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algorithms.eod_public.1.0.schemas.breast.json Maven / Gradle / Ivy
{
"id" : "breast",
"algorithm" : "eod_public",
"version" : "1.0",
"name" : "Breast",
"title" : "Breast",
"notes" : "C500 Nipple \nC501 Central portion of breast \nC502 Upper-inner quadrant of breast \nC503 Lower-inner quadrant of breast \nC504 Upper-outer quadrant of breast \nC505 Lower-outer quadrant of breast \nC506 Axillary Tail of breast \nC508 Overlapping lesion of breast \nC509 Breast, NOS \n\n**Note 1:** The following sources were used in the development of this schema\n* SEER Extent of Disease 1988: Codes and Coding Instructions (3rd Edition, 1998) (https://seer.cancer.gov/archive/manuals/EOD10Dig.3rd.pdf)\n* SEER Summary Staging Manual-2000: Codes and Coding Instructions (https://seer.cancer.gov/tools/ssm/)\n* Collaborative Stage Data Collection System, version 02.05: https://cancerstaging.org/cstage/Pages/default.aspx \n* Chapter 48 *Breast*, in the AJCC Cancer Staging Manual, Eighth Edition (2017) published by Springer International Publishing. Used with permission of the American College of Surgeons, Chicago, Illinois.\n\n**Note 2:** In addition to coding *EOD Primary Tumor, EOD Regional Nodes* and *EOD Mets*, the following data items are also needed to assign a stage group for Breast.\n* ER Summary\n* PR Summary\n* HER2 Summary\n* Oncotype Dx Recurrence Score",
"schema_selection_table" : "schema_selection_breast",
"inputs" : [ {
"key" : "year_dx",
"name" : "Year of Diagnosis",
"naaccr_item" : 390,
"table" : "year_dx_validation",
"used_for_staging" : false
}, {
"key" : "site",
"name" : "Primary Site",
"naaccr_item" : 400,
"table" : "primary_site",
"used_for_staging" : true
}, {
"key" : "hist",
"name" : "Histology",
"naaccr_item" : 522,
"table" : "histology",
"used_for_staging" : true
}, {
"key" : "behavior",
"name" : "Behavior",
"naaccr_item" : 523,
"table" : "behavior",
"used_for_staging" : true
}, {
"key" : "size_clin",
"name" : "Tumor Size Clinical",
"naaccr_item" : 752,
"table" : "tumor_size_clinical_60979",
"used_for_staging" : false
}, {
"key" : "size_path",
"name" : "Tumor Size Pathological",
"naaccr_item" : 754,
"table" : "tumor_size_pathological_25597",
"used_for_staging" : false
}, {
"key" : "size_summary",
"name" : "Tumor Size Summary",
"naaccr_item" : 756,
"default" : "999",
"table" : "tumor_size_summary_63115",
"used_for_staging" : true
}, {
"key" : "nodes_pos",
"name" : "Regional Nodes Positive",
"naaccr_item" : 820,
"default" : "99",
"table" : "nodes_pos_fab",
"used_for_staging" : false
}, {
"key" : "nodes_exam",
"name" : "Regional Nodes Examined",
"naaccr_item" : 830,
"default" : "99",
"table" : "nodes_exam_76029",
"used_for_staging" : false
}, {
"key" : "radiation_surg_seq",
"name" : "RX Summ Surgery/Radiation Sequence",
"naaccr_item" : 1380,
"table" : "radiation_surg_seq",
"used_for_staging" : false
}, {
"key" : "systemic_surg_seq",
"name" : "RX Summ Systemic/Surgery Sequence",
"naaccr_item" : 1639,
"table" : "systemic_surg_seq",
"used_for_staging" : false
}, {
"key" : "eod_primary_tumor",
"name" : "EOD Primary Tumor",
"naaccr_item" : 772,
"default" : "999",
"table" : "extension_bak",
"used_for_staging" : true
}, {
"key" : "eod_regional_nodes",
"name" : "EOD Regional Nodes",
"naaccr_item" : 774,
"default" : "999",
"table" : "nodes_daj",
"used_for_staging" : true
}, {
"key" : "eod_mets",
"name" : "EOD Mets",
"naaccr_item" : 776,
"default" : "00",
"table" : "mets_hau",
"used_for_staging" : true
}, {
"key" : "ss2018",
"name" : "SS2018",
"naaccr_item" : 764,
"table" : "ss2018_breast_69079",
"used_for_staging" : false
}, {
"key" : "grade_clin",
"name" : "Grade Clinical",
"naaccr_item" : 3843,
"default" : "9",
"table" : "grade_clinical_91491",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "grade_path",
"name" : "Grade Pathological",
"naaccr_item" : 3844,
"default" : "9",
"table" : "grade_pathological_47031",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "grade_post_therapy",
"name" : "Grade Post Therapy",
"naaccr_item" : 3845,
"table" : "grade_post_therapy_61120",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "ln_pos_axillary_level_1_2",
"name" : "Lymph Nodes Positive Axillary Level I-II",
"description" : "Number of Positive Ipsilateral Level I-II Axillary Lymph Nodes",
"naaccr_item" : 3882,
"default" : "X9",
"table" : "number_of_positive_ipsilateral_level_i_ii_axillary_lymph_nodes_79439",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "er",
"name" : "ER Summary",
"naaccr_item" : 3827,
"default" : "9",
"table" : "er_summary_44166",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "er_percent_positive",
"name" : "ER Percent Positive",
"naaccr_item" : 3826,
"default" : "XX8",
"table" : "er_percent_positive_61867",
"used_for_staging" : false,
"metadata" : [ "NPCR_REQUIRED", "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "er_allred_score",
"name" : "ER Allred Score",
"naaccr_item" : 3828,
"default" : "X8",
"table" : "er_allred_score_36612",
"used_for_staging" : false,
"metadata" : [ "NPCR_REQUIRED", "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "pr",
"name" : "PR Summary",
"naaccr_item" : 3915,
"default" : "9",
"table" : "pr_summary_49534",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "pr_percent_positive",
"name" : "PR Percent Positive",
"naaccr_item" : 3914,
"default" : "XX8",
"table" : "pr_percent_positive_94563",
"used_for_staging" : false,
"metadata" : [ "NPCR_REQUIRED", "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "pr_allred_score",
"name" : "PR Allred Score",
"naaccr_item" : 3916,
"default" : "X8",
"table" : "pr_allred_score_83938",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "her2_summary",
"name" : "HER2 Overall Summary",
"naaccr_item" : 3855,
"default" : "9",
"table" : "her2_summary_30512",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "her2_ihc_summary",
"name" : "HER2 IHC Summary",
"naaccr_item" : 3850,
"default" : "8",
"table" : "her2_ihc_summary_57693",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "her2_ish_summary",
"name" : "HER2 ISH Summary",
"naaccr_item" : 3854,
"default" : "8",
"table" : "her2_ish_summary_40783",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "her2_ish_dp_ratio",
"name" : "HER2 ISH DP Ratio",
"naaccr_item" : 3852,
"default" : "XX.8",
"table" : "her2_ish_dual_probe_ration_4635",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "her2_ish_dp_copy_no",
"name" : "HER2 ISH DP Copy No",
"naaccr_item" : 3851,
"default" : "XX.8",
"table" : "her2_ish_dp_copy_no_89821",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "her2_ish_sp_copy_no",
"name" : "HER2 ISH SP Copy No",
"naaccr_item" : 3853,
"default" : "XX.8",
"table" : "her2_ish_sp_copy_no_95955",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "ki67",
"name" : "Ki-67 (MIB-1)",
"naaccr_item" : 3863,
"default" : "XXX.8",
"table" : "ki67_8355",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "oncotype_dx_score",
"name" : "Oncotype DX Recur Score",
"naaccr_item" : 3904,
"default" : "XX9",
"table" : "oncotype_dx_recur_score_73667",
"used_for_staging" : true,
"metadata" : [ "COC_REQUIRED", "NPCR_REQUIRED", "SSDI", "CCCR_REQUIRED", "SEER_REQUIRED" ]
}, {
"key" : "oncotype_dx_risk_level",
"name" : "Oncotype Dx Risk Level Invasive",
"naaccr_item" : 3906,
"default" : "8",
"table" : "oncotype_dx_risk_level_11033",
"used_for_staging" : false,
"metadata" : [ "NPCR_REQUIRED", "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "oncotype_dx_score_dcis",
"name" : "Oncotype DX Recur Score - DCIS",
"naaccr_item" : 3903,
"default" : "XX8",
"table" : "oncotype_dx_recurrence_score_dcis_70549",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "oncotype_dx_risk_level_dcis",
"name" : "Oncotype Dx Risk Level - DCIS",
"naaccr_item" : 3905,
"default" : "8",
"table" : "oncotype_dx_risk_level_dcis_53080",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "multigene_signature_method",
"name" : "Multigene Signature Method",
"naaccr_item" : 3894,
"default" : "8",
"table" : "multigene_signature_method_85043",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "multigene_signature_result",
"name" : "Multigene Signature Result",
"naaccr_item" : 3895,
"default" : "X8",
"table" : "multigene_signature_result_37000",
"used_for_staging" : false,
"metadata" : [ "NPCR_REQUIRED", "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
}, {
"key" : "response_neoadjuv_therapy",
"name" : "Response Neoadjuv Therapy",
"naaccr_item" : 3922,
"default" : "8",
"table" : "response_to_neoadjuvant_therapy_57695",
"used_for_staging" : false,
"metadata" : [ "COC_REQUIRED", "SSDI", "SEER_REQUIRED" ]
} ],
"outputs" : [ {
"key" : "naaccr_schema_id",
"name" : "Schema ID",
"naaccr_item" : 3800,
"default" : "00480"
}, {
"key" : "ajcc_id",
"name" : "AJCC ID",
"naaccr_item" : 995,
"default" : "XX"
}, {
"key" : "derived_version",
"name" : "Derived Version",
"default" : "{{ctx_alg_version}}"
}, {
"key" : "eod_2018_t",
"name" : "Derived EOD 2018 T",
"naaccr_item" : 785,
"default" : "88"
}, {
"key" : "eod_2018_n",
"name" : "Derived EOD 2018 N",
"naaccr_item" : 815,
"default" : "88"
}, {
"key" : "eod_2018_m",
"name" : "Derived EOD 2018 M",
"naaccr_item" : 795,
"default" : "88"
}, {
"key" : "eod_2018_stage_group",
"name" : "Derived EOD 2018 Stage Group",
"naaccr_item" : 818,
"default" : "88"
}, {
"key" : "ss2018_derived",
"name" : "Derived Summary Stage 2018",
"naaccr_item" : 762,
"default" : "9"
} ],
"mappings" : [ {
"id" : "summary_stage_2018",
"name" : "Summary Stage 2018",
"initial_context" : [ {
"key" : "ss2018_derived",
"value" : "90"
} ],
"tables" : [ {
"id" : "extension_bak",
"inputs" : [ "hist", "size_summary", "eod_primary_tumor", "behavior" ],
"outputs" : [ "eod_2018_t", "ss2018_t" ]
}, {
"id" : "nodes_daj",
"inputs" : [ "ln_pos_axillary_level_1_2", "eod_regional_nodes" ],
"outputs" : [ "eod_2018_n", "ss2018_n", "stage_table_for_n" ]
}, {
"id" : "mets_hau",
"inputs" : [ "eod_mets" ],
"outputs" : [ "eod_2018_m", "ss2018_m" ]
}, {
"id" : "summary_stage_rpa",
"inputs" : [ "ss2018_m", "ss2018_n", "ss2018_t" ],
"outputs" : [ "ss2018_derived" ]
} ]
}, {
"id" : "ajcc_chapter_calculation",
"name" : "AJCC Chapter Calculation",
"tables" : [ {
"id" : "ajcc_chapter_calculation_15027",
"inputs" : [ "site", "hist", "behavior" ],
"outputs" : [ "ajcc_id" ]
} ]
}, {
"id" : "eod_2018_stage_group",
"name" : "EOD 2018 Stage Group",
"inclusion_tables" : [ {
"id" : "tnm8_inclusions_tpg",
"inputs" : [ "ajcc_id" ]
} ],
"initial_context" : [ {
"key" : "eod_2018_stage_group",
"value" : "90"
} ],
"tables" : [ {
"id" : "parse_t_2177",
"input_mapping" : [ {
"from" : "eod_2018_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "root_t",
"to" : "tmp_eod_t"
} ],
"inputs" : [ "eod_2018_t" ],
"outputs" : [ "t_prefix", "tmp_eod_t" ]
}, {
"id" : "parse_n_67182",
"input_mapping" : [ {
"from" : "eod_2018_n",
"to" : "n"
} ],
"output_mapping" : [ {
"from" : "root_n",
"to" : "tmp_eod_n"
} ],
"inputs" : [ "eod_2018_n" ],
"outputs" : [ "n_prefix", "tmp_eod_n" ]
}, {
"id" : "parse_m_47057",
"input_mapping" : [ {
"from" : "eod_2018_m",
"to" : "m"
} ],
"output_mapping" : [ {
"from" : "root_m",
"to" : "tmp_eod_m"
} ],
"inputs" : [ "eod_2018_m" ],
"outputs" : [ "m_prefix", "tmp_eod_m" ]
}, {
"id" : "oncotype_less_than_11_10827",
"inputs" : [ "oncotype_dx_score" ],
"outputs" : [ "oncotype11" ]
}, {
"id" : "combined_grade_56638",
"inputs" : [ "grade_path", "grade_clin" ],
"outputs" : [ "grade_combined" ]
}, {
"id" : "temp_eod_prefixes_52976",
"input_mapping" : [ {
"from" : "stage_table_for_n",
"to" : "prefix_n_in"
} ],
"inputs" : [ "stage_table_for_n" ],
"outputs" : [ "eod_t_source", "eod_n_source", "eod_m_source" ]
}, {
"id" : "tnm_8_combined_group_breast_93916",
"input_mapping" : [ {
"from" : "eod_m_source",
"to" : "cmb_m_prefix"
}, {
"from" : "grade_combined",
"to" : "grade"
}, {
"from" : "eod_n_source",
"to" : "cmb_n_prefix"
}, {
"from" : "eod_t_source",
"to" : "cmb_t_prefix"
}, {
"from" : "tmp_eod_n",
"to" : "n"
}, {
"from" : "tmp_eod_m",
"to" : "m"
}, {
"from" : "tmp_eod_t",
"to" : "t"
} ],
"output_mapping" : [ {
"from" : "stage",
"to" : "eod_2018_stage_group"
} ],
"inputs" : [ "pr", "oncotype11", "eod_t_source", "eod_n_source", "eod_m_source", "tmp_eod_n", "grade_combined", "her2_summary", "tmp_eod_m", "tmp_eod_t", "er" ],
"outputs" : [ "eod_2018_stage_group" ]
} ]
}, {
"id" : "eod_tnm_cleanup",
"name" : "EOD TNM Cleanup",
"exclusion_tables" : [ {
"id" : "tnm8_inclusions_tpg",
"inputs" : [ "ajcc_id" ]
} ],
"tables" : [ {
"id" : "eod_tnm_component_cleanup_58170",
"inputs" : [ "ajcc_id" ],
"outputs" : [ "eod_2018_n", "eod_2018_m", "eod_2018_t", "eod_2018_stage_group" ]
} ]
} ],
"involved_tables" : [ "her2_ish_sp_copy_no_95955", "er_percent_positive_61867", "oncotype_dx_recur_score_73667", "her2_ish_summary_40783", "grade_pathological_47031", "parse_t_2177", "schema_selection_breast", "ss2018_breast_69079", "histology", "nodes_exam_76029", "nodes_pos_fab", "tumor_size_summary_63115", "grade_post_therapy_61120", "er_summary_44166", "her2_summary_30512", "temp_eod_prefixes_52976", "her2_ish_dp_copy_no_89821", "her2_ish_dual_probe_ration_4635", "oncotype_less_than_11_10827", "tnm_8_stage_group_breast_16868", "nodes_daj", "tumor_size_pathological_25597", "systemic_surg_seq", "tnm8_inclusions_tpg", "her2_ihc_summary_57693", "tnm_8_path_stage_group_breast_21522", "parse_m_47057", "pr_allred_score_83938", "morphology_with_primary_tumor_for_ajcc_t_82996", "summary_stage_rpa", "extension_bak", "pr_summary_49534", "radiation_surg_seq", "ajcc_chapter_calculation_15027", "oncotype_dx_risk_level_11033", "multigene_signature_result_37000", "ki67_8355", "parse_n_67182", "oncotype_dx_recurrence_score_dcis_70549", "tumor_size_with_primary_tumor_for_ajcc_t_16997", "response_to_neoadjuvant_therapy_57695", "er_allred_score_36612", "grade_clinical_91491", "pr_percent_positive_94563", "combined_grade_56638", "mets_hau", "behavior", "num_pos_aln_with_regional_nodes_for_ajcc_n_30002", "tnm_8_combined_group_breast_93916", "multigene_signature_method_85043", "behavior_with_primary_tumor_for_ss2018_t_69793", "tumor_size_clinical_60979", "primary_site", "eod_tnm_component_cleanup_58170", "number_of_positive_ipsilateral_level_i_ii_axillary_lymph_nodes_79439", "year_dx_validation", "oncotype_dx_risk_level_dcis_53080" ],
"on_invalid_input" : "FAIL_WHEN_USED_FOR_STAGING",
"last_modified" : "2018-03-12T16:42:02.404Z"
}
