{ "schema_name": "soa-table-extraction", "schema_version": "1.0", "extraction_metadata": { "extracted_at": "2026-09-27T12:58:17+00:00", "extractor": "Claude, PDF_TO_JSON_PROMPT single-pass", "prompt_version": "3.8.1", "source_document": { "filename": "NCT04184622_soa.pdf", "document_type": "protocol", "document_version": "I8F-MC-GPHK(b)" }, "extraction_status": "ready_for_resolution", "extraction_notes": "All printed '*' markers in this table point to the 'Additional Information Regarding Activities Described in Schedule of Activities' table printed after Table 2 (document pages 25-28), per the source note '*Please see table below for corresponding additional information'. Because every marker prints as the same '*', each Additional Information note was given a synthesized id (n1..n27, identical across Tables 1 and 2) and bound to the starred element whose label matches that note's Activity cell (method text_match). The Additional Information table itself is not emitted as a table (its rows key to SoA elements; soa_table_type_definitions 'reference' rule). Abbreviation lists dropped (no in-grid abbreviation markers). Grid read by pdftotext -bbox column binning to Visit-row centres; row bands from raster rule lines.", "model": "claude-opus-5-5" }, "table_metadata": { "table_number": 1, "table_type": "main_soa", "table_title": "Schedule of Activities covering visits to primary study endpoint", "table_purpose": "Main 72-week treatment schedule (screening, treatment to primary endpoint at Week 72, Visit 99, early discontinuation and safety follow-up Visit 801) for all participants.", "page_start": 18, "page_end": 21 }, "schedule_properties": [ { "table_number": 1, "row_position": 1, "property_name": "Visit", "property_name_source": { "row_position": 1, "column_position": 1, "cell_value": "Visit*" }, "property_type": "visit", "property_comment": "Visit identifiers (1–21, 99, ED, 801 in Table 1; 101–116, 199, ED, 802 in Table 2); a named/numbered visit per column, so property_type visit. Uniquely identifies every column.", "hierarchical_level": 1, "annotation_markers": "n1" }, { "table_number": 1, "row_position": 2, "property_name": "Week of Treatment", "property_name_source": { "row_position": 2, "column_position": 1, "cell_value": "Week of Treatment" }, "property_type": "week", "property_comment": "Week of treatment relative to randomization (negative weeks = screening/lead-in; last column reads \"N wks Post TxP\"). Numeric week labels, so property_type week. ED column is empty.", "hierarchical_level": 2 }, { "table_number": 1, "row_position": 3, "property_name": "Allowable Deviation (days)", "property_name_source": { "row_position": 3, "column_position": 1, "cell_value": "Allowable Deviation (days)*" }, "property_type": "window", "property_comment": "Visit window in days (±3, +7, ±7). Allowed deviation around the target date, so property_type window. Empty for the first visit and for ED.", "hierarchical_level": 3, "annotation_markers": "n6" }, { "table_number": 1, "row_position": 4, "property_name": "Fasting Visit", "property_name_source": { "row_position": 4, "column_position": 1, "cell_value": "Fasting Visit*" }, "property_type": "other", "property_comment": "X marks visits at which the participant must attend fasting. A per-visit attribute/requirement flag, not a timing level; does not distinguish columns, so hierarchical_level null and property_type other.", "hierarchical_level": null, "structure_method": "inferred_from_layout", "annotation_markers": "n1" }, { "table_number": 1, "row_position": 5, "property_name": "Telephone Visit", "property_name_source": { "row_position": 5, "column_position": 1, "cell_value": "Telephone Visit" }, "property_type": "modality", "property_comment": "X marks visits conducted by telephone (these columns are grey-shaded in the body). Visit type/modality, so property_type modality; does not distinguish columns, so hierarchical_level null.", "hierarchical_level": null, "structure_method": "inferred_from_layout" } ], "schedule_grid": [ { "table_number": 1, "row_position": 1, "column_position": 2, "cell_value": "1" }, { "table_number": 1, "row_position": 1, "column_position": 3, "cell_value": "2" }, { "table_number": 1, "row_position": 1, "column_position": 4, "cell_value": "3", "annotation_markers": "n2" }, { "table_number": 1, "row_position": 1, "column_position": 5, "cell_value": "4" }, { "table_number": 1, "row_position": 1, "column_position": 6, "cell_value": "5" }, { "table_number": 1, "row_position": 1, "column_position": 7, "cell_value": "6" }, { "table_number": 1, "row_position": 1, "column_position": 8, "cell_value": "7" }, { "table_number": 1, "row_position": 1, "column_position": 9, "cell_value": "8" }, { "table_number": 1, "row_position": 1, "column_position": 10, "cell_value": "9" }, { "table_number": 1, 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without eating, drinking (except water), or any significant physical activity. Since some screening procedures need to be completed in the fasting state, Visit 1 may be conducted over more than 1 day to ensure necessary conditions are met.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_property", "row_position": 1, "method": "text_match" }, { "table_number": 1, "location_type": "schedule_property", "row_position": 4, "method": "text_match" } ] }, { "annotation_marker": "n2", "annotation_type": "footnote", "annotation_text": "Baseline assessments must be completed before processing in the IWRS.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 4, "method": "text_match" } ] }, { "annotation_marker": "n3", "annotation_type": "footnote", "annotation_text": "Participants wanting to discontinue the study before Week 72 will be asked to return for Visit 99 at 72 weeks ± 7 days after randomization primarily for body weight measurement and assessment of adverse events. If the participant is unwilling to attend Visit 99, it should be documented in the participant medical record that the participant has refused to attend. Participants wanting to discontinue the study after Week 72 but before Week 176 will be asked to return for Visit 199 primarily for the body weight measurement and assessment of adverse events. Refusal to attend should be documented.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 23, "method": "text_match" } ] }, { "annotation_marker": "n4", "annotation_type": "footnote", "annotation_text": "Participants who are unable or unwilling to continue the study treatment for any reason will perform an ED visit. If the participant is discontinuing during an unscheduled visit or a scheduled visit, that visit should be performed as the ED visit.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 24, "method": "text_match" } ] }, { "annotation_marker": "n5", "annotation_type": "footnote", "annotation_text": "For participants who discontinue or complete the study within the first 72 weeks, Visit 801 (safety follow-up visit) should be performed 4 weeks after the last visit during the 72-week treatment period. Participants with prediabetes continuing to Week 78 should not perform Visit 801. For participants with prediabetes who complete the 176 weeks or discontinue after Week 72, Visit 802 should be performed 17 weeks after the last visit during the additional 2-year treatment period for participants with prediabetes at randomization.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 1, "column_position": 25, "method": "text_match" } ] }, { "annotation_marker": "n6", "annotation_type": "footnote", "annotation_text": "The visit date is determined in relation to the date of the randomization visit (± the allowed visit window).", "marker_locations": [ { "table_number": 1, "location_type": "schedule_property", "row_position": 3, "method": "text_match" } ] }, { "annotation_marker": "n7", "annotation_type": "footnote", "annotation_text": "Medical history includes assessment of preexisting conditions (for example, history of gallbladder disease, cardiovascular disease, and medullary thyroid carcinoma) and substance usage (such as alcohol and tobacco).", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 10, "method": "text_match" } ] }, { "annotation_marker": "n8", "annotation_type": "footnote", "annotation_text": "Weight measurements should be obtained per the instructions in Section 10.7. Body weight must be measured in fasting state. If the participant is not fasting, the participant should be called in for a new visit within the visit window to have the fasting body weight measured.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 13, "method": "text_match" } ] }, { "annotation_marker": "n9", "annotation_type": "footnote", "annotation_text": "ECG measurements should be obtained per the instructions in Section 10.7. ECGs will be performed in triplicate at Weeks 0 and 36. All other ECGs will be single measurements. ECGs should be collected at least 30 minutes prior to collection of blood samples for laboratory testing, including PK samples.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 15, "method": "text_match" } ] }, { "annotation_marker": "n10", "annotation_type": "footnote", "annotation_text": "Vital-sign measurements should be taken before obtaining an ECG tracing and before collection of blood samples for laboratory testing, per the instruction in Section 10.7.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 16, "method": "text_match" } ] }, { "annotation_marker": "n11", "annotation_type": "footnote", "annotation_text": "All training should be repeated as needed to ensure participant compliance.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 20, "method": "text_match" } ] }, { "annotation_marker": "n12", "annotation_type": "footnote", "annotation_text": "Data from diary, as well as study drug compliance, should be reviewed.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 21, "method": "text_match" } ] }, { "annotation_marker": "n13", "annotation_type": "footnote", "annotation_text": "Counselling on diet and exercise, to be performed by a dietician or equivalent qualified delegate, to include calculation of individualized energy requirement and methods to change dietary composition and amount of physical activity. The Lifestyle Program Instruction may be delivered on a separate day from the rest of that visit’s study procedures but must occur within the visit window. Beginning at Week 8, the Lifestyle Program Instruction may be delivered by phone.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 22, "method": "text_match" } ] }, { "annotation_marker": "n14", "annotation_type": "footnote", "annotation_text": "All training should be repeated as needed to ensure participant compliance. Study personnel to provide reinforcement and encouragement for lifestyle modifications.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 23, "method": "text_match" } ] }, { "annotation_marker": "n15", "annotation_type": "footnote", "annotation_text": "All training should be repeated as needed to ensure participant compliance", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 24, "method": "text_match" } ] }, { "annotation_marker": "n16", "annotation_type": "footnote", "annotation_text": "This applies only to those participants going into the additional 2-year treatment period for participants with prediabetes at randomization.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 25, "column_position": 22, "method": "text_match" } ] }, { "annotation_marker": "n17", "annotation_type": "footnote", "annotation_text": "Participants should administer their first dose of study drug at the end of the Visit 3, after other study procedures are completed", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 26, "method": "text_match" } ] }, { "annotation_marker": "n18", "annotation_type": "footnote", "annotation_text": "A serum pregnancy test will be performed at Visit 1 for women of childbearing potential only.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 29, "method": "text_match" } ] }, { "annotation_marker": "n19", "annotation_type": "footnote", "annotation_text": "A urine pregnancy test must be performed at Visit 3 with the result available prior to randomization and first injection of study drug(s) for women of childbearing potential only. Additional pregnancy tests (beyond those required per the Schedule of Activities) should be performed at any time during the trial if a menstrual period is missed, there is clinical suspicion of pregnancy, or as required by local law or regulation.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 30, "method": "text_match" } ] }, { "annotation_marker": "n20", "annotation_type": "footnote", "annotation_text": "Follicle-stimulating hormone test performed at Visit 1 for postmenopausal women at least 40 years of age with an intact uterus, not on hormone therapy, and who have had spontaneous amenorrhea for more than 1 year without an alternative medical cause.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 31, "method": "text_match" } ] }, { "annotation_marker": "n21", "annotation_type": "footnote", "annotation_text": "2-hour OGTT testing should be omitted at visits following a protocol-defined diabetes diagnosis.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 32, "method": "text_match" } ] }, { "annotation_marker": "n22", "annotation_type": "footnote", "annotation_text": "Screening visit assessment will be used to confirm eligibility. If calcitonin results are not available, a final review of eligibility will occur at Visit 3 before randomization can proceed.", "marker_locations": [ { "table_number": 1, "location_type": "schedule_cell", "row_position": 38, "column_position": 2, "method": "text_match" }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 39, "column_position": 2, "method": "text_match" }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 40, "column_position": 2, "method": "text_match" }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 41, "column_position": 2, "method": "text_match" }, { "table_number": 1, "location_type": "schedule_cell", "row_position": 44, "column_position": 2, "method": "text_match" } ] }, { "annotation_marker": "n23", "annotation_type": "footnote", "annotation_text": "The CKD-EPI equation will be used by the central lab to estimate and report eGFR.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 33, "method": "text_match" } ] }, { "annotation_marker": "n24", "annotation_type": "footnote", "annotation_text": "PK samples for immunogenicity must be taken prior to drug administration at these visits. In the event of systemic drug hypersensitivity reactions (immediate or nonimmediate), additional blood samples will be collected including ADA, PK, and exploratory biomarker samples.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 45, "method": "text_match" } ] }, { "annotation_marker": "n25", "annotation_type": "footnote", "annotation_text": "PK samples will be collected at these visits at time windows of 1 to 24 hours, 24 to 96 hours, or 120 to 168 hours post dose, as assigned by IWRS at randomization. Dependent on the time windows to which a participant is assigned, they may be required to come to site for PK-specific visits.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 46, "method": "text_match" } ] }, { "annotation_marker": "n26", "annotation_type": "footnote", "annotation_text": "The C-SSRS, Self-Harm Supplement Form and PHQ-9 should be administered after assessment of adverse events. For this study, the C-SSRS is adapted for the assessment of the ideation and behavior categories only. The Intensity of Ideation and Lethality of Behavior sections are removed.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 50, "method": "text_match" }, { "table_number": 1, "location_type": "activity_name", "row_position": 51, "method": "text_match" }, { "table_number": 1, "location_type": "activity_name", "row_position": 52, "method": "text_match" }, { "table_number": 1, "location_type": "activity_name", "row_position": 53, "method": "text_match" } ] }, { "annotation_marker": "n27", "annotation_type": "footnote", "annotation_text": "Self-Harm Follow-up Form is only required if triggered by the Self-Harm Supplement Form, per instructions in the form.", "marker_locations": [ { "table_number": 1, "location_type": "activity_name", "row_position": 54, "method": "text_match" } ] } ], "review_items": [ { "id": "D1", "severity": "high", "location": { "page": 18, "row_position": 1, "annotation_marker": "n1" }, "call_made": "Every '*' in the table was treated as pointing to one specific note of the 'Additional Information' table (pages 25-28): each note got its own id (n1-n27) and was attached to the starred row, visit or cell whose name matches that note's Activity cell.", "alternative": "Treat '*' as a single generic pointer ('see table below') and emit one annotation bound to every starred element, leaving the note-to-element matching to a later step.", "report_section": "3.1" }, { "id": "D2", "severity": "high", "location": { "page": 19, "row_position": 25, "column_position": 22, "annotation_marker": "n16" }, "call_made": "The note 'Dispense study drug Visit 72' (only for participants continuing into the prediabetes 2-year period) is attached only to the starred X of Dispense study drug at Visit 21 (Week 72), the one cell printed 'X*'.", "alternative": "Attach the note to the whole Dispense study drug row (all visits), since the note's own label names 'Visit 72', which does not exist as a visit number.", "report_section": "3.2" }, { "id": "D3", "severity": "high", "location": { "page": 20, "row_positions": [ 38, 39, 40, 41, 44 ], "column_position": 2, "annotation_marker": "n22" }, "call_made": "The eligibility note for Urinary albumin/creatinine, Cystatin-c, Calcitonin, Hematology and TSH ('Screening visit assessment will be used to confirm eligibility ...') is attached only to their starred Visit 1 cells, where the '*' is printed.", "alternative": "Attach it to the five activity rows as a whole (all visits), and also to the same-named rows of Table 2 which carry no '*'.", "report_section": "3.2" }, { "id": "D4", "severity": "medium", "location": { "page": 18, "row_positions": [ 4, 5 ] }, "call_made": "'Fasting Visit' and 'Telephone Visit' (blue-shaded header rows reprinted on every page) are recorded as header properties (Fasting = other, Telephone = modality), not as activities.", "alternative": "Record them as activity rows with X marks at the fasting / telephone visits.", "report_section": "3.3" }, { "id": "D5", "severity": "medium", "location": { "page": 21, "row_position": 51 }, "call_made": "The activity name is transcribed literally as printed: 'C-SSRS (Baseline/Screening) Version)', including the stray parenthesis.", "alternative": "Normalise to 'C-SSRS (Baseline/Screening Version)', the spelling used in the Additional Information table.", "report_section": "3.4" } ] }