├── .cruft.json ├── .env.example ├── .github └── workflows │ ├── deploy-docs.yml │ ├── qc.yml │ ├── release.yml │ └── uniprot_s3_dump.yml ├── .gitignore ├── Jenkinsfile ├── LICENSE.txt ├── Makefile ├── README.md ├── check_transform_chars.py ├── data └── raw │ ├── exclusion_branches.tsv │ └── nlp │ ├── output │ ├── chebi_ner.tsv │ ├── chebi_ner_unmatched.tsv │ ├── go_ner.tsv │ └── go_ner_unmatched.tsv │ └── stopwords │ └── stopWords.txt ├── docs ├── Makefile ├── conf.py ├── index.rst ├── kg_microbe.rst ├── kg_microbe.transform_utils.ontology.rst ├── kg_microbe.transform_utils.rst ├── kg_microbe.transform_utils.traits.rst ├── kg_microbe.utils.rst ├── make.bat ├── modules.rst ├── query_utils.rst ├── run.rst ├── setup.rst ├── sources │ ├── Bacteria-archaea-traits.md │ ├── carbon_substrates.md │ ├── cell_shape.md │ ├── cell_shape_enum.md │ ├── class.md │ ├── coding_genes.md │ ├── d1_lo.md │ ├── d1_up.md │ ├── d2_lo.md │ ├── d2_up.md │ ├── data_source.md │ ├── data_source_enum.md │ ├── doubling_h.md │ ├── family.md │ ├── gc_content.md │ ├── genome_size.md │ ├── genus.md │ ├── gram_stain.md │ ├── gram_stain_enum.md │ ├── growth_tmp.md │ ├── index.md │ ├── isolation_source.md │ ├── metabolism.md │ ├── metabolism_enum.md │ ├── motility.md │ ├── motility_enum.md │ ├── optimum_ph.md │ ├── optimum_tmp.md │ ├── order.md │ ├── org_name.md │ ├── pathways.md │ ├── phylum.md │ ├── rRNA16S_genes.md │ ├── rRNA16S_genes_enum.md │ ├── range_salinity.md │ ├── range_salinity_enum.md │ ├── range_tmp.md │ ├── range_tmp_enum.md │ ├── ref_id.md │ ├── species.md │ ├── species_tax_id.md │ ├── sporulation.md │ ├── sporulation_enum.md │ ├── superkingdom.md │ ├── superkingdom_enum.md │ ├── tRNA_genes.md │ ├── tax_id.md │ └── types │ │ ├── Boolean.md │ │ ├── Date.md │ │ ├── Datetime.md │ │ ├── Decimal.md │ │ ├── Double.md │ │ ├── Float.md │ │ ├── Integer.md │ │ ├── Ncname.md │ │ ├── Nodeidentifier.md │ │ ├── Objectidentifier.md │ │ ├── String.md │ │ ├── Time.md │ │ ├── Uri.md │ │ └── Uriorcurie.md ├── static │ └── intro.md └── tests.rst ├── download.yaml ├── hpc ├── kg_microbe_train_binary_medium.sl ├── run_kg_transform.sl ├── run_kg_transform_uniprot.sl ├── run_kg_transform_uniref.sl └── run_parallel_transform.slurm ├── kg-microbe.Makefile ├── kg-microbe.png ├── kg_microbe ├── __init__.py ├── bactotraits_to_mongo.py ├── download.py ├── merge_utils │ ├── __init__.py │ └── merge_kg.py ├── query.py ├── run.py ├── transform.py ├── transform_utils │ ├── __init__.py │ ├── bacdive │ │ ├── __init__.py │ │ ├── bacdive.py │ │ ├── cas-rn_map.txt │ │ ├── metabolite_mapping.json │ │ └── tmp │ │ │ ├── .keep │ │ │ ├── bacdive.tsv │ │ │ ├── bacdive_mappings.tsv │ │ │ ├── bacdive_name_tax_classification.tsv │ │ │ └── yaml │ │ │ └── .keep │ ├── bactotraits │ │ ├── __init__.py │ │ ├── bactotraits.py │ │ └── tmp │ │ │ ├── BactoTraits.tsv │ │ │ └── BactoTraits_mapping.tsv │ ├── constants.py │ ├── ctd │ │ ├── __init__.py │ │ └── ctd.py │ ├── custom_curies.yaml │ ├── disbiome │ │ ├── __init__.py │ │ ├── disbiome.py │ │ └── tmp │ │ │ ├── Disbiome_Labels.csv │ │ │ └── Disbiome_Microbe_Labels.csv │ ├── example_transform │ │ ├── __init__.py │ │ └── example_transform.py │ ├── madin_etal │ │ ├── __init__.py │ │ ├── chebi_manual_annotation.tsv │ │ └── madin_etal.py │ ├── mediadive │ │ ├── __init__.py │ │ ├── mediadive.py │ │ └── tmp │ │ │ ├── .keep │ │ │ ├── mediadive.tsv │ │ │ ├── medium_strain_yaml │ │ │ └── .keep │ │ │ └── medium_yaml │ │ │ └── .keep │ ├── ontologies │ │ ├── __init__.py │ │ ├── ontologies_transform.py │ │ ├── trees │ │ │ └── go_category_trees.tsv │ │ └── xrefs │ │ │ └── mondo_gene_ids.tsv │ ├── prefixmap.json │ ├── rhea_mappings │ │ ├── __init__.py │ │ └── rhea_mappings.py │ ├── transform.py │ ├── translation_table.yaml │ ├── uniprot_functional_microbes │ │ ├── __init__.py │ │ ├── tmp │ │ │ ├── go_obsolete_terms.tsv │ │ │ └── relevant_files.tsv │ │ └── uniprot_functional_microbes.py │ ├── uniprot_human │ │ ├── __init__.py │ │ ├── tmp │ │ │ └── go_obsolete_terms.tsv │ │ └── uniprot_human.py │ ├── uniprot_trembl │ │ ├── __init__.py │ │ ├── tmp │ │ │ └── .keep │ │ └── uniprot_trembl.py │ └── wallen_etal │ │ ├── __init__.py │ │ ├── tmp │ │ └── Wallen_etal_Microbe_Labels.csv │ │ └── wallen_etal.py └── utils │ ├── __init__.py │ ├── download_bacdive.py │ ├── dummy_tqdm.py │ ├── mapping_file_utils.py │ ├── ner_utils.py │ ├── oak_utils.py │ ├── ontology_utils.py │ ├── pandas_utils.py │ ├── parse_taxon_rank.py │ ├── robot_utils.py │ ├── sanitize_curies.py │ ├── string_coding.py │ ├── trembl_utils.py │ ├── unipathways_utils.py │ └── uniprot_utils.py ├── mappings ├── chemical_mappings.tsv └── chemical_mappings_mismatches.tsv ├── merge.minimal.yaml ├── merge.yaml ├── merge.yaml_biomed ├── merged_graph_stats.yaml ├── notebooks ├── BacDive-exploration.ipynb ├── MergedKG_exploration.ipynb ├── README.md ├── bacdive-api-test.ipynb ├── bacdive_mapping_resource.ipynb ├── feba.ipynb ├── get_taxa_features.ipynb ├── kg_microbe_summary.ipynb ├── metacyc_pathway_hierarchy.ipynb ├── pivot-kg-edges │ ├── data │ │ ├── merged-kg_edges.tsv.gz │ │ ├── merged-kg_edges_NCBITaxon_clean.tsv.gz │ │ └── pivot_merged-kg_edges_NCBITaxon.tsv.gz │ ├── pivot-merged-kg-edges-NCBITaxon.ipynb │ └── test-pivot-kg-subset.ipynb ├── schema-1.png ├── schema-2.png ├── schema.pdf └── schema.png ├── poetry.lock ├── pyproject.toml ├── query_utils ├── __init__.py └── query.py ├── sample-merge-config.yml ├── schemas ├── chemicals.sssom.tsv ├── distinct_carbon_substrates.txt ├── pathways.sssom.tsv └── trait_condensed.yaml ├── scripts └── combine_chemical_mappings.py ├── stopwords.yaml ├── templates ├── README.build └── README.toplevel ├── tests ├── __init__.py └── demo_test.py └── tox.ini /.cruft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-microbe/HEAD/.cruft.json -------------------------------------------------------------------------------- /.env.example: 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