metpo/.gitignore at main · berkeleybop/metpo · GitHub

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# ODK-managed rules, do not modify
# If you need to add your own ignore rules, you may do so below
# the "End ODK-managed rules" marker at the end of this file.
.DS_Store
semantic.cache
bin/

*.tmp
*.tmp.obo
*.tmp.owl
*.tmp.json
*-relation-graph.tsv.gz
.template.db

.github/token.txt

/metpo.owl
/metpo.obo
/metpo.json
/metpo.db
/metpo-base.*
/metpo-basic.*
/metpo-full.*
/metpo-simple.*
/metpo-simple-non-classified.*
/mappings/
/patterns/
/reports/
/subsets/

src/ontology/mirror
src/ontology/mirror/*
src/ontology/reports/*
!src/ontology/reports/release-diff.md
src/ontology/metpo.owl
src/ontology/metpo.obo
src/ontology/metpo.json
src/ontology/metpo.db
src/ontology/metpo-base.*
src/ontology/metpo-basic.*
src/ontology/metpo-full.*
src/ontology/metpo-simple.*
src/ontology/metpo-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-metpo-edit.owl
src/ontology/metpo-edit.properties

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

src/ontology/run.sh.conf
src/ontology/run.sh.env

src/ontology/imports/*_terms_combined.txt

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

# End of ODK-managed rules

# METPO commits release artifacts to the repo rather than using GitHub Releases.
# Override the ODK-managed ignore rules above so these files stay tracked.
!/metpo.owl
!/metpo.obo
!/metpo.json
!/metpo-base.owl
!/metpo-base.obo
!/metpo-base.json
!/metpo-full.owl
!/metpo-full.obo
!/metpo-full.json

*.db
*sqlite
.env
.idea/
.litellm_cache
.venv/
downloads/
large/
local/
**/__pycache__/
*.pyc
*.pyo


literature_mining/random-*-pmids.txt

# Large log files from literature mining
literature_mining/logs/*.log
literature_mining/outputs/**/*.log

# Literature mining workspace (untracked working files)
literature_mining/workspace/

# Large reference files
assets/chebi.lex
assets/*.zip

# Jupyter notebook checkpoints
.ipynb_checkpoints/
**/.ipynb_checkpoints/

# ChromaDB directories (vector databases can be multi-GB)
notebooks/*.db
notebooks/metpo_relevant_chroma/
notebooks/oba_chroma/
notebooks/chroma*/
notebooks/*_chroma/
chroma_*/
embeddings_chroma/

# Ontology pipeline tracking files
.ontology_manifest.json
.ontology_fetch.log
.robot_query.log

# ROBOT quality control report (regenerate with: make metpo-report.tsv)
metpo-report.tsv

# N4L phenotypic ontology generated docs (4000+ HTML files)
assets/N4L_phenotypic_ontology_2016/N4L_phenotypic_ontology/20160406_docs/
assets/N4L_phenotypic_ontology_2016/N4L_phenotypic_ontology/20160406_docs/doc/

# Ontologies directory - ignore large OWL files but keep analysis results
# External ontology files
# Tracked in git since total size is reasonable (~17 MB)
# Only ignore derived databases
external/databases/*.db
.~lock.*#
data/chromadb/chroma_ols20_nonols4/

# MCP cache files
.channels_cache_v2.json
.mcp.json
.users_cache.json