{
  "argo95_sft": {
    "n_files": 95,
    "n_terms": 955,
    "assessment_counts": {
      "CNN": 682,
      "NPI": 113,
      "UNC": 60,
      "LSP": 43,
      "REP": 29,
      "COR": 23,
      "PLI": 5
    },
    "n_discordant": 147,
    "n_discordant_tagged": 85,
    "n_discordant_untagged": 62,
    "untagged_by_assessment": {
      "NPI": 62
    },
    "error_type_term_counts": {
      "FREQUENCY_BIAS": 29,
      "PATHWAY_CONTEXT_IGNORED": 14,
      "NAMING_INCONSISTENCY": 13,
      "PSEUDOENZYME_OVERANNOTATION": 9,
      "TAXON_CONSTRAINT_VIOLATION": 7,
      "PARALOG_OVERANNOTATION": 5,
      "LOCALIZATION_DEFAULT": 4,
      "TRAINING_DATA_CONTAMINATION": 2,
      "CURATION_MISTAKE": 1,
      "MULTIPLE_FUNCTIONS": 1
    },
    "error_type_gene_counts": {
      "FREQUENCY_BIAS": 29,
      "NAMING_INCONSISTENCY": 11,
      "PATHWAY_CONTEXT_IGNORED": 9,
      "TAXON_CONSTRAINT_VIOLATION": 7,
      "LOCALIZATION_DEFAULT": 4,
      "PARALOG_OVERANNOTATION": 3,
      "PSEUDOENZYME_OVERANNOTATION": 3,
      "CURATION_MISTAKE": 1,
      "MULTIPLE_FUNCTIONS": 1,
      "TRAINING_DATA_CONTAMINATION": 1
    },
    "error_type_genes": {
      "TAXON_CONSTRAINT_VIOLATION": [
        "ARATH/COP1",
        "BACSU/aprE",
        "BACSU/sigK",
        "ECOLI/DnaJ",
        "ECOLI/DnaK",
        "rat/Hspa5",
        "yeast/RAS2"
      ],
      "NAMING_INCONSISTENCY": [
        "ARATH/ETR1",
        "BACSU/fliY",
        "BACSU/spoIIGA",
        "ECOLI/mrdA",
        "PSEPK/pedH",
        "SCHPO/ura7",
        "human/NFE2L2",
        "rat/Rgn",
        "worm/hsf-1",
        "worm/hsp-90",
        "yeast/HSP104"
      ],
      "FREQUENCY_BIAS": [
        "BACSU/aprE",
        "BACSU/comK",
        "BACSU/secA",
        "BACSU/sigF",
        "BACSU/sigK",
        "BACSU/spo0A",
        "BACSU/spoIIE",
        "DROME/CRY",
        "DROME/Git",
        "ECOLI/ftsI",
        "ECOLI/mrdA",
        "ECOLI/surA",
        "SCHPO/SPCC16C4.02c",
        "SCHPO/Shu1",
        "SCHPO/atg101",
        "SCHPO/atg13",
        "SCHPO/atg16",
        "SCHPO/atg38",
        "SCHPO/atg5",
        "SCHPO/pol5",
        "SCHPO/snx41",
        "SCHPO/tam10",
        "SCHPO/tim10",
        "human/CYCS",
        "mouse/Calm1",
        "worm/pgl-1",
        "yeast/RAS2",
        "yeast/SIR2",
        "yeast/TOR1"
      ],
      "PATHWAY_CONTEXT_IGNORED": [
        "BACSU/comK",
        "BACSU/divIVA",
        "BACSU/fliY",
        "BACSU/secA",
        "BACSU/sigF",
        "BACSU/sigK",
        "BACSU/spoIIE",
        "yeast/HSP60",
        "yeast/SSA1"
      ],
      "PARALOG_OVERANNOTATION": [
        "DROME/LysB",
        "SCHPO/SPAC8E11.10",
        "SCHPO/alo1"
      ],
      "CURATION_MISTAKE": [
        "ECOLI/DnaJ"
      ],
      "MULTIPLE_FUNCTIONS": [
        "ECOLI/SecB"
      ],
      "LOCALIZATION_DEFAULT": [
        "PSEPK/pedH",
        "SCHPO/Shu1",
        "SCHPO/cps1",
        "yeast/HSP60"
      ],
      "PSEUDOENZYME_OVERANNOTATION": [
        "SCHPO/Epe1",
        "SCHPO/cts2",
        "SCHPO/pmp20"
      ],
      "TRAINING_DATA_CONTAMINATION": [
        "human/NFE2L2"
      ]
    }
  },
  "argo139_gogpt": {
    "n_files": 139,
    "n_terms": 5923,
    "assessment_counts": {
      "UNC": 3899,
      "CNN": 1897,
      "NPI": 124,
      "LSP": 3
    },
    "n_discordant": 124,
    "n_discordant_tagged": 0,
    "n_discordant_untagged": 124,
    "untagged_by_assessment": {
      "NPI": 124
    },
    "error_type_term_counts": {},
    "error_type_gene_counts": {},
    "error_type_genes": {}
  },
  "mode_table": [
    {
      "mode": "1 pseudo-enzyme",
      "error_types": [
        "PSEUDOENZYME_OVERANNOTATION"
      ],
      "argo95_sft_terms": 9,
      "argo95_sft_genes": 3,
      "argo139_gogpt_terms": 0,
      "argo139_gogpt_genes": 0
    },
    {
      "mode": "2 localization default",
      "error_types": [
        "LOCALIZATION_DEFAULT"
      ],
      "argo95_sft_terms": 4,
      "argo95_sft_genes": 4,
      "argo139_gogpt_terms": 0,
      "argo139_gogpt_genes": 0
    },
    {
      "mode": "3 paralog indistinguishability",
      "error_types": [
        "PARALOG_OVERANNOTATION"
      ],
      "argo95_sft_terms": 5,
      "argo95_sft_genes": 3,
      "argo139_gogpt_terms": 0,
      "argo139_gogpt_genes": 0
    },
    {
      "mode": "5 neo-functionalization/moonlighting",
      "error_types": [
        "MULTIPLE_FUNCTIONS"
      ],
      "argo95_sft_terms": 1,
      "argo95_sft_genes": 1,
      "argo139_gogpt_terms": 0,
      "argo139_gogpt_genes": 0
    },
    {
      "mode": "7 cross-kingdom fold bias",
      "error_types": [
        "TAXON_CONSTRAINT_VIOLATION"
      ],
      "argo95_sft_terms": 7,
      "argo95_sft_genes": 7,
      "argo139_gogpt_terms": 0,
      "argo139_gogpt_genes": 0
    },
    {
      "mode": "9 wrong input data",
      "error_types": [
        "WRONG_INPUT_SEQUENCE"
      ],
      "argo95_sft_terms": 0,
      "argo95_sft_genes": 0,
      "argo139_gogpt_terms": 0,
      "argo139_gogpt_genes": 0
    }
  ],
  "rl_text_flags": {
    "n_reviews": 139,
    "n_performance_reviews": 138,
    "markers": {
      "2 localization default": "wrong (?:sub)?cellular (?:location|localization|compartment)|wrong locali[sz]ation|locali[sz]ation (?:is |was )?(?:wrong|incorrect)|locali[sz]ation error|mis-?locali[sz]|incorrect locali[sz]ation|locali[sz]ation incorrect|is (?:emphatically )?not (?:cytosolic|cytoplasmic|nuclear)",
      "9 wrong input data": "wrong (?:input|protein|sequence|gene)"
    },
    "counts_performance_set": {
      "2 localization default": 16,
      "9 wrong input data": 0
    },
    "counts_excluded_inputs": {
      "2 localization default": 0,
      "9 wrong input data": 1
    },
    "flagged_genes": {
      "2 localization default": [
        "ANOGA/PGRPLB",
        "ARATH/ETR1",
        "BACSU/spoIIE",
        "ECOLI/CpxP",
        "ECOLI/Skp",
        "ECOLI/mrdA",
        "PSEPK/mrcA",
        "PSEPK/pedH",
        "SCHPO/alo1",
        "SCHPO/cps1",
        "SCHPO/cts2",
        "SCHPO/pol5",
        "worm/ire-1",
        "worm/pgl-1",
        "yeast/CAT2",
        "yeast/IRE1"
      ],
      "9 wrong input data": [
        "worm/csr-1"
      ]
    }
  }
}