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config.yml
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config.yml
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merged_files_allbiomes:
abundance: "data/EDA/Abundance_tables/Merged_tables/All_biomes_filtstud/all_biomes_merged_abund_tables_species_filtstud.csv"
taxonomy: "data/EDA/Abundance_tables/Merged_tables/All_biomes_filtstud/all_biomes_merged_taxa_tables_species_filtstud.csv"
samples: "data/EDA/Samples_metadata/Merged_tables/all_biomes_merged_samples_metadata_filtstud.csv"
study_ids: "data/EDA/Abundance_tables/Merged_tables/All_biomes_filtstud/all_biomes_studies_per_sample_filtstud.csv"
merged_files_per_biome:
Wastewater:
abundance: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater/Wastewater_merged_abund_tables_species.csv"
taxonomy: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater/Wastewater_merged_taxa_tables_species.csv"
Wastewater_Water_and_sludge:
abundance: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater_Water_and_sludge/Wastewater_Water_and_sludge_merged_abund_tables_species.csv"
taxonomy: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater_Water_and_sludge/Wastewater_Water_and_sludge_merged_taxa_tables_species.csv"
Wastewater_Industrial_wastewater:
abundance: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater_Industrial_wastewater/Wastewater_Industrial_wastewater_merged_abund_tables_species.csv"
taxonomy: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater_Industrial_wastewater/Wastewater_Industrial_wastewater_merged_taxa_tables_species.csv"
Wastewater_Activated_Sludge:
abundance: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater_Activated_Sludge/Wastewater_Activated_Sludge_merged_abund_tables_species.csv"
taxonomy: "data/EDA/Abundance_tables/Merged_tables/Biomes/Wastewater_Activated_Sludge/Wastewater_Activated_Sludge_merged_taxa_tables_species.csv"
microbial_asso_nets:
Activated_sludge:
Assembly: "data/Microb_asso_nets/Activated_sludge/Assembly/ActivatedSludge_assembly_nosinglt_cclasso_10"
Metagenomics: "data/Microb_asso_nets/Activated_sludge/Metagenomics/ActivatedSludge_metagenomic_nosinglt_cclasso_70"
Metatranscriptomics: "data/Microb_asso_nets/Activated_sludge/Metatranscriptomics/ActivatedSludge_metatranscriptomic_nosinglt_cclasso_40"
Wastewater:
Assembly: "data/Microb_asso_nets/Wastewater/Assembly/Wastewater_assembly_nosinglt_cclasso_10"
Metagenomics: "data/Microb_asso_nets/Wastewater/Metagenomics/Wastewater_metagenomic_nosinglt_cclasso_25"
Metatranscriptomics: "data/Microb_asso_nets/Wastewater/Metatranscriptomics/Wastewater_metatranscriptomic_nosinglt_cclasso_60"
Industrial_wastewater:
Metagenomics: "data/Microb_asso_nets/Industrial_wastewater/Industrial_wastewater_metagenomic_nosinglt_cclasso_50"
Water_and_sludge:
Metagenomics: "data/Microb_asso_nets/Water_and_sludge/Water_and_sludge_metagenomic_nosinglt_cclasso_70"
knowledge_graphs:
Activated_sludge:
Assembly: "data/KG/Activated_sludge/ActivatedSludge_assembly"
Metagenomics: "data/KG/Activated_sludge/ActivatedSludge_metagenomics"
Metatranscriptomics: "data/KG/Activated_sludge/ActivatedSludge_metatranscriptomics"
Wastewater:
Assembly: "data/KG/Wastewater/Wastewater_assembly"
Metagenomics: "data/KG/Wastewater/Wastewater_metagenomics"
Metatranscriptomics: "data/KG/Wastewater/Wastewater_metatrasncriptomics"
Industrial_wastewater:
Metagenomics: "data/KG/Industrial_wastewater/IndustrialWastewater_metagenomics"
Water_and_sludge:
Metagenomics: "data/KG/Water_and_sludge/WaterSludge_metagenomics"
Complete_kg: "data/KG/Complete_KG/MicW2Graph"
case_studies:
Wastewater_and_metagenomics_association_cluster1: "data/Case_studies/Wastewater_and_metagenomics_association_cluster1"
Wastewater_and_metagenomics_association_cluster2: "data/Case_studies/Wastewater_and_metagenomics_association_cluster2"
Wastewater_and_metagenomics_functional_cluster: "data/Case_studies/Wastewater_and_metagenomics_functional_cluster"
Activated_sludge_and_metagenomics_association_cluster: "data/Case_studies/Activated_sludge_and_metagenomics_association_cluster"
kg_nodes:
Class:
color: '#d6d211ff'
border-color: '#888408ff'
Family:
color: '#2793146b'
border-color: '#31c17aff'
Genus:
color: '#7ad1ffff'
border-color: '#009bedff'
Kingdom:
color: '#e9ccaaff'
border-color: '#cf8f44ff'
Order:
color: '#c5aae9ff'
border-color: '#9b6bd9ff'
Phylum:
color: '#b5e3ecff'
border-color: '#47b9d1ff'
Species:
color: '#e3cd72ff'
border-color: '#a48f23ff'
ActivityAndBehavior:
color: '#77b3ddc9'
border-color: '#256491c9'
BiologicalProcess:
color: '#cdfb98ff'
border-color: '#76d30aff'
ChemicalEntity:
color: '#e9aaaaff'
border-color: '#d65c5cff'
EnvironmentalFeature:
color: '#ecb5ebff'
border-color: '#d761d6ff'
PhenotypicFeature:
color: '#f3ab8eff'
border-color: '#e75d24ff'
kg_edges:
ASSOCIATED_WITH:
color: '#B53C44FF'
PARTICIPATES_IN:
color: '#11449cff'
CAPABLE_OF:
color: '#11449cff'
PRODUCES:
color: '#11449cff'
HAS_PHENOTYPE:
color: '#11449cff'
LOCATED_IN:
color: '#11449cff'
HAS_NUTRIENT:
color: '#11449cff'
SUBCLASS_OF:
color: '#a5abb6ff'
urls: