.gitignore

# General
# - directories
__pycache__/
/.idea/
/.run/
bin/
cache/
semantic.cache/
# - patterns
*.code-workspace
*.tmp
*.tmp.obo
*.tmp.owl
*.tmp.json
*.db
!/tests/input/**/*.db
.vscode/*

# - static
.DS_Store

# Specific files, patterns, and directories
*relation-graph*
mondo-ingest.owl
mondo-ingest.obo
mondo-ingest.json
mondo-ingest-full.owl
mondo-ingest-full.obo
mondo-ingest-full.json
mondo-ingest-base.owl
mondo-ingest-base.obo
mondo-ingest-base.json

.github/workflows/diff.yml
.github/workflows/qc.yml

imports/*

# src/mappings/
src/mappings/mondo-sources-all-lexical.sssom.tsv
src/mappings/mondo-sources-all-lexical-2.sssom.tsv

# src/ontology/
src/ontology/.template.db
src/ontology/mondo-ingest.owl
src/ontology/mondo-ingest.obo
src/ontology/mondo-ingest.json
src/ontology/mondo-ingest-base.*
src/ontology/mondo-ingest-basic.*
src/ontology/mondo-ingest-full.*
src/ontology/mondo-ingest-simple.*
src/ontology/mondo-ingest-simple-non-classified.*
src/ontology/seed.txt
src/ontology/dosdp-tools.log
src/ontology/ed_definitions_merged.owl
src/ontology/ontologyterms.txt
src/ontology/simple_seed.txt
src/ontology/patterns
src/ontology/merged-mondo-ingest-edit.owl

# src/ontology/components/
src/ontology/components/*

# src/ontology/imports/
src/ontology/imports/*.owl
!src/ontology/imports/do_import.owl
!src/ontology/imports/omo_import.owl
!src/ontology/imports/ro_import.owl
src/ontology/imports/*.json
src/ontology/imports/*_terms_combined.txt

# src/ontology/mirror/
src/ontology/mirror
src/ontology/mirror/*

# src/ontology/reports/
src/ontology/reports/*.ttl
src/ontology/reports/*.subclass.direct-in-mondo-only.tsv
src/ontology/reports/mondo-ingest-edit.owl-obo-report.tsv
!src/ontology/reports/README.md
!src/ontology/reports/*excluded_terms_in_mondo_xrefs.tsv
!src/ontology/reports/*exclusion_reasons.robot.template.tsv
!src/ontology/reports/*excluded_terms.txt
# todo: These ! patterns don't seem to be an exception to anything that would currently be ignoring them, so I don't think they're needed. Commented out. - Joe 2023/11/16
#!src/ontology/reports/README.md
#!src/ontology/reports/*excluded_terms_in_mondo_xrefs.tsv
#!src/ontology/reports/*exclusion_reasons.robot.template.tsv
#!src/ontology/reports/*excluded_terms.txt

# src/ontology/target/
src/ontology/target/

# src/ontology/tmp/
src/ontology/tmp/*
!src/ontology/tmp/.gitkeep
!src/ontology/tmp/README.md

# src/patterns/
src/patterns/data/**/*.ofn
src/patterns/data/**/*.txt
src/patterns/pattern_owl_seed.txt
src/patterns/all_pattern_terms.txt

src/scripts/.ipynb_checkpoints/*
src/scripts/mondo_unmapped.tsv

# Test
tests/output/*
!tests/output/.gitkeep
src/scripts/dataframes/*
src/ontology/reports/gard.subclass.added-obsolete.robot.tsv
src/ontology/reports/gard.subclass.added.robot.tsv
src/ontology/reports/gard.subclass.confirmed.robot.tsv
src/ontology/reports/basic-report.tsv