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problematic env_braod_scale and env_material #39

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merged 2 commits into from
Feb 16, 2024
Merged

problematic env_braod_scale and env_material #39

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55cfb4f
problematic env_braod_scale and env_material
turbomam Feb 16, 2024
ac97511
problematic_triads.tsv in data-vs-ontology-all
turbomam Feb 16, 2024
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27 changes: 26 additions & 1 deletion data-vs-ontology-reports.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ data-vs-ontology-all: data-vs-ontology-clean \
data-vs-ontology-reports/report-id-ranges.tsv \
data-vs-ontology-reports/envo-id-ranges-report.tsv \
data-vs-ontology-reports/fma-usage-report.tsv \
data-vs-ontology-reports/nmdco-envo-classes-with-id-owner.tsv
data-vs-ontology-reports/nmdco-envo-classes-with-id-owner.tsv \
data-vs-ontology-reports/problematic_triads.tsv

data-vs-ontology-clean:
rm -rf data-vs-ontology-reports/*
Expand Down Expand Up @@ -89,3 +90,27 @@ data-vs-ontology-reports/nmdco-envo-classes-with-id-owner.tsv: data-vs-ontology-
--nmdco-classes-json-input $(word 2,$^) \
--output $@

data-vs-ontology-reports/envo-biomes.txt: downloads/envo.db
$(RUN) runoak \
--input $< descendants -p i biome | sort -t '!' -k2,2 > $@

data-vs-ontology-reports/envo-environmental-materials.txt: downloads/envo.db
$(RUN) runoak \
--input $< descendants -p i 'environmental material' | sort -t '!' -k2,2 > $@


data-vs-ontology-reports/envo-all-classes.txt: downloads/envo.db
$(RUN) runoak \
--input $< descendants -p i entity | sort -t '!' -k2,2 > $@

data-vs-ontology-reports/problematic_triads.tsv: data-vs-ontology-reports/envo-all-classes.txt \
data-vs-ontology-reports/envo-biomes.txt \
data-vs-ontology-reports/biosample-triad-report.tsv \
data-vs-ontology-reports/envo-environmental-materials.txt
$(RUN) find-biosamples-with-problematic-triads \
--all-envo-classes-file $(word 1, $^) \
--biomes-file $(word 2, $^) \
--biosamples-file $(word 3, $^) \
--materials-file $(word 4, $^) \
--output $@ \
--output-summary data-vs-ontology-reports/problematic_triad_summary.yaml
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