METRIN-KG

Files associated with MEtabolomes, TRaits, and INteractions-Knowledge Graph (METRIN-KG). Contains input and output files used in mapping taxonomy, metadata, ontology and knowledge graph construction. Associated github repositories are metrin-kg and earth_metabolome_ontology

Directory structure looks like the following. This directory can be used in combination with the code at the github repo metrin-kg.

└── metrin-kg-data
    ├── ontology
    │   └── emi.ttl.gz
    ├── processed
    │   ├── globi
    │   │   ├── correctedBiologicalSexNames.tsv
    │   │   ├── correctedBodyPartNamesGlobi.csv
    │   │   ├── correctedLifeStageNamesGlobi.csv
    │   │   ├── mappedBiologicalSexNames.tsv
    │   │   ├── unmappedBiologicalSexNames.tsv
    │   │   ├── verbatim_mappedBodyPartNamesGlobi.csv
    │   │   ├── verbatim_mappedLifeStageNamesGlobi.csv
    │   │   ├── verbatim_unmappedBodyPartNamesGlobi_mod.csv
    │   │   └── verbatim_unmappedLifeStageNamesGlobi_mod.csv
    │   ├── KG
    │   │   ├── dbgi-emi-rdf-v3.zip
    │   │   ├── globi_output.ttl.gz
    │   │   ├── taxonomy_output.ttl.gz
    │   │   └── trydb_output.ttl.gz
    │   ├── trydb
    │   │   ├── EmiMappingToTryDb.txt
    │   │   ├── qudtMappingToTryDb_full.txt
    │   │   └── qudtMappingToTryDb.txt
    │   ├── wdTax_duplicates.txt
    │   ├── wdTax_GloBI.txt.gz
    │   ├── wdTax_SPARQL_lineage_filtered_aligned.txt.gz
    │   ├── wdTax_SPARQL_lineage_filtered.txt.gz
    │   ├── wdTax_SPARQL_lineage.txt.gz
    │   ├── wdTax_SPARQL.txt.gz
    │   └── wdTax_TRYdb.txt.gz
    └── raw
        ├── enpkg_wd_pfId.csv.gz
        ├── Try20243712146549_TRY6.0_SpeciesList_TaxonomicHarmonization.csv
        └── TRYdb_40340.txt.gz