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algorithms.tnm.2.0.schemas.gist_rectum.json Maven / Gradle / Ivy
{
"id" : "gist_rectum",
"algorithm" : "tnm",
"version" : "2.0",
"name" : "GIST Rectum",
"title" : "Gastrointestinal Stromal Tumor of Rectum and Rectosigmoid Junction",
"notes" : "C199 Rectosigmoid junction\nC209 Rectum, NOS\n\n**Note 1:** This schema is based on the UICC chapter *Gastrointestinal Stromal Tumour (GIST),* pages 78-81.\n* Primary site C199 is not listed in this chapter of the UICC manual; however, it is included in this schema and TNM staged\n\n**Note 2:** In addition to directly assigning TNM, Summary Stage 2000 (SS2000) must be captured. If directly assigning SS2000, use the *Rectum* chapter on page 100 of the [SS2000 on-line manual](https://seer.cancer.gov/tools/ssm/ssm2000/SSSM2000-122012.pdf#page=100).",
"schema_selection_table" : "schema_selection_gist_rectum",
"inputs" : [ {
"key" : "year_dx",
"name" : "Year of Diagnosis",
"naaccr_item" : 390,
"naaccr_xml_id" : "dateOfDiagnosis",
"table" : "year_dx_validation",
"used_for_staging" : false
}, {
"key" : "site",
"name" : "Primary Site",
"naaccr_item" : 400,
"naaccr_xml_id" : "primarySite",
"table" : "primary_site",
"used_for_staging" : true
}, {
"key" : "hist",
"name" : "Histology",
"naaccr_item" : 522,
"naaccr_xml_id" : "histologicTypeIcdO3",
"table" : "histology",
"used_for_staging" : true
}, {
"key" : "systemic_surg_seq",
"name" : "RX Summ Systemic/Surgery Sequence",
"naaccr_item" : 1639,
"naaccr_xml_id" : "rxSummSystemicSurSeq",
"table" : "systemic_surg_seq",
"used_for_staging" : true
}, {
"key" : "radiation_surg_seq",
"name" : "RX Summ Surgery/Radiation Sequence",
"naaccr_item" : 1380,
"naaccr_xml_id" : "rxSummSurgRadSeq",
"table" : "radiation_surg_seq",
"used_for_staging" : true
}, {
"key" : "nodes_pos",
"name" : "Regional Nodes Positive",
"naaccr_item" : 820,
"naaccr_xml_id" : "regionalNodesPositive",
"table" : "nodes_pos_fpa",
"used_for_staging" : true
}, {
"key" : "clin_t",
"name" : "Clinical T",
"naaccr_item" : 940,
"naaccr_xml_id" : "tnmClinT",
"table" : "clin_t_gist_rectum_83293",
"used_for_staging" : true
}, {
"key" : "clin_n",
"name" : "Clinical N",
"naaccr_item" : 950,
"naaccr_xml_id" : "tnmClinN",
"table" : "clin_n_gist_rectum_58109",
"used_for_staging" : true
}, {
"key" : "clin_m",
"name" : "Clinical M",
"naaccr_item" : 960,
"naaccr_xml_id" : "tnmClinM",
"table" : "clin_m_hcc",
"used_for_staging" : true
}, {
"key" : "path_t",
"name" : "Pathologic T",
"naaccr_item" : 880,
"naaccr_xml_id" : "tnmPathT",
"table" : "gist_rectum_t_7125",
"used_for_staging" : true
}, {
"key" : "path_n",
"name" : "Pathologic N",
"naaccr_item" : 890,
"naaccr_xml_id" : "tnmPathN",
"table" : "gist_rectum_n_35223",
"used_for_staging" : true
}, {
"key" : "path_m",
"name" : "Pathologic M",
"naaccr_item" : 900,
"naaccr_xml_id" : "tnmPathM",
"table" : "path_m_hcc",
"used_for_staging" : true
}, {
"key" : "ssf11",
"name" : "Mitotic Count",
"naaccr_item" : 2865,
"naaccr_xml_id" : "csSiteSpecificFactor11",
"default" : "999",
"table" : "ssf11_spk",
"used_for_staging" : true
}, {
"key" : "ssf12",
"name" : "KIT Gene Immunohistochemistry (IHC)",
"naaccr_item" : 2866,
"naaccr_xml_id" : "csSiteSpecificFactor12",
"default" : "988",
"table" : "ssf12_spl",
"used_for_staging" : false,
"metadata" : [ {
"name" : "COC_REQUIRED"
}, {
"name" : "CCCR_REQUIRED"
} ]
}, {
"key" : "ssf13",
"name" : "KIT Gene Mutations",
"naaccr_item" : 2867,
"naaccr_xml_id" : "csSiteSpecificFactor13",
"default" : "988",
"table" : "ssf13_spm",
"used_for_staging" : false
}, {
"key" : "ssf14",
"name" : "PDGFRA Gene Mutation",
"naaccr_item" : 2868,
"naaccr_xml_id" : "csSiteSpecificFactor14",
"default" : "988",
"table" : "ssf14_spn",
"used_for_staging" : false
}, {
"key" : "ssf15",
"name" : "Tumor Multiplicity",
"naaccr_item" : 2869,
"naaccr_xml_id" : "csSiteSpecificFactor15",
"default" : "988",
"table" : "ssf15_spo",
"used_for_staging" : false
}, {
"key" : "clin_stage_group_direct",
"name" : "TNM Clin Stage Group",
"naaccr_item" : 970,
"naaccr_xml_id" : "tnmClinStageGroup",
"default" : "99",
"table" : "stage_group_c_86666",
"used_for_staging" : true,
"metadata" : [ {
"name" : "NPCR_REQUIRED"
}, {
"name" : "COC_REQUIRED"
} ]
}, {
"key" : "path_stage_group_direct",
"name" : "TNM Path Stage Group",
"naaccr_item" : 910,
"naaccr_xml_id" : "tnmPathStageGroup",
"default" : "99",
"table" : "stage_group_p_82525",
"used_for_staging" : true,
"metadata" : [ {
"name" : "NPCR_REQUIRED"
}, {
"name" : "COC_REQUIRED"
} ]
} ],
"outputs" : [ {
"key" : "derived_version",
"name" : "Derived Version",
"default" : "{{ctx_alg_version}}"
}, {
"key" : "clin_stage_group",
"name" : "Derived SEER Clin Stage Group",
"naaccr_item" : 3610,
"naaccr_xml_id" : "derivedSeerClinStgGrp",
"default" : "88"
}, {
"key" : "path_stage_group",
"name" : "Derived SEER Path Stage Group",
"naaccr_item" : 3605,
"naaccr_xml_id" : "derivedSeerPathStgGrp",
"default" : "88"
}, {
"key" : "combined_stage_group",
"name" : "Derived SEER Combined Stage Group",
"naaccr_item" : 3614,
"naaccr_xml_id" : "derivedSeerCmbStgGrp",
"default" : "88"
}, {
"key" : "combined_t",
"name" : "Derived SEER Combined T",
"naaccr_item" : 3616,
"naaccr_xml_id" : "derivedSeerCombinedT",
"default" : "88"
}, {
"key" : "combined_n",
"name" : "Derived SEER Combined N",
"naaccr_item" : 3618,
"naaccr_xml_id" : "derivedSeerCombinedN",
"default" : "88"
}, {
"key" : "combined_m",
"name" : "Derived SEER Combined M",
"naaccr_item" : 3620,
"naaccr_xml_id" : "derivedSeerCombinedM",
"default" : "88"
}, {
"key" : "source_t",
"name" : "Derived SEER Combined T Source",
"naaccr_item" : 3622,
"naaccr_xml_id" : "derivedSeerCmbTSrc"
}, {
"key" : "source_n",
"name" : "Derived SEER Combined N Source",
"naaccr_item" : 3624,
"naaccr_xml_id" : "derivedSeerCmbNSrc"
}, {
"key" : "source_m",
"name" : "Derived SEER Combined M Source",
"naaccr_item" : 3626,
"naaccr_xml_id" : "derivedSeerCmbMSrc"
} ],
"mappings" : [ {
"id" : "tnm7_stage",
"name" : "TNM 7 Stage",
"inclusion_tables" : [ {
"id" : "tnm7_inclusions_tpo",
"inputs" : [ "hist" ]
} ],
"initial_context" : [ {
"key" : "clin_stage_group",
"value" : "90"
}, {
"key" : "path_stage_group",
"value" : "90"
} ],
"tables" : [ {
"id" : "parse_t_2177",
"input_mapping" : [ {
"from" : "clin_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "root_t",
"to" : "tmp_clin_t"
}, {
"from" : "t_prefix",
"to" : "clin_t_prefix"
} ],
"inputs" : [ "clin_t" ],
"outputs" : [ "clin_t_prefix", "tmp_clin_t" ]
}, {
"id" : "parse_n_67182",
"input_mapping" : [ {
"from" : "clin_n",
"to" : "n"
} ],
"output_mapping" : [ {
"from" : "root_n",
"to" : "tmp_clin_n"
}, {
"from" : "n_prefix",
"to" : "clin_n_prefix"
} ],
"inputs" : [ "clin_n" ],
"outputs" : [ "clin_n_prefix", "tmp_clin_n" ]
}, {
"id" : "parse_m_47057",
"input_mapping" : [ {
"from" : "clin_m",
"to" : "m"
} ],
"output_mapping" : [ {
"from" : "m_prefix",
"to" : "clin_m_prefix"
}, {
"from" : "root_m",
"to" : "tmp_clin_m"
} ],
"inputs" : [ "clin_m" ],
"outputs" : [ "tmp_clin_m", "clin_m_prefix" ]
}, {
"id" : "parse_t_2177",
"input_mapping" : [ {
"from" : "path_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "root_t",
"to" : "tmp_path_t"
}, {
"from" : "t_prefix",
"to" : "path_t_prefix"
} ],
"inputs" : [ "path_t" ],
"outputs" : [ "tmp_path_t", "path_t_prefix" ]
}, {
"id" : "parse_n_67182",
"input_mapping" : [ {
"from" : "path_n",
"to" : "n"
} ],
"output_mapping" : [ {
"from" : "root_n",
"to" : "tmp_path_n"
}, {
"from" : "n_prefix",
"to" : "path_n_prefix"
} ],
"inputs" : [ "path_n" ],
"outputs" : [ "tmp_path_n", "path_n_prefix" ]
}, {
"id" : "parse_m_47057",
"input_mapping" : [ {
"from" : "path_m",
"to" : "m"
} ],
"output_mapping" : [ {
"from" : "root_m",
"to" : "tmp_path_m"
}, {
"from" : "m_prefix",
"to" : "path_m_prefix"
} ],
"inputs" : [ "path_m" ],
"outputs" : [ "tmp_path_m", "path_m_prefix" ]
}, {
"id" : "determine_default_t",
"input_mapping" : [ {
"from" : "tmp_path_t",
"to" : "path_t_in"
}, {
"from" : "tmp_clin_t",
"to" : "clin_t_in"
} ],
"output_mapping" : [ {
"from" : "source_t_out",
"to" : "source_t"
}, {
"from" : "path_t_out",
"to" : "tmp_path_t"
}, {
"from" : "clin_t_out",
"to" : "tmp_clin_t"
}, {
"from" : "combined_t_out",
"to" : "tmp_combined_t"
} ],
"inputs" : [ "tmp_path_t", "tmp_clin_t" ],
"outputs" : [ "source_t", "tmp_path_t", "tmp_clin_t", "tmp_combined_t" ]
}, {
"id" : "determine_default_n",
"input_mapping" : [ {
"from" : "tmp_path_n",
"to" : "path_n_in"
}, {
"from" : "tmp_clin_n",
"to" : "clin_n_in"
} ],
"output_mapping" : [ {
"from" : "path_n_out",
"to" : "tmp_path_n"
}, {
"from" : "source_n_out",
"to" : "source_n"
}, {
"from" : "combined_n_out",
"to" : "tmp_combined_n"
}, {
"from" : "clin_n_out",
"to" : "tmp_clin_n"
} ],
"inputs" : [ "tmp_clin_n", "tmp_path_n" ],
"outputs" : [ "tmp_combined_n", "tmp_clin_n", "tmp_path_n", "source_n" ]
}, {
"id" : "determine_default_m",
"input_mapping" : [ {
"from" : "tmp_path_m",
"to" : "path_m_in"
}, {
"from" : "tmp_clin_m",
"to" : "clin_m_in"
} ],
"output_mapping" : [ {
"from" : "source_m_out",
"to" : "source_m"
}, {
"from" : "combined_m_out",
"to" : "tmp_combined_m"
}, {
"from" : "clin_m_out",
"to" : "tmp_clin_m"
}, {
"from" : "path_m_out",
"to" : "tmp_path_m"
} ],
"inputs" : [ "tmp_path_m", "tmp_clin_m" ],
"outputs" : [ "tmp_path_m", "tmp_combined_m", "tmp_clin_m", "source_m" ]
}, {
"id" : "gist_appendix_mitotic_rate_calculation",
"inputs" : [ "ssf11" ],
"outputs" : [ "mitotic_rate" ]
}, {
"id" : "tnm7_stage_gist_small_intestine_upy",
"input_mapping" : [ {
"from" : "tmp_clin_n",
"to" : "n"
}, {
"from" : "tmp_clin_m",
"to" : "m"
}, {
"from" : "tmp_clin_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "stage",
"to" : "clin_stage_group"
} ],
"inputs" : [ "mitotic_rate", "tmp_clin_n", "tmp_clin_m", "tmp_clin_t" ],
"outputs" : [ "clin_stage_group" ]
}, {
"id" : "tnm7_path_stage_gist_small_intestine_upy",
"input_mapping" : [ {
"from" : "tmp_path_m",
"to" : "m"
}, {
"from" : "tmp_path_n",
"to" : "n"
}, {
"from" : "tmp_path_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "stage",
"to" : "path_stage_group"
} ],
"inputs" : [ "tmp_path_m", "mitotic_rate", "tmp_path_n", "tmp_path_t" ],
"outputs" : [ "path_stage_group" ]
}, {
"id" : "adjustments_for_no_clin_or_no_path_26261",
"output_mapping" : [ {
"from" : "source_t_out",
"to" : "source_t"
}, {
"from" : "source_m_out",
"to" : "source_m"
}, {
"from" : "combined_m_out",
"to" : "tmp_combined_m"
}, {
"from" : "source_n_out",
"to" : "source_n"
}, {
"from" : "combined_t_out",
"to" : "tmp_combined_t"
}, {
"from" : "combined_n_out",
"to" : "tmp_combined_n"
} ],
"inputs" : [ "tmp_path_t", "clin_n", "clin_m", "clin_t", "path_t", "tmp_path_m", "tmp_clin_n", "tmp_clin_m", "clin_stage_group_direct", "tmp_path_n", "path_m", "tmp_clin_t", "path_stage_group_direct", "path_n" ],
"outputs" : [ "tmp_combined_n", "tmp_combined_m", "source_t", "clin_stage_group", "path_stage_group", "source_n", "tmp_combined_t", "source_m" ]
} ]
}, {
"id" : "combined_stage",
"name" : "Combined Stage",
"inclusion_tables" : [ {
"id" : "tnm7_inclusions_tpo",
"inputs" : [ "hist" ]
} ],
"initial_context" : [ {
"key" : "combined_m",
"value" : "90"
}, {
"key" : "combined_n",
"value" : "90"
}, {
"key" : "combined_stage_group",
"value" : "90"
}, {
"key" : "combined_t",
"value" : "90"
} ],
"tables" : [ {
"id" : "stop_if_no_clin_and_no_path_24035",
"inputs" : [ "clin_t", "path_t", "clin_stage_group_direct", "path_m", "clin_n", "path_stage_group_direct", "clin_m", "path_n" ],
"outputs" : [ "combined_m", "combined_n", "source_t", "tmp_continue", "combined_t", "combined_stage_group", "source_n", "source_m" ]
}, {
"id" : "combined_t_no_tis",
"input_mapping" : [ {
"from" : "tmp_path_t",
"to" : "path_t_in"
}, {
"from" : "tmp_combined_t",
"to" : "combined_t_in"
}, {
"from" : "tmp_clin_t",
"to" : "clin_t_in"
} ],
"output_mapping" : [ {
"from" : "source_t_out",
"to" : "source_t"
}, {
"from" : "combined_t_out",
"to" : "tmp_combined_t"
} ],
"inputs" : [ "radiation_surg_seq", "tmp_path_t", "tmp_clin_t", "systemic_surg_seq", "tmp_combined_t" ],
"outputs" : [ "source_t", "tmp_combined_t" ]
}, {
"id" : "combined_n_no_tis_path_n_cn0_allowed_73884",
"input_mapping" : [ {
"from" : "tmp_path_n",
"to" : "path_n_in"
}, {
"from" : "tmp_combined_n",
"to" : "combined_n_in"
}, {
"from" : "tmp_clin_n",
"to" : "clin_n_in"
} ],
"output_mapping" : [ {
"from" : "source_n_out",
"to" : "source_n"
}, {
"from" : "combined_n_out",
"to" : "tmp_combined_n"
} ],
"inputs" : [ "nodes_pos", "tmp_combined_n", "tmp_clin_n", "radiation_surg_seq", "tmp_path_n", "systemic_surg_seq" ],
"outputs" : [ "tmp_combined_n", "source_n" ]
}, {
"id" : "combined_m",
"input_mapping" : [ {
"from" : "tmp_combined_m",
"to" : "combined_m_in"
}, {
"from" : "tmp_path_m",
"to" : "path_m_in"
}, {
"from" : "tmp_clin_m",
"to" : "clin_m_in"
} ],
"output_mapping" : [ {
"from" : "source_m_out",
"to" : "source_m"
}, {
"from" : "combined_m_out",
"to" : "tmp_combined_m"
} ],
"inputs" : [ "tmp_path_m", "tmp_combined_m", "tmp_clin_m" ],
"outputs" : [ "tmp_combined_m", "tmp_source_m", "source_m" ]
}, {
"id" : "determine_combined_prefix_91402",
"input_mapping" : [ {
"from" : "clin_t_prefix",
"to" : "clin_prefix"
}, {
"from" : "source_t",
"to" : "cmb_source"
}, {
"from" : "path_t_prefix",
"to" : "path_prefix"
} ],
"output_mapping" : [ {
"from" : "cmb_prefix",
"to" : "cmb_t_prefix"
} ],
"inputs" : [ "clin_t_prefix", "source_t", "path_t_prefix" ],
"outputs" : [ "cmb_t_prefix" ]
}, {
"id" : "determine_combined_prefix_91402",
"input_mapping" : [ {
"from" : "path_n_prefix",
"to" : "path_prefix"
}, {
"from" : "source_n",
"to" : "cmb_source"
}, {
"from" : "clin_n_prefix",
"to" : "clin_prefix"
} ],
"output_mapping" : [ {
"from" : "cmb_prefix",
"to" : "cmb_n_prefix"
} ],
"inputs" : [ "clin_n_prefix", "path_n_prefix", "source_n" ],
"outputs" : [ "cmb_n_prefix" ]
}, {
"id" : "determine_combined_prefix_91402",
"input_mapping" : [ {
"from" : "tmp_source_m",
"to" : "cmb_source"
}, {
"from" : "path_m_prefix",
"to" : "path_prefix"
}, {
"from" : "clin_m_prefix",
"to" : "clin_prefix"
} ],
"output_mapping" : [ {
"from" : "cmb_prefix",
"to" : "cmb_m_prefix"
} ],
"inputs" : [ "clin_m_prefix", "tmp_source_m", "path_m_prefix" ],
"outputs" : [ "cmb_m_prefix" ]
}, {
"id" : "concatenate_t_51262",
"input_mapping" : [ {
"from" : "tmp_combined_t",
"to" : "root_t"
}, {
"from" : "cmb_t_prefix",
"to" : "t_prefix"
} ],
"output_mapping" : [ {
"from" : "t",
"to" : "combined_t"
} ],
"inputs" : [ "cmb_t_prefix", "tmp_combined_t" ],
"outputs" : [ "combined_t" ]
}, {
"id" : "concatenate_n_43246",
"input_mapping" : [ {
"from" : "cmb_n_prefix",
"to" : "n_prefix"
}, {
"from" : "tmp_combined_n",
"to" : "root_n"
} ],
"output_mapping" : [ {
"from" : "n",
"to" : "combined_n"
} ],
"inputs" : [ "cmb_n_prefix", "tmp_combined_n" ],
"outputs" : [ "combined_n" ]
}, {
"id" : "concatenate_m_40642",
"input_mapping" : [ {
"from" : "tmp_combined_m",
"to" : "root_m"
}, {
"from" : "cmb_m_prefix",
"to" : "m_prefix"
} ],
"output_mapping" : [ {
"from" : "m",
"to" : "combined_m"
} ],
"inputs" : [ "cmb_m_prefix", "tmp_combined_m" ],
"outputs" : [ "combined_m" ]
}, {
"id" : "tnm7_path_stage_gist_small_intestine_upy",
"input_mapping" : [ {
"from" : "tmp_combined_n",
"to" : "n"
}, {
"from" : "tmp_combined_m",
"to" : "m"
}, {
"from" : "tmp_combined_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "stage",
"to" : "combined_stage_group"
} ],
"inputs" : [ "mitotic_rate", "tmp_combined_n", "tmp_combined_m", "tmp_combined_t" ],
"outputs" : [ "combined_stage_group" ]
} ]
} ],
"involved_tables" : [ "clin_n_gist_rectum_58109", "determine_default_t", "tnm7_path_stage_gist_small_intestine_upy", "radiation_surg_seq", "ssf15_spo", "ssf11_spk", "determine_default_m", "nodes_pos_fpa", "parse_t_2177", "concatenate_n_43246", "gist_rectum_t_7125", "gist_rectum_n_35223", "parse_n_67182", "stage_group_p_82525", "determine_default_n", "schema_selection_gist_rectum", "tnm7_stage_gist_small_intestine_upy", "clin_m_hcc", "histology", "concatenate_m_40642", "combined_t_no_tis", "combined_n_no_tis_path_n_cn0_allowed_73884", "ssf14_spn", "concatenate_t_51262", "ssf13_spm", "adjustments_for_no_clin_or_no_path_26261", "gist_appendix_mitotic_rate_calculation", "tnm7_inclusions_tpo", "determine_combined_prefix_91402", "stage_group_c_86666", "stop_if_no_clin_and_no_path_24035", "systemic_surg_seq", "parse_m_47057", "primary_site", "combined_m", "path_m_hcc", "year_dx_validation", "clin_t_gist_rectum_83293", "ssf12_spl" ],
"last_modified" : "2020-06-30T19:47:48.184Z",
"on_invalid_input" : "FAIL_WHEN_USED_FOR_STAGING"
}
