Thesis #3 · working method manuscript · 20 September 2026
Disease Profiles for Complex Pathologies: A Gated Method for Systemic Personalized-Medicine Research Objects
Abstract
Personalized medicine is often described as if a molecular chart of a person would yield a dose. That leap is a product claim. Complex pathologies — triple-negative breast cancer with coupled metabolic and immune exclusion, glioblastoma with hypoxic and invasive niches, pancreatic ductal adenocarcinoma with a desmoplastic stromal barrier, and dormant or occult residual disease — do not become usable research objects by pasting a knowledge-graph page into an ordinary differential equation.
This thesis defines the Disease Profile as a versioned research object for systemic personalized-medicine research. Completing a four-question thinking laboratory (who is asking; which disease, not “cancer”; regime; where the system is stuck) exports a profile with observables, candidate mechanisms, an explicit non-parameter list, admitted hypotheses, Vancouver citations, and a fixed research-only disclaimer. Admission is gated:
Knowledge ≠ Evidence ≠ Mechanism ≠ Parameter ≠ Prediction
OnCo knowledge, OnCo confidence.probability, Idea maturity, and the legacy
gene-to-parameter map must not enter Θ. Profiles feed HypothesisObject records
aimed at named public datasets (TCGA-BRCA, TCGA-GBM, TCGA-PAAD, CCLE metabolomics,
GEO GSE71729 / GSE62452 / GSE28735, Ivy GAP). They do not write coefficients.
The method sits beside CONFLUENCE adapter P0 (pull request #9) and Complexity Science
CaseCards. Worked examples are qualitative boards, not outcomes.
Keywords
Contents of the PDF
- Introduction — two meanings of personalized medicine; research objects versus charts
- Aims — contract, four questions, gates, case pack, HypothesisObjects, P0 / CaseCard sit
- Methods — proposed schema
1.0.0; export rules; named public datasets - Worked examples — TNBC, GBM, PDAC, dormancy/occult qualitative boards
- Discussion — efficiency of adding a new complex disease without an ODE edit
- Limitations and future work
- Vancouver references (verified DOIs only) and the product-refusal disclaimer
Independence from the exporter pull request
If pull request #11
(Disease Profile exporter) is still dirty, Thesis #3 remains a self-contained method paper.
The schema in the PDF is a proposed contract. Merging this thesis does not
require merging the exporter, and this thesis does not edit CancerODE.
Related artefacts (cited, not over-claimed)
- CONFLUENCE P0 adapter (PR #9) — read-only OnCo client; knowledge is not a parameter
- Thesis evidence ledger — burden statistics keep their estimate year
- Thinking laboratory — the four questions
- Complexity Science CaseCards (PR #2) — YAML templates for the same four diseases; draft companion
Disclaimer
This document is not personalized medicine as a clinical product. Disease Profiles are computational research artefacts. They are not a medical device, not CDS, not a diagnosis, not a dose, and not a cure. Data from OnCo (onco.cc), CC BY-NC 4.0; commercial use needs a licence.