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Merge pull request #4 from Knowledge-Graph-Hub/build_graphs
create all graphs for paper
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| # download-transforms: | ||
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| # wget "XXX" -O data/raw/merged-kg_nodes.tsv | ||
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| # merge-kg-microbe-function: | ||
| # PWD=$(pwd) | ||
| # poetry run kg merge -y $(PWD)/merged_yamls/kg_base_merge.yaml | ||
| # poetry run kg duckdb_merge -base-n $(PWD)/data/merged/merged-kg_nodes.tsv -subset-n $(PWD)/data/transformed/nodes.tsv -base-e $(PWD)/data/merged/merged-kg_edges.tsv -subset-e $(PWD)/data/transformed/edges.tsv | ||
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| # merge-kg-microbe-biomedical: | ||
| # PWD=$(pwd) | ||
| # poetry run kg merge -y $(PWD)/merged_yamls/kg_biomedical_merge.yaml | ||
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| # merge-kg-microbe-biomedical-function: | ||
| # PWD=$(pwd) | ||
| # poetry run kg merge -y $(PWD)/merged_yamls/kg_biomedical_merge.yaml | ||
| # poetry run kg duckdb_merge -base-n $(PWD)/data/merged/merged-kg_nodes.tsv -subset-n $(PWD)/data/transformed/nodes.tsv -base-e $(PWD)/data/merged/merged-kg_edges.tsv -subset-e $(PWD)/data/transformed/edges.tsv | ||
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| # !For testing | ||
| # merge-kg-microbe-biomedical-function: | ||
| # poetry run kg merge -y merge_yamls/merge.yaml -m duckdb -base-n '/Users/brooksantangelo/Documents/LozuponeLab/FRMS_2024/duckdb/merged-kg_kg-microbe-base/merged-kg_nodes.tsv' -base-e '/Users/brooksantangelo/Documents/LozuponeLab/FRMS_2024/duckdb/merged-kg_kg-microbe-base/merged-kg_edges.tsv' -subset-n '/Users/brooksantangelo/Documents/Repositories/kg-microbe/data/transformed/uniprot_genome_features/nodes.tsv' -subset-e '/Users/brooksantangelo/Documents/Repositories/kg-microbe/data/transformed/uniprot_genome_features/edges.tsv' | ||
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| datamodel: | ||
| poetry run gen-python kg_microbe_merge/schema/merge_schema.yaml > kg_microbe_merge/schema/merge_datamodel.py | ||
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| kg-microbe-core: | ||
| poetry run kg merge -m duckdb -s "bacdive, mediadive, madin_etal, rhea_mappings, bactotraits, chebi, ec, envo, go, ncbitaxon, upa" --merge-label $@ | ||
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| kg-microbe-function: | ||
| poetry run kg merge -m duckdb -n 1000000 -e 100000 -s "bacdive, mediadive, madin_etal, rhea_mappings, bactotraits, chebi, ec, envo, go, ncbitaxon, upa, uniprot_functional_microbes" --merge-label $@ | ||
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| kg-microbe-biomedical: | ||
| poetry run kg merge -m duckdb -n 1000000 -e 100000 -s "bacdive, mediadive, madin_etal, rhea_mappings, bactotraits, chebi, ec, envo, go, ncbitaxon, upa, hp, mondo, ctd, wallen_etal, uniprot_human" --merge-label $@ | ||
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| subset-merge: | ||
| poetry run kg merge -m duckdb -s "bacdive, bactotraits, chebi, ncbitaxon" | ||
| kg-microbe-biomedical-function-merge: | ||
| poetry run kg merge -m duckdb -n 1000000 -e 100000 -s "bacdive, mediadive, madin_etal, rhea_mappings, bactotraits, chebi, ec, envo, go, ncbitaxon, upa, hp, mondo, ctd, wallen_etal, uniprot_human, uniprot_functional_microbes" --merge-label $@ |