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Update ThothII presentation tour, annotated screenshots and speaker notes

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# Outline v3 (FINAL structure — proposal A) — Role of AI in the Analysis of Unstructured Clinical Databases
# Outline v4 — Role of AI in the Analysis of Unstructured Clinical Databases
Updated 2026-09-18 against the actual deck, rather than the earlier proposed structure.
Deck: [`../deck/index.html`](../deck/index.html) — Reveal.js 5.1.0, **14 slides**, 16:9
(1280 × 720), with local fonts and speaker notes on every slide.
Review status: [`../prototype/deck-overview.html`](../prototype/deck-overview.html).
The titles below are the actual slide headings; some overview labels are shorter or older.
Deck: `deck/index.html` (Reveal.js, 15 slides, fonts embedded).
Presenters: **MP** = Dr. Marco Pancotti · **SP** = Dr.ssa Sara Paratico.
The notes explicitly identify Sara on slides 05–08. The final handoff around slide 04
and the remaining speaker allocation should be confirmed during rehearsal.
Per-slide timings and total running time need a new rehearsal; the previous 15-slide
timing estimate no longer describes this deck.
| # | Slide | Master | By | Time | Status |
|----|------------------------------------------------|--------------|----|------|--------|
| 01 | Title | title | MP | 40s | ✅ final |
| 02 | Where we started (4 systems + 2 missing) | interactive | MP | 65s | ✅ final |
| 03 | The project at a glance (flow + brain popups) | architecture | MP | 75s | ✅ final |
| 04 | What the text miner reads (numbers) | stats | SP | 60s | ✅ real data |
| 05 | The hard problems of clinical NLP | concept | SP | 75s | 🟡 draft |
| 06 | Building the clinical ontology | concept | SP | 75s | 🟡 draft |
| 07 | Trust the text: validation & human review | concept | SP | 75s | 🟡 draft |
| 08 | AI as co-engineer (mapping YAMLs) | artifact | MP | 70s | ✅ real |
| 09 | Genetic data — many sources, one patient | architecture | MP | 60s | ⚠️ wording TBD (a/b) |
| 10 | ThothII: ask the warehouse in plain English | concept | MP | 75s | 🟡 draft |
| 11 | From datamarts to predictive statistics & ML | concept | MP | 60s | 🟡 draft |
| 12 | Live demo cue (star schema · Superset · ThothII)| divider | MP | ~2min live | ✅ |
| 13 | Lessons learned | concept | MP | 60s | 🟡 draft |
| 14 | (merged into 15) | — | — | — | — |
| 15 | Thank you + Q&A (+ Substack pointer) | closing | MP | 25s | 🟡 draft |
## Actual slide sequence
Talk ≈ 13.4 min + ~2 min demo. 15 slides = user cap reached.
| # | Actual slide title | Content / format | Slide review status | Speaker notes |
|---|---|---|---|---|
| 01 | Role of AI in the Analysis of Unstructured Clinical Databases | AritmoLab introduction, clinical data platform and presenters | FINAL | Present; no DRAFT marker |
| 02 | Four islands and four missing pieces | Interactive map: Cardioref, Genetic data, Omics Portal and ECG subsystems; Clinical Intelligence, Datawarehouse, ML-ready data and Professional Portal as missing pieces | FINAL | Present; no DRAFT marker |
| 03 | What we wanted to build | Architecture and data flow toward the patient portal and research warehouse; clickable AI contribution cards | FINAL | Present; no DRAFT marker |
| 04 | The clinical truth lives in unstructured columns | Italian clinical sentence with English translation; why free text needs structured interpretation | FINAL | DRAFT |
| 05 | Deterministic AI, audited numbers | Text-mining outputs: 58,438 letters, 73,389 pathologies, 10,908 tests and 2,307 Brugada patients; extraction pipeline | FINAL | DRAFT — Sara |
| 06 | Reading clinical text is not keyword matching | Clinical NLP challenges, including negation and distinguishing family history from the patient's conditions | FINAL | DRAFT — Sara |
| 07 | Two tiers, one clinical order | Clinical ontology: 11 arrhythmic and 5 structural categories; text becomes recorded data | FINAL | DRAFT — Sara |
| 08 | Trusting the text is a process, not a promise | Five centered detail lenses: four validation controls and the three advantages | REFINED | ~120 words; five hover cues |
| 09 | AritmoLab — a quick tour | Portal tour; currently six screenshot placeholders | DRAFT | DRAFT |
| 10 | The warehouse speaks SQL. Research needs more. | Gap between the warehouse and clinical/research use: SQL access, aggregates and research cohorts | DRAFT | DRAFT |
| 11 | Ask the warehouse in plain English | ThothII: natural-language question, SQL proposal, human review and a research-ready datamart | DRAFT | DRAFT |
| 12 | From question to datamart — the app | ThothII walkthrough; currently six screenshot placeholders | DRAFT | DRAFT |
| 13 | One datamart — many questions answered | Multivariate analysis and machine learning; two chart placeholders with an illustrative-data disclosure | DRAFT | DRAFT — charts still to be created |
| 14 | Thank you | Questions and invitation to future technical walkthroughs on Substack | DRAFT | DRAFT |
## Confirmed decisions
- Project named **AritmoLab** everywhere (internal codename never appears).
- Slide 02 (Where we started): map of legacy systems — Cardioref / Genetic data /
Omics Portal / ECG subsystems, each clickable → popup (usage + problem box);
two dashed "MISSING" cards (Health Intelligence, ML-ready datamarts).
- Slide 03 flow: 3 sources + "Future sources" (dashed) → staging → integration 🧠
→ star schema → datamarts 🧠 → AritmoLab (DWH + Portal); brain popups =
The mappings / Reading the clinical text / Datamarts from plain English.
- Text-analysis block (SP): slides 04–07. Scripts to be validated by SP.
- Speaker view (S): Tall layout customized — upcoming 25%, timer bottom-left,
notes 1.45em. Default: upcoming 20%, notes 80%.
- Fonts embedded (Source Sans 3 + Source Serif 4, OFL) — no Google dependency.
`FINAL` and `REFINED` reproduce the overview's recorded review status. They do not imply
that speaker notes or clinical claims have received a separate final validation.
Figures above describe the content currently displayed in the deck.
## OPEN
- Slide 09 genetics wording: (a) deterministic reconciliation [recommended] vs
(b) AI upstream (only if MP confirms it happens outside the ETL).
- Draft slides 05-07, 10-11, 13-15: review one by one.
- Dark theme of the whole deck: final pass.
- "twenty years" (slide 01 script + slide 02): confirm real data span.
## Current presentation behavior
- Slide 02 has four clickable source systems and four clickable missing pieces,
each opening an explanatory popup.
- Slide 03 has clickable brain icons that open AI contribution cards with a connector
to the selected icon.
- Slide 08 has four centered lens popups. In the presenter console, hovering over
a numbered control or its corresponding heading in the notes opens the detail
in both preview and audience view. Escape closes it. Its quality wording separates
the original procedure-accuracy target from pathology coverage. The ~893
false-positive records and v1.3.1 negation fix are confirmed in the ETL sources;
see [source notes](08-validation-sources.md) for precise scope and limitations.
- Its advantages panel highlights on hover and opens a fifth centered lens on
click, explaining speed, precision and determinism. The fifth speaker-note cue
and presenter control open the same popup.
- Slide changes use a fade transition. Popups fade in and their cards move/scale into
place; clickable source icons and brain buttons have hover effects.
- A dropdown on each slide jumps to another slide. Reveal.js provides keyboard
navigation and the overview.
- The `S` key opens the Reveal.js speaker view when served locally. Speaker scripts
live in each slide's `<aside class="notes">` in `deck/index.html`.
- Source Sans 3 and Source Serif 4 are bundled under `deck/fonts/`; the deck does not
depend on Google Fonts.
## Remaining work
- Review slide 08 for final approval and slides 09–14 individually.
- Replace the six placeholders on slide 09 with real anonymized or demo portal
screenshots. The in-slide authoring note still requests 6–7 screenshots; settle
that count when inserting the images.
- Replace the six placeholders on slide 12 with screenshots of the ThothII workflow.
Its authoring note likewise still requests 6–7 screenshots.
- Create the two charts on slide 13, identify the supporting literature, and preserve
the disclosure if the data remain illustrative rather than measured results.
- Validate the speaker scripts on slides 04–14, including Sara's clinical section
on slides 05–08, and confirm the handoff between presenters.
- Confirm the “twenty years” wording, clinical figures, and quality-gate claims before
presenting them as final facts.
- Confirm the closing Substack reference and whether the promised videos will be
available by the talk.
- Rehearse the actual 14-slide sequence and set timings, including popup explanations
and any live demo chosen in addition to the screenshot walkthroughs.
The previous standalone slides on AI co-engineering, genetic reconciliation, lessons
learned and a live-demo divider are not separate slides in the current sequence.
Their old slide numbers, review tasks and timings should not be reused.
## Local preview
From the repository root:
```bash
python3 -m http.server 8000 --bind 127.0.0.1 --directory presentation
```
- Deck: <http://localhost:8000/deck/index.html>
- Review overview: <http://localhost:8000/prototype/deck-overview.html>
- Presenter console: <http://localhost:8000/presenter/> — notes, interactive preview,
popup controls and a separate audience window for an extended HDMI display.
See [`../presenter/README.md`](../presenter/README.md) for operation and scope.
Keep `presentation/` as the server root: the overview uses absolute `/deck/` URLs.
Stop the server with Ctrl+C.