Input and enriched files for the pf1600 dataset - ENPKG

<p>Input files (.mgf spectra and .tsv metadata) and enriched files (metabolite annotation, molecular networks and taxonomical resolution results) for the pf1600 dataset described at <a href="https://doi.org/10.1093/gigascience/giac124">https://doi.org/10.1093/gigascience/giac124</a> and used prior to their semantic enrichment and conversion to knowledge graphs as described in&nbsp;<a href="https://doi.org/10.1021/acscentsci.3c00800">https://doi.org/10.1021/acscentsci.3c00800</a>.</p> <p>&nbsp;</p> <p>A typical directory looks like :</p> <p>&nbsp;</p> <p>├── neg<br>│ &nbsp; ├── isdb&nbsp; &nbsp;<br>│ &nbsp; │ &nbsp; ├── config.yaml<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_isdb_neg.tsv<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_isdb_reweighted_flat_neg.tsv<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_isdb_reweighted_neg.tsv<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_treemap_chemo_counted_neg.html<br>│ &nbsp; │ &nbsp; └── VGF159_A02_treemap_chemo_intensity_neg.html<br>│ &nbsp; ├── molecular_network<br>│ &nbsp; │ &nbsp; ├── config.yaml<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_mn_metadata_neg.tsv<br>│ &nbsp; │ &nbsp; └── VGF159_A02_mn_neg.graphml<br>│ &nbsp; ├── VGF159_A02_features_ms2_neg.mgf<br>│ &nbsp; ├── VGF159_A02_features_quant_neg.csv<br>│ &nbsp; ├── VGF159_A02_lcms_method_params_neg.txt<br>│ &nbsp; ├── VGF159_A02_lcms_processing_params_neg.xml<br>│ &nbsp; ├── VGF159_A02_sirius_neg.mgf<br>│ &nbsp; └── VGF159_A02_WORKSPACE_SIRIUS<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_compound_summary.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_formula_summary_adducts.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_formula_summary.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_neg.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_npc_neg.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_npc.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── compound_identifications_adducts.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── compound_identifications.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── csi_fingerid_neg.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── csi_fingerid.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── formula_identifications_adducts.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── formula_identifications.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── params.yml<br>│ &nbsp; &nbsp; &nbsp; └── report.mztab<br>├── pos<br>│ &nbsp; ├── isdb<br>│ &nbsp; │ &nbsp; ├── config.yaml<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_isdb_pos.tsv<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_isdb_reweighted_flat_pos.tsv<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_isdb_reweighted_pos.tsv<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_treemap_chemo_counted_pos.html<br>│ &nbsp; │ &nbsp; └── VGF159_A02_treemap_chemo_intensity_pos.html<br>│ &nbsp; ├── molecular_network<br>│ &nbsp; │ &nbsp; ├── config.yaml<br>│ &nbsp; │ &nbsp; ├── VGF159_A02_mn_metadata_pos.tsv<br>│ &nbsp; │ &nbsp; └── VGF159_A02_mn_pos.graphml<br>│ &nbsp; ├── VGF159_A02_features_ms2_pos.mgf<br>│ &nbsp; ├── VGF159_A02_features_quant_pos.csv<br>│ &nbsp; ├── VGF159_A02_lcms_method_params_pos.txt<br>│ &nbsp; ├── VGF159_A02_lcms_processing_params_pos.xml<br>│ &nbsp; ├── VGF159_A02_sirius_pos.mgf<br>│ &nbsp; └── VGF159_A02_WORKSPACE_SIRIUS<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_neg.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_summary_adducts.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus_summary.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── canopus.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── compound_identifications_adducts.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── compound_identifications.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── csi_fingerid_neg.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── csi_fingerid.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── formula_identifications_adducts.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── formula_identifications.tsv<br>│ &nbsp; &nbsp; &nbsp; ├── npc_summary.csv<br>│ &nbsp; &nbsp; &nbsp; ├── params.yml<br>│ &nbsp; &nbsp; &nbsp; └── report.mztab<br>├── rdf<br>│ &nbsp; └── graph_params.yaml<br>├── taxo_output<br>│ &nbsp; ├── params.yaml<br>│ &nbsp; ├── VGF159_A02_species.json<br>│ &nbsp; ├── VGF159_A02_taxo_metadata.tsv<br>│ &nbsp; └── VGF159_A02_taxon_info.json<br>└── VGF159_A02_metadata.tsv</p>