data/taxonomy/extractions.csv

extraction_id,source_id,page,verbatim_text,extracted_by,note
ex_cap_histotype_element,cap_uterus/5.1.0.0,5,Histologic Type (Note C),agent:claude-fable-5,"Names the element and points at Note C, which is where CAP reproduces the WHO classification."
ex_cap_histotype_endometrioid,cap_uterus/5.1.0.0,5,___ Endometrioid carcinoma,agent:claude-fable-5,Checklist choice.
ex_cap_histotype_serous,cap_uterus/5.1.0.0,5,___ Serous carcinoma,agent:claude-fable-5,Checklist choice.
ex_cap_histotype_clear_cell,cap_uterus/5.1.0.0,5,___ Clear cell carcinoma,agent:claude-fable-5,Checklist choice.
ex_cap_histotype_carcinosarcoma,cap_uterus/5.1.0.0,5,___ Carcinosarcoma,agent:claude-fable-5,Checklist choice.
ex_cap_histotype_dedifferentiated,cap_uterus/5.1.0.0,5,___ Dedifferentiated carcinoma,agent:claude-fable-5,Checklist choice. CAP separates dedifferentiated from undifferentiated; endopath's Histotype fuses them.
ex_cap_histotype_undifferentiated,cap_uterus/5.1.0.0,5,___ Undifferentiated carcinoma,agent:claude-fable-5,Checklist choice.
ex_cap_histotype_mixed,cap_uterus/5.1.0.0,5,___ Mixed carcinoma (specify types and percentages),agent:claude-fable-5,Checklist choice.
ex_cap_histotype_other,cap_uterus/5.1.0.0,5,___ Other histologic type not listed (specify),agent:claude-fable-5,Checklist choice: the residual bucket that makes the sibling set exhaustive.
ex_cap_mucinous_absorbed,cap_uterus/5.1.0.0,19,carcinoma with extensive mucinous differentiation (previously known as mucinous carcinoma),agent:claude-fable-5,Why there is no standalone mucinous histotype in CAP 5.1.0.0.
ex_cap_grade_element,cap_uterus/5.1.0.0,5,Histologic Grade# (Note D),agent:claude-fable-5,Names the element.
ex_cap_grade_1,cap_uterus/5.1.0.0,20,FIGO Grade 1 5% or less non-squamous solid growth pattern,agent:claude-fable-5,The quantity behind grade 1. Numbers stay numbers.
ex_cap_grade_2,cap_uterus/5.1.0.0,20,FIGO Grade 2 6% to 50% non-squamous solid growth pattern,agent:claude-fable-5,The quantity behind grade 2.
ex_cap_grade_3,cap_uterus/5.1.0.0,20,FIGO Grade 3 >50% non-squamous solid growth pattern,agent:claude-fable-5,The quantity behind grade 3.
ex_cap_grade_high_grade_non_endometrioid,cap_uterus/5.1.0.0,5,___ High-grade (non-endometrioid carcinoma),agent:claude-fable-5,Grade is gated on histotype: this is the choice for the non-endometrioid branch.
ex_cap_lvsi_equivalence,cap_uterus/5.1.0.0,9,Lymphatic and / or Vascular Invasion (LVI) is equivalent to the FIGO term Lymphovascular Space Invasion (LVSI).,agent:claude-fable-5,CAP's LVI and FIGO's LVSI are the same dimension under two names.
ex_cap_lvsi_count_instruction,cap_uterus/5.1.0.0,9,Report the maximum number of LVI foci present on the single slide with the highest number of foci.,agent:claude-fable-5,"CAP asks for a count, which is the primitive quantity the categories derive from."
ex_cap_lvsi_not_identified,cap_uterus/5.1.0.0,9,___ Not identified,agent:claude-fable-5,Checklist choice under Lymphatic and / or Vascular Invasion.
ex_cap_lvsi_present,cap_uterus/5.1.0.0,9,___ Present,agent:claude-fable-5,Checklist choice under Lymphatic and / or Vascular Invasion.
ex_cap_lvsi_le4,cap_uterus/5.1.0.0,9,___ Less than or equal to 4 foci,agent:claude-fable-5,Sub-choice under Present.
ex_cap_lvsi_ge5,cap_uterus/5.1.0.0,9,___ Greater than or equal to 5 foci,agent:claude-fable-5,Sub-choice under Present. The 5-focus cut is the same one FIGO 2023 uses for substantial.
ex_cap_lvsi_cannot_be_determined,cap_uterus/5.1.0.0,9,___ Cannot be determined (explain),agent:claude-fable-5,"indeterminate is a value, not a blank."
ex_cap_promise_pole,cap_uterus/5.1.0.0,7,___ POLE-mutated carcinoma,agent:claude-fable-5,ProMisE-style checklist choice.
ex_cap_promise_mmrd,cap_uterus/5.1.0.0,7,___ Mismatch repair-deficient carcinoma,agent:claude-fable-5,ProMisE-style checklist choice.
ex_cap_promise_p53abn,cap_uterus/5.1.0.0,7,___ p53-abnormal carcinoma,agent:claude-fable-5,ProMisE-style checklist choice.
ex_cap_promise_nsmp,cap_uterus/5.1.0.0,7,___ No specific molecular profile (NSMP),agent:claude-fable-5,ProMisE-style checklist choice.
ex_cap_promise_double,cap_uterus/5.1.0.0,7,___ Double classifier (explain),agent:claude-fable-5,"Two classifiers at once is its own value, not a tie to be broken silently."
ex_cap_tcga_ultramutated,cap_uterus/5.1.0.0,7,___ POLE-mutated (ultramutated) carcinoma,agent:claude-fable-5,"TCGA-style checklist choice, a separate value set from ProMisE."
ex_cap_tcga_msi_high,cap_uterus/5.1.0.0,7,___ Microsatellite instability high (hypermutated) carcinoma,agent:claude-fable-5,TCGA-style checklist choice.
ex_cap_tcga_cn_low,cap_uterus/5.1.0.0,7,___ Copy number low carcinoma,agent:claude-fable-5,TCGA-style checklist choice.
ex_cap_tcga_cn_high,cap_uterus/5.1.0.0,7,___ Copy number high carcinoma,agent:claude-fable-5,TCGA-style checklist choice. UCEC_CN_HIGH is the surrogate that routes to p53abn.
ex_cap_ajcc_pn0i_plus,cap_uterus/5.1.0.0,14,___ pN0(i+): Isolated tumor cells in regional lymph node(s) no greater than 0.2 mm,agent:claude-fable-5,"AJCC 8 category, reproduced by CAP. Note the bound: no greater than 0.2 mm."
ex_cap_ajcc_pn1mi,cap_uterus/5.1.0.0,14,___ pN1mi: Regional lymph node metastasis (greater than 0.2 mm but not greater than 2.0 mm in,agent:claude-fable-5,"AJCC 8 category, reproduced by CAP."
ex_cap_ajcc_pn1a,cap_uterus/5.1.0.0,14,___ pN1a: Regional lymph node metastasis (greater than 2.0 mm in diameter) to pelvic lymph nodes,agent:claude-fable-5,"AJCC 8 category, reproduced by CAP."
ex_cap_ajcc_8_named,cap_uterus/5.1.0.0,4,"Standard(s): AJCC 8, FIGO 2009 Staging (2018 Annual Report), FIGO 2023 Staging",agent:claude-fable-5,CAP names the standards it reproduces. This is what licenses every derived_from citation through CAP.
ex_cap_figo2009_retained,cap_uterus/5.1.0.0,3,Added back FIGO 2009 Staging while retaining FIGO 2023 Staging,agent:claude-fable-5,"CAP 5.1.0.0 carries both editions, which is why one document can source both."
ex_cap_figo2009_element,cap_uterus/5.1.0.0,14,+FIGO Stage (FIGO 2009 Staging / 2018 FIGO Cancer Report) (Note N),agent:claude-fable-5,The FIGO 2009 stage element.
ex_figo2023_itc_threshold,figo_endo/2023,7,isolated tumor cells are up to 0.2 mm in size and up to 200,agent:claude-fable-5,"Correct ITC bound. The page-4 footnote of this same PDF says '≥0.2 mm', which is the error the paywalled corrigendum fixes. Cite page 7."
ex_figo2023_micromet_threshold,figo_endo/2023,7,micrometastases are 0.2–2 mm in size,agent:claude-fable-5,"Correct micrometastasis bound, body text."
ex_figo2023_lvsi_thresholds,figo_endo/2023,10,“LVSI negative” (0 vessels); “LVSI focal” (<5 vessels),agent:claude-fable-5,The vessel counts behind the FIGO 2023 LVSI categories.
ex_figo2023_lvsi_substantial_rule,figo_endo/2023,6,for staging purposes the recommendation by WHO 2020 (≥5 vessels) is adopted [3].,agent:claude-fable-5,"The substantial cut. Note this page says WHO 2020 and page 4 says WHO 2021, in the same paper."
ex_figo2023_lvsi_who_footnote,figo_endo/2023,4,"LVSI as defined in WHO 2021: extensive/substantial, ≥5 vessels involved.",agent:claude-fable-5,Table 1 footnote. Dates WHO as 2021 where page 6 says 2020.
ex_fhir_dar_canonical_url,fhir_dar/1.0.0,,"""url"" : ""http://terminology.hl7.org/CodeSystem/data-absent-reason""",agent:claude-fable-5,The canonical URL an export cites. Pinned so a future fetch that changes it fails loudly.
ex_fhir_dar_not_applicable,fhir_dar/1.0.0,,There is no proper value for this element (e.g. last menstrual period for a male).,agent:claude-fable-5,Definition of `not-applicable`. Exactly what a gate asserts: FIGO grade on a serous carcinoma.
ex_fhir_dar_asked_unknown,fhir_dar/1.0.0,,The source was asked but does not know the value.,agent:claude-fable-5,Definition of `asked-unknown`. The escalating search asked the report; the report does not say.
ex_fhir_dar_not_asked,fhir_dar/1.0.0,,The workflow didn't lead to this value being known.,agent:claude-fable-5,Definition of `not-asked`. Evidence for why the silent-report state is `asked-unknown` and not this: the search did ask.
ex_fhir_dar_unknown,fhir_dar/1.0.0,,The value is expected to exist but is not known.,agent:claude-fable-5,"Definition of `unknown`. Evidence for why `indeterminate` is not coded here: a report asserting non-assessability is not a source that does not know, it is a source that answered."
ex_figo2023_aggressive_types,figo_endo/2023,3,"aggressive histological types, i.e. serous, high-grade endometrioid, clear cell, carcinosarcomas, undifferentiated, mixed, and other unusual types",agent:claude-fable-5,Histotype aggressiveness becomes a staging input in 2023. It was not one in 2009.
ex_figo2023_stage_ia1,figo_endo/2023,4,IA1 Non-aggressive histological type limited to an endometrial polyp OR confined to the endometrium,agent:claude-fable-5,"Requires two variables FIGO 2009 stage I never needed: histotype aggressiveness, and whether invasion is zero."
ex_figo2023_stage_ia2,figo_endo/2023,4,IA2 Non-aggressive histological types involving less than half of the myometrium with no or focal LVSI,agent:claude-fable-5,A non-aggressive case with under half invasion falls out of IA2 if LVSI is substantial. It becomes IIB.
ex_figo2023_stage_ia3,figo_endo/2023,4,IA3 Low-grade endometrioid carcinomas limited to the uterus and ovary,agent:claude-fable-5,"Ovarian involvement, which FIGO 2009 stages IIIA, can be stage IA3 in 2023. A stage III to stage I move."
ex_figo2023_stage_ib,figo_endo/2023,4,"Non-aggressive histological types with invasion of half or more of the myometrium, and with no or focal LVSI",agent:claude-fable-5,IB. Substantial LVSI removes a case from IB and places it in IIB.
ex_figo2023_stage_ic,figo_endo/2023,4,limited to a polyp or confined to the endometrium,agent:claude-fable-5,IC. An aggressive type with no myometrial invasion. Requires the polyp or zero-invasion determination.
ex_figo2023_stage_iia,figo_endo/2023,4,Invasion of the cervical stroma of non-aggressive histological types,agent:claude-fable-5,IIA.
ex_figo2023_stage_iib,figo_endo/2023,4,of non-aggressive histological types,agent:claude-fable-5,IIB. Substantial LVSI alone raises a non-aggressive case from stage I to stage II.
ex_figo2023_stage_iic,figo_endo/2023,4,with any myometrial involvement,agent:claude-fable-5,"IIC. Any myometrial invasion of an aggressive type is stage II, whatever the depth."
ex_figo2023_ia3_criteria,figo_endo/2023,4,"1) no more than superficial myometrial invasion is present (<50%); 2) absence of extensive/substantial LVSI; 3) absence of additional metastases; and 4) the ovarian tumor is unilateral, limited to the ovary, without capsule invasion/rupture (equivalent to pT1a).",agent:claude-fable-5,"The four criteria separating IA3 from IIIA1. Criterion 4 needs ovarian capsule status, which pathology reports of this era rarely record. Note that page 7 words this as 'capsule invasion/breach', not 'rupture'."
ex_figo2023_stage_iam_polemut,figo_endo/2023,5,"POLEmut endometrial carcinoma, confined to the uterine corpus or with cervical extension, regardless of the degree of LVSI or histological type",agent:claude-fable-5,"IAmPOLEmut. A downstage, and it overrides both LVSI and histotype."
ex_figo2023_stage_iicm_p53abn,figo_endo/2023,5,"p53abn endometrial carcinoma confined to the uterine corpus with any myometrial invasion, with or without cervical invasion, and regardless of",agent:claude-fable-5,"IICmp53abn. An upstage, and it overrides both LVSI and histotype."
ex_figo2023_node_micro_macro,figo_endo/2023,4,IIIC1i Micrometastasis,agent:claude-fable-5,"FIGO 2023 subdivides nodal metastasis by deposit size. FIGO 2009 does not, so the size is an extra variable."
ex_figo2023_itc_not_metastatic,figo_endo/2023,4,The prognostic significance of ITCs is unclear. The presence of ITCs should be,agent:claude-fable-5,ITCs are recorded pN0(i+) and do not upstage. A 2009 IIIC case whose only nodal finding is ITCs is not stage III in 2023.
ex_abu_rustum_1988_stage_i,abu_rustum/2011,3,"IA (570), IB (593), and IC (144)",agent:claude-opus-4-8,"The 1988 stage-I sub-staging by myometrial depth: IA, IB and IC are distinct extents. Evidences the three 1988 stage-I codes."
ex_figo2009_stage_ia,figo_endo/2009,2,No or less than half myometrial invasion,agent:claude-opus-4-8,FIGO 2009 stage IA definition on the corpus uteri table.
ex_figo2009_stage_ib,figo_endo/2009,2,Invasion equal to or more than half of the myometrium,agent:claude-opus-4-8,FIGO 2009 stage IB definition. Opposite extent to 1988 IB.
ex_figo2009_stage_ii,figo_endo/2009,2,"Tumor invades cervical stroma, but does not extend beyond the uterus",agent:claude-opus-4-8,FIGO 2009 stage II definition.
ex_iccr_histotype_element,iccr_endo/5,1,HISTOLOGICAL TUMOUR TYPE (select all that apply) (Note 8),agent:claude-opus-4-8,"Names the ICCR histological tumour type element; the value list is the WHO 2020 classification (Core and Non-core, Note 8)."
ex_iccr_histotype_endometrioid,iccr_endo/5,1,Endometrioid carcinoma,agent:claude-opus-4-8,Checklist response option under HISTOLOGICAL TUMOUR TYPE (Note 8).
ex_iccr_histotype_serous,iccr_endo/5,1,Serous carcinoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_clear_cell,iccr_endo/5,1,Clear cell carcinoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_undifferentiated,iccr_endo/5,1,"Carcinoma, undifferentiated",agent:claude-opus-4-8,Checklist response option (Note 8). ICCR lists no separate dedifferentiated option.
ex_iccr_histotype_mixed,iccr_endo/5,1,Mixed cell carcinoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_mesonephric,iccr_endo/5,1,Mesonephric carcinoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_squamous,iccr_endo/5,1,Squamous cell carcinoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_mucinous_gi,iccr_endo/5,1,"Mucinous carcinoma, gastrointestinal type",agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_mesonephric_like,iccr_endo/5,1,Mesonephric-like carcinoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_neuroendocrine,iccr_endo/5,1,Neuroendocrine carcinomas,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histotype_carcinosarcoma,iccr_endo/5,1,Carcinosarcoma,agent:claude-opus-4-8,Checklist response option (Note 8).
ex_iccr_histologic_grade_1,iccr_endo/5,2,Grade 1 (low),agent:claude-opus-4-8,"Grade response option (Core, Note 9); ICCR labels grade 1 as low grade."
ex_iccr_histologic_grade_2,iccr_endo/5,2,Grade 2 (low),agent:claude-opus-4-8,"Grade response option (Core, Note 9); low grade in the binary grouping."
ex_iccr_histologic_grade_3,iccr_endo/5,2,Grade 3 (high),agent:claude-opus-4-8,"Grade response option (Core, Note 9); high grade in the binary grouping."
ex_iccr_histologic_grade_not_applicable,iccr_endo/5,10,high grade by definition should be recorded as ‘not applicable’ in the reporting guide. The value of the FIGO,agent:claude-opus-4-8,Non-endometrioid tumours are high grade by definition and grade is recorded as not applicable (Note 9).
ex_iccr_myometrial_invasion_bands,iccr_endo/5,11,"recorded as none, <50%, or ≥50%; this is a core element. In addition, the absolute percentage of myometrial",agent:claude-opus-4-8,"The core three-category myometrial invasion value set: none, <50%, >=50% (Note 10)."
ex_iccr_myometrial_invasion_percent_noncore,iccr_endo/5,11,wall thickness that is invaded by carcinoma can be recorded as a non-core element.,agent:claude-opus-4-8,Absolute percentage of myometrial wall thickness invaded is a non-core element (Note 10).
ex_iccr_cervical_stromal_involvement_involved,iccr_endo/5,14,Cervical stromal invasion indicates Stage IIA endometrial carcinoma according to the FIGO 2023 staging,agent:claude-opus-4-8,Cervical stromal invasion is a core element (Note 14); it stages non-aggressive types as FIGO 2023 IIA.
ex_iccr_cervical_stromal_involvement_not_involved,iccr_endo/5,2,Not involved,agent:claude-opus-4-8,The 'Not involved' response option under CERVICAL STROMA (Note 14).
ex_iccr_cervical_stromal_involvement_depth_noncore,iccr_endo/5,14,carcinoma.78 Absolute depth of cervical stromal invasion and percentage of cervical stromal invasion are,agent:claude-opus-4-8,Depth and percentage of cervical stromal invasion are non-core elements (Note 15).
ex_iccr_lvsi_not_identified,iccr_endo/5,13,The absence of LVI is defined as no tumour cells within vessels.33 There is controversial data regarding the,agent:claude-opus-4-8,LVI absence: no tumour cells within vessels (Note 11).
ex_iccr_lvsi_focal,iccr_endo/5,13,with ‘focal’ or ‘no’ LVI.67-69 Recording the degree of LVI (focal or substantial/extensive) is regarded as a core,agent:claude-opus-4-8,Recording the degree of LVI (focal or substantial/extensive) is a core element (Note 11).
ex_iccr_lvsi_substantial,iccr_endo/5,13,cut off for ‘substantial (extensive)’ LVI. ‘Substantial LVI’ is defined as the presence of three or more vessels,agent:claude-opus-4-8,ICCR/ISGyP substantial LVI cut-off is three or more involved vessels (Note 11).
ex_iccr_lvsi_indeterminate,iccr_endo/5,13,A value of ‘indeterminate’ should be used sparingly and only in cases where there is genuine doubt as to,agent:claude-opus-4-8,LVI 'indeterminate' is genuine doubt whether LVI is present (Note 11).
ex_iccr_regional_lymph_node_status_itc,iccr_endo/5,3,c Isolated tumour cells (≤0.2 mm and ≤200 cells).,agent:claude-opus-4-8,"Isolated tumour cells bound (<=0.2 mm and <=200 cells), footnote to the FIGO 2023 staging table."
ex_iccr_regional_lymph_node_status_deposit_bounds,iccr_endo/5,3,d Micrometastasis (>0.2 mm and ≤2 mm); Macrometastasis (>2 mm).,agent:claude-opus-4-8,"Micrometastasis (>0.2 mm and <=2 mm) and macrometastasis (>2 mm) bounds, FIGO 2023 staging table footnote."
ex_iccr_molecular_classification_polemut,iccr_endo/5,22,"According to this simplified algorithm, tumours with pathogenic POLE mutation correspond to ultramutated",agent:claude-opus-4-8,"TCGA surrogate algorithm: pathogenic POLE mutation = ultramutated group (Note 26, non-core)."
ex_iccr_molecular_classification_mmrd,iccr_endo/5,22,tumours. MSH6 or PMS2 abnormal expression defines tumours in the hypermutated group. Abnormal,agent:claude-opus-4-8,TCGA surrogate: MSH6/PMS2 abnormal expression = hypermutated group (Note 26).
ex_iccr_molecular_classification_p53abn,iccr_endo/5,22,"expression of p53 (mutated pattern), characterises the copy number high group. Finally, NSMP is defined by",agent:claude-opus-4-8,TCGA surrogate: abnormal p53 (mutated pattern) = copy-number-high group (Note 26).
ex_iccr_molecular_classification_nsmp,iccr_endo/5,4,"(POLEmut, MMRd, NSMP, p53abn) is encouraged in all patients with",agent:claude-opus-4-8,Names the four molecular classes; NSMP corresponds to the TCGA copy-number-low group.
ex_iccr_molecular_classification_noncore,iccr_endo/5,21,Reporting of TCGA-based molecular classification of endometrial carcinomas is a non-core parameter.,agent:claude-opus-4-8,TCGA-based molecular classification is a non-core parameter (Note 26).
ex_iccr_stage_element,iccr_endo/5,3,PROVISIONAL PATHOLOGICAL STAGING (Note 28),agent:claude-opus-4-8,Pathological staging is a core element (Note 28); ICCR uses FIGO 2023.
ex_iccr_stage_IA1,iccr_endo/5,3,IA1 Non-aggressive histological type limited to an,agent:claude-opus-4-8,FIGO 2023 stage IA1 (Note 28).
ex_iccr_stage_IA2,iccr_endo/5,3,IA2 Non-aggressive histological types involving less,agent:claude-opus-4-8,FIGO 2023 stage IA2 (Note 28).
ex_iccr_stage_IA3,iccr_endo/5,3,IA3 Low grade endometrioid carcinomas limited to the,agent:claude-opus-4-8,FIGO 2023 stage IA3 (Note 28).
ex_iccr_stage_IB,iccr_endo/5,3,Non-aggressive histological types with invasion of half,agent:claude-opus-4-8,FIGO 2023 stage IB (Note 28).
ex_iccr_stage_IC,iccr_endo/5,3,Aggressive histological typesh limited to a polyp or,agent:claude-opus-4-8,FIGO 2023 stage IC (Note 28).
ex_iccr_stage_IIA,iccr_endo/5,3,Invasion of the cervical stroma of non-aggressive,agent:claude-opus-4-8,FIGO 2023 stage IIA (Note 28).
ex_iccr_stage_IIB,iccr_endo/5,3,Substantial LVSI,agent:claude-opus-4-8,FIGO 2023 stage IIB (Note 28).
ex_iccr_stage_IIC,iccr_endo/5,3,Aggressive histological typesh with any myometrial,agent:claude-opus-4-8,FIGO 2023 stage IIC (Note 28).