ba5350e41c26185f48dd56d074219d3a2eab7aed
mspeir
  Thu Jul 2 10:32:20 2026 -0700
New otto framework for G2P track, refs #36736

diff --git src/hg/utils/otto/g2p/g2p.as src/hg/utils/otto/g2p/g2p.as
new file mode 100644
index 00000000000..5c1f3427489
--- /dev/null
+++ src/hg/utils/otto/g2p/g2p.as
@@ -0,0 +1,35 @@
+table g2p
+"All panels in the Gene2Phenotype (G2P) database - BED 9+20"
+(
+    string chrom;        "Reference sequence chromosome or scaffold"
+    uint   chromStart;    "Start position of feature on chromosome"
+    uint   chromEnd;      "End position of feature on chromosome"
+    string name;          "Gene symbol"
+    uint   score;         "Score"
+    char[1] strand;       "+ or - for strand"
+    uint   thickStart;    "Coding region start"
+    uint   thickEnd;      "Coding region end"
+    uint   itemRGB;       "Color based on confidence (R,G,B values)"
+
+    # ----- 20 additional custom fields -----
+    string g2p_id;                           "G2P ID"
+    string   gene_mim;                         "Gene MIM ID"
+    string   hgnc_id;                          "HGNC ID"
+    string previous_gene_symbols;            "List of previous gene symbols"
+    lstring disease_name;                     "Disease name"
+    string disease_mim;                      "Disease MIM ID"
+    string disease_MONDO;                    "MONDO ID"
+    string allelic_requirement;              "Number of alleles affected to cause the relevant disease"
+    string cross_cutting_modifier;           "Optional cross-cutting modifiers giving extra info"
+    string confidence;                       "Likelihood that the gene-disease association is true"
+    string variant_consequence;              "SO terms for the variant consequence"
+    lstring variant_types;                    "SO terms for variant types"
+    string molecular_mechanism;              "Molecular mechanism"
+    string molecular_mechanism_categorisation; "Categorisation of the molecular mechanism"
+    lstring molecular_mechanism_evidence;     "Evidence to determine the disease mechanism"
+    lstring phenotypes;                       "Human phenotype ontology IDs"
+    lstring publications;                     "Pubmed IDs"
+    string panel;                            "Disease grouping or defined clinical category"
+    lstring comments;                         "Comments added by online curators"
+    string date_of_last_review;              "Date of last review"
+)