ba10a7b1b7fae45ac511702425528670042b8c9f
angie
  Tue Jun 3 11:26:10 2025 -0700
Taxonium config file for SRA Mtb tree with Ash's ranchero metadata.

diff --git src/hg/utils/otto/mtb/taxonium.annotated.config.json src/hg/utils/otto/mtb/taxonium.annotated.config.json
new file mode 100644
index 00000000000..f1e2076841f
--- /dev/null
+++ src/hg/utils/otto/mtb/taxonium.annotated.config.json
@@ -0,0 +1,93 @@
+{ "customNames": {
+    "meta_host_commonname": "Host common name",
+    "meta_host_scienname": "Host scientific name",
+    "meta_run_index": "SRA run accession",
+    "meta_tbprof_sublin": "Lineage from TBProfiler",
+    "meta_tbprofiler_lineage_usher": "Lineage assigned by UShER",
+    "meta_lineage": "Lineage from literature / BioSample",
+    "meta_organism": "Scientific name inferred from submission data",
+    "meta_strain": "Strain from submission or literature",
+    "meta_tbprof_drtype": "TBProfiler drug resistance type",
+    "meta_pheno_AMIKACIN": "Amikacin susceptibility",
+    "meta_pheno_CAPREOMYCIN": "Capreomycin susceptibility",
+    "meta_pheno_CIPROFLOXACIN": "Ciprofloxacin susceptibility",
+    "meta_pheno_CYCLOSERINE": "Cycloserine susceptibility",
+    "meta_pheno_ETHAMBUTOL": "Ethambutol susceptibility",
+    "meta_pheno_ETHIONAMIDE": "Ethionamide susceptibility",
+    "meta_pheno_ISONIAZID": "Isoniazid susceptibility",
+    "meta_pheno_KANAMYCIN": "Kanamycin susceptibility",
+    "meta_pheno_MOXIFLOXACIN": "Moxifloxacin susceptibility",
+    "meta_pheno_OFLOXACIN": "Ofloxacin susceptibility",
+    "meta_pheno_PAS": "PAS susceptibility",
+    "meta_pheno_PYRAZINAMIDE": "Pyrazinamide susceptibility",
+    "meta_pheno_RIFAMPICIN": "Rifampicin susceptibility",
+    "meta_pheno_STREPTOMYCIN": "Streptomycin susceptibility",
+    "meta_pheno_BEDAQUILINE": "Bedaquiline susceptibility",
+    "meta_pheno_CLOFAZIMINE": "Clofazimine susceptibility",
+    "meta_pheno_DELAMANID": "Delamanid susceptibility",
+    "meta_pheno_LEVOFLOXACIN": "Levofloxacin susceptibility",
+    "meta_pheno_LINEZOLID": "Linezolid susceptibility",
+    "meta_pheno_RIFABUTIN": "Rifabutin susceptibility",
+    "meta_pheno_source": "Source(s) of susceptibility data"
+  },
+  "defaultColorByField": "meta_tbprofiler_lineage_usher",
+  "colorBy": {
+      "colorByOptions": [
+          "meta_continent", "meta_country", "meta_region",
+          "meta_host_commonname", "meta_host_scienname",
+          "meta_tbprof_sublin", "meta_tbprofiler_lineage_usher", "meta_lineage",
+          "meta_organism", "meta_strain",
+          "meta_tbprof_drtype",
+          "meta_pheno_AMIKACIN", "meta_pheno_CAPREOMYCIN",
+          "meta_pheno_CIPROFLOXACIN", "meta_pheno_CYCLOSERINE",
+          "meta_pheno_ETHAMBUTOL", "meta_pheno_ETHIONAMIDE",
+          "meta_pheno_ISONIAZID", "meta_pheno_KANAMYCIN",
+          "meta_pheno_MOXIFLOXACIN", "meta_pheno_OFLOXACIN",
+          "meta_pheno_PAS", "meta_pheno_PYRAZINAMIDE",
+          "meta_pheno_RIFAMPICIN", "meta_pheno_STREPTOMYCIN",
+          "meta_pheno_BEDAQUILINE", "meta_pheno_CLOFAZIMINE",
+          "meta_pheno_DELAMANID", "meta_pheno_LEVOFLOXACIN",
+          "meta_pheno_LINEZOLID", "meta_pheno_RIFABUTIN"
+      ]
+  },
+  "defaultColorByField": "meta_tbprof_sublin",
+  "search_types": [
+      { "name": "name", "label": "Name", "type": "text_match" },
+      { "name": "meta_country", "label": "Country", "type": "text_match" },
+      { "name": "meta_region", "label": "Region", "type": "text_match" },
+      { "name": "meta_host_commonname", "label": "Host common name", "type": "text_match" },
+      { "name": "meta_host_scienname", "label": "Host scientific name", "type": "text_match" },
+      { "name": "meta_tbprof_sublin", "label": "Lineage from TBProfiler", "type": "text_exact" },
+      { "name": "meta_tbprofiler_lineage_usher", "label": "Lineage assigned by UShER", "type": "text_exact" },
+      { "name": "meta_lineage", "label": "Lineage from literature / BioSample", "type": "text_exact" },
+      { "name": "meta_organism", "label": "Scientific name inferred from submission data", "type": "text_exact" },
+      { "name": "meta_strain", "label": "Strain from submission or literature", "type": "text_exact" },
+      { "name": "meta_tbprof_drtype", "label": "TBProfiler drug resistance type", "type": "text_exact" },
+      { "name": "meta_pheno_AMIKACIN", "label": "Amikacin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_CAPREOMYCIN", "label": "Capreomycin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_CIPROFLOXACIN", "label": "Ciprofloxacin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_CYCLOSERINE", "label": "Cycloserine susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_ETHAMBUTOL", "label": "Ethambutol susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_ETHIONAMIDE", "label": "Ethionamide susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_ISONIAZID", "label": "Isoniazid susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_KANAMYCIN", "label": "Kanamycin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_MOXIFLOXACIN", "label": "Moxifloxacin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_OFLOXACIN", "label": "Ofloxacin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_PAS", "label": "PAS susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_PYRAZINAMIDE", "label": "Pyrazinamide susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_RIFAMPICIN", "label": "Rifampicin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_STREPTOMYCIN", "label": "Streptomycin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_BEDAQUILINE", "label": "Bedaquiline susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_CLOFAZIMINE", "label": "Clofazimine susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_DELAMANID", "label": "Delamanid susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_LEVOFLOXACIN", "label": "Levofloxacin susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_LINEZOLID", "label": "Linezolid susceptibility", "type": "text_exact" },
+      { "name": "meta_pheno_RIFABUTIN", "label": "Rifabutin susceptibility", "type": "text_exact" },
+      { "name": "mutation", "label": "Mutation", "type": "mutation" },
+      { "name": "genotype", "label": "Genotype", "type": "genotype" },
+      { "name": "revertant", "label": "Revertant", "type": "revertant" },
+      { "name": "num_tips", "label": "Number of tips", "type": "number" },
+      { "name": "boolean", "label": "Boolean", "type": "boolean" }
+  ],
+  "source": "SRA"
+}