT | 191,123 | 169,937 | 5,221 | 5,199 | 15,965 | 3,675 | 12,290 | 77.0% |
| ICD11FOUNDATION | 100,382 | 30,335 | 6,587 | 6,587 | 64,451 | 0 | 64,451 | 100.0% |
| ORDO | 15,402 | 6,212 | 1,391 | 1,165 | 9,190 | 9,137 | 53 | 0.6% |
| DOID | 14,082 | 2,656 | 2,484 | 2,468 | 11,424 | 11,391 | 33 | 0.3% |
| OMIM | 29,382 | 19,278 | 1,364 | 1,318 | 8,741 | 8,739 | 2 | 0.0% |
The diffs are as I would expect. These are just newly added synonyms. There are a lot of unmapped terms, so the diff is large.
@matentzn You agree that this is expected?
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However, notice that the diff for NCIT and DOID is very small. I looked, and for some reason, the unmapped/*.owl files for these sources don't have any synonyms or labels (or really any properties in them), even though the components*.owl files do. I created an issue for this:
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FYI: newer build
Since this build initially froze, I had to run it several times. It looks like #609 is the final build that ran. I just pushed it after noticing that my local files in the clone where I ran the build were different than what was here in #601. Note that there are 21 more files changed in that PR than in this one.
I probably just forgot to --force push when finishing that final build. Sorry.
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