data/taxonomy/gap_report.csv

dimension,surface_form,n_reports,channel,bucket,mapped_concept_id,note
lvsi,lvsi_sf_identified,232,text,covered,cap_uterus.lvsi.present,LVSI asserted present. CAP and FIGO 2023 both name it.
lvsi,lvsi_sf_present,149,text,covered,cap_uterus.lvsi.present,
lvsi,lvsi_sf_negative,148,text,covered,cap_uterus.lvsi.not_identified,Also figo_endo_2023.lvsi.negative.
lvsi,lvsi_sf_not_identified,113,text,covered,cap_uterus.lvsi.not_identified,
lvsi,lvsi_sf_absent,64,text,covered,cap_uterus.lvsi.not_identified,
lvsi,lvsi_sf_none,28,text,covered,cap_uterus.lvsi.not_identified,
lvsi,lvsi_sf_focal,34,text,covered,figo_endo_2023.lvsi.focal,FIGO 2023 names focal. CAP counts foci instead and has no focal choice.
lvsi,lvsi_sf_extensive,42,text,in_data_not_in_reference,endopath.lvsi.extensive,An adjective is not the five-vessel count FIGO 2023 defines substantial by. Left constrained (dec_012).
lvsi,lvsi_sf_suspicious,12,text,in_data_not_in_reference,endopath.lvsi.suspicious,Pathologist hedge with no home in CAP or FIGO. endopath/1 extension so it survives export uncoerced (dec_016).
lvsi,lvsi_sf_indeterminate,3,text,in_data_not_in_reference,endopath.lvsi.indeterminate,Equivocal or indeterminate result. Distinct from CAP 'cannot be determined' which asserts non-assessability (dec_016).
lvsi,lvsi_sf_cannot_be_determined,0,text,covered,cap_uterus.lvsi.cannot_be_determined,"Asserted non-assessability. A value, not a blank."
lvsi,lvsi_ref_le_4_foci,0,text,in_reference_not_in_data,cap_uterus.lvsi.le_4_foci,CAP requires a focus count. No report states one.
lvsi,lvsi_ref_ge_5_foci,0,text,in_reference_not_in_data,cap_uterus.lvsi.ge_5_foci,CAP's five-or-more-foci choice. No report states a count.
lvsi,lvsi_ref_substantial,0,text,in_reference_not_in_data,figo_endo_2023.lvsi.substantial,FIGO 2023 substantial is a count of five or more vessels. Unreachable from this corpus (dec_012).
grade,grd_sf_grade_3,227,text,covered,cap_uterus.histologic_grade.3,
grade,grd_sf_grade_2,190,text,covered,cap_uterus.histologic_grade.2,
grade,grd_sf_grade_1,113,text,covered,cap_uterus.histologic_grade.1,
grade,grd_sf_high_grade,44,text,covered,cap_uterus.histologic_grade.high_grade_non_endometrioid,High grade resolves to G3 on the endometrioid branch or the non-endometrioid choice. #36 disambiguates on histotype.
grade,grd_sf_low_grade,3,text,covered,cap_uterus.histologic_grade.1,Low grade groups FIGO G1 and G2.
grade,grd_sf_solid_percent,44,text,covered,,Percent non-squamous solid growth. The quantity FIGO grade is cut from (5 / 6-50 / >50).
histotype,hst_sf_endometrioid,427,text,covered,who_fgt.histotype.endometrioid,
histotype,hst_sf_serous,197,text,covered,who_fgt.histotype.serous,
histotype,hst_sf_mixed,33,text,covered,who_fgt.histotype.mixed,
histotype,hst_sf_clear_cell,30,text,covered,who_fgt.histotype.clear_cell,
histotype,hst_sf_carcinosarcoma,24,text,covered,who_fgt.histotype.carcinosarcoma,MMMT is the old name for the same entity.
histotype,hst_sf_mucinous,25,text,covered,icdo3.histotype.8480_3,WHO 2020 absorbed standalone mucinous into endometrioid. ICD-O-3 keeps 8480/3 (#36).
stage,stg_sf_ia,54,text,covered,gdc.stage.stage_ia,Edition ambiguous between FIGO 1988 and 2009. #35 infers the edition.
stage,stg_sf_ib,62,text,covered,gdc.stage.stage_ib,IB denotes opposite extents under FIGO 1988 and 2009. #35 infers the edition.
stage,stg_sf_ic,19,text,covered,gdc.stage.stage_ic,Stage IC exists only under FIGO 1988. Its presence dates the report.
stage,stg_sf_edition_1988_marker,25,text,covered,gdc.stage.stage_ic,T1c or IC marker. FIGO 2009 abolished stage IC.
stage,stg_sf_t1a,10,text,covered,gdc.stage.stage_ia,
stage,stg_sf_t1b,23,text,covered,gdc.stage.stage_ib,
stage,stg_sf_t1c,9,text,covered,gdc.stage.stage_ic,Exists only under FIGO 1988 / AJCC 6-7.
cervical_involvement,cvx_sf_present,150,text,covered,,Cervical stromal involvement present. CAP and FIGO field it.
cervical_involvement,cvx_sf_absent,133,text,covered,,
cervical_involvement,cvx_sf_quantity,70,text,covered,,Depth or percent of cervical wall involved. CAP's own element.
cervical_involvement,cvx_sf_glandular_only,4,text,covered,,Mucosal or glandular-only involvement. FIGO 1988 IIA named it. FIGO 2009 dropped it from stage II. The distinction is preserved.
myometrial_invasion,myo_sf_depth_quantity,269,text,covered,,Invasion depth in mm or cm. The primitive quantity. Numbers stay numbers.
myometrial_invasion,myo_sf_percent,144,text,covered,,Invasion as a percent of wall thickness.
myometrial_invasion,myo_sf_word_fraction,85,text,covered,,Word fraction of the myometrium invaded.
myometrial_invasion,myo_sf_numeric_fraction,74,text,covered,,Numeric fraction of the myometrium invaded.
myometrial_invasion,myo_sf_half_or_more,60,text,covered,,Half-or-more invasion category derived from the quantity (dec_011).
myometrial_invasion,myo_sf_less_than_half,58,text,covered,,Less-than-half invasion category (dec_011).
myometrial_invasion,myo_sf_no_invasion,39,text,covered,,"Zero invasion. A distinct category, not a blank (dec_011)."
nodes,nod_sf_count,358,text,covered,,Positive over examined node count. Numbers stay numbers.
nodes,nod_sf_negative,304,text,covered,,
nodes,nod_sf_positive,167,text,covered,,
nodes,nod_sf_none_submitted,31,text,covered,,No regional nodes submitted. A not-applicable gate value.
nodes,nod_sf_micromet,2,text,covered,ajcc_8.regional_lymph_node_status.pN1mi,Micrometastasis. 2 reports (0.4%).
nodes,nod_ref_itc,0,text,in_reference_not_in_data,ajcc_8.regional_lymph_node_status.pN0_i_plus,Isolated tumor cells. No report states them. FIGO 2023 IIIC*i/ii needs the micro-vs-macro-vs-ITC deposit distinction the corpus lacks (dec_017).
molecular_classification,tcga_subtype_pole,49,structured,covered,tcga_ucec.molecular_classification.pole_ultramutated,"From cBioPortal. determined_by_join, not asserted from the report."
molecular_classification,tcga_subtype_msi,148,structured,covered,tcga_ucec.molecular_classification.msi_hypermutated,"From cBioPortal. determined_by_join, not asserted from the report."
molecular_classification,tcga_subtype_cn_low,147,structured,covered,tcga_ucec.molecular_classification.copy_number_low,"From cBioPortal. determined_by_join, not asserted from the report."
molecular_classification,tcga_subtype_cn_high,163,structured,covered,tcga_ucec.molecular_classification.copy_number_high,From cBioPortal. determined_by_join. Routes to p53abn as a ~95% surrogate (T9 open decision 3).
stage,IA3,0,structured,in_reference_not_in_data,figo2023.stage.ia3,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IAmPOLEmut,0,structured,in_reference_not_in_data,figo2023.stage.iampolemut,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IICmp53abn,0,structured,in_reference_not_in_data,figo2023.stage.iicmp53abn,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IIIB1,0,structured,in_reference_not_in_data,figo2023.stage.iiib1,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IIIB2,0,structured,in_reference_not_in_data,figo2023.stage.iiib2,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IIIC1i,0,structured,in_reference_not_in_data,figo2023.stage.iiic1i,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IIIC1ii,0,structured,in_reference_not_in_data,figo2023.stage.iiic1ii,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IIIC2i,0,structured,in_reference_not_in_data,figo2023.stage.iiic2i,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.
stage,IIIC2ii,0,structured,in_reference_not_in_data,figo2023.stage.iiic2ii,no equivalent in GDC's figo_stage enum; a GDC round-trip drops this code.