Program
PROJECT STRANDSHIFT
Deliverable Code
STRANDSHIFT-ALID-0.10
Classification
Disease Intelligence Infrastructure Deliverable
Objective
To create a continuously expanding, evidence-ranked, multi-omic literature intelligence platform that captures, classifies, scores, and integrates all relevant scientific knowledge pertaining to:
- Huntington disease
- HTT biology
- CAG repeat instability
- DNA repair modifiers
- Neurodegeneration
- Neurodevelopment
- Trauma biology
- Psychoneuroimmunology
- Neuroimmune activation
- Viral mimicry
- Endogenous retroelements
- Circadian biology
- Apoptosis
- Mitochondrial dysfunction
- Angiogenesis
- Biomarker discovery
- Therapeutic development
The database serves as the primary knowledge engine supporting all subsequent STRANDSHIFT phases.
SECTION 1
DATABASE ARCHITECTURE
Knowledge Domains
Domain A
Disease Intelligence
Subdomains:
- Huntington disease
- Juvenile HD
- Late-onset HD
- PolyQ disorders
- Neurodegenerative diseases
- Neurodevelopmental disorders
Domain B
Genomics
Subdomains:
- HTT
- CAG repeats
- Repeat instability
- Somatic expansion
- Germline transmission
- DNA repair modifiers
Domain C
DNA Repair Biology
Subdomains:
- MSH3
- MSH2
- MLH1
- PMS1
- PMS2
- FAN1
- EXO1
- LIG1
- PCNA
- ATM
- ATR
- PARP1
Domain D
Epigenomics
Subdomains:
- DNA methylation
- Histone modification
- Chromatin remodeling
- Non-coding RNA
- Trauma epigenomics
Domain E
Neuroimmune Biology
Subdomains:
- Microglia
- Astrocytes
- Complement
- Cytokines
- Inflammasomes
- Neuroinflammation
Domain F
Psychoneuroimmunology
Subdomains:
- Stress biology
- HPA axis
- Trauma
- Neuroimmune interactions
- Sleep biology
- Circadian regulation
Domain G
Viragenesis
Subdomains:
- Viral mimicry
- cGAS-STING
- Interferon signaling
- HERV activation
- LINE-1
- Retrotransposons
Domain H
Cell Fate Biology
Subdomains:
- Apoptosis
- Senescence
- Autophagy
- Necroptosis
- Ferroptosis
Domain I
Systems Neuroscience
Subdomains:
- Connectomics
- Cortico-striatal circuitry
- Functional networks
- Executive function
- Cognitive decline
Domain J
Therapeutic Development
Subdomains:
- HTT lowering
- ASO therapeutics
- Gene editing
- DNA repair modulation
- Neuroimmune therapeutics
- Mitochondrial therapeutics
SECTION 2
LITERATURE CLASSIFICATION SYSTEM
Tier 1 Evidence
Highest confidence.
Includes:
- Phase III trials
- Meta-analyses
- Systematic reviews
- Consensus statements
- Major cohort studies
Evidence Weight:
100
Tier 2 Evidence
High confidence.
Includes:
- Phase I/II trials
- Longitudinal cohort studies
- Large observational studies
Evidence Weight:
80
Tier 3 Evidence
Moderate confidence.
Includes:
- Mechanistic laboratory studies
- Multi-omic studies
- Animal models
Evidence Weight:
60
Tier 4 Evidence
Exploratory.
Includes:
- Pilot studies
- Single-center studies
- Novel hypotheses
Evidence Weight:
40
Tier 5 Evidence
Hypothesis generation.
Includes:
- Theoretical frameworks
- Computational predictions
- Emerging concepts
Evidence Weight:
20
SECTION 3
MASTER DATA FIELDS
Every literature record contains:
Field | Description |
Record ID | Unique identifier |
PMID | PubMed identifier |
DOI | DOI |
Title | Publication title |
Authors | Author list |
Journal | Publication source |
Publication Year | Year |
Evidence Tier | Evidence ranking |
Disease Domain | Primary disease category |
Biological Domain | Mechanistic category |
Gene Targets | Associated genes |
Biomarkers | Associated biomarkers |
Cell Types | Relevant cell populations |
Tissue Type | Relevant tissue |
Species | Human/animal/in vitro |
Clinical Relevance | Translational significance |
STRANDSHIFT Relevance Score | Program importance score |
SECTION 4
STRANDSHIFT RELEVANCE SCORING SYSTEM
Score 100
Critical Core Evidence
Examples:
- HTT expansion
- MSH3
- FAN1
- Somatic expansion
- Mutant huntingtin
Score 90
Major Disease Modifiers
Examples:
- DNA repair biology
- Neuroimmune activation
- Mitochondrial dysfunction
Score 80
Important Disease Amplifiers
Examples:
- Stress biology
- Circadian disruption
- Cytokine signaling
Score 70
Supporting Systems
Examples:
- Trauma epigenomics
- Connectomics
- Behavioral phenotypes
Score <70
Peripheral evidence.
SECTION 5
SPECIALIZED STRANDSHIFT LIBRARIES
Library A
HTT Knowledge Repository
Contents:
- HTT genetics
- CAG instability
- Protein biology
- Clinical studies
Library B
DNA Repair Intelligence Repository
Contents:
- MSH3
- FAN1
- Mismatch repair
- Somatic expansion studies
Library C
Trauma–Epigenomic Repository
Contents:
- Trauma biology
- Epigenetic programming
- Stress physiology
- Neuroimmune adaptation
Library D
PNI Repository
Contents:
- Psychoneuroimmunology
- Cortisol biology
- Cytokine networks
- Neuroimmune stress
Library E
Circadian Repository
Contents:
- REM sleep
- Circadian genes
- Sleep disruption
- Glymphatic biology
Library F
Viragenesis Repository
Contents:
- HERVs
- LINE-1
- Viral mimicry
- cGAS-STING
- Interferon biology
SECTION 6
AUTOMATED KNOWLEDGE EXTRACTION
For every publication:
Gene Extraction
Identify:
- genes
- loci
- variants
Biomarker Extraction
Identify:
- proteins
- cytokines
- metabolites
Pathway Extraction
Identify:
- signaling pathways
- repair pathways
- inflammatory pathways
Therapeutic Extraction
Identify:
- targets
- interventions
- outcomes
SECTION 7
AI-ASSISTED KNOWLEDGE GRAPH
Core Nodes
- HTT
- MSH3
- FAN1
- DNA Injury
- Cortisol
- IL-6
- TNF-α
- cGAS
- STING
- HERV-K
- LINE-1
- BDNF
- PGC-1α
Edge Types
- activates
- suppresses
- correlates
- predicts
- repairs
- amplifies
- protects
- destabilizes
SECTION 8
STRANDSHIFT-SPECIFIC RESEARCH COLLECTIONS
Collection 1
HTT–DNA Repair Convergence
Purpose:
Support Phases 1–8.
Collection 2
Trauma–Epigenomic Convergence
Purpose:
Support Phase 5.
Collection 3
Stress–DNA Injury Convergence
Purpose:
Support PNI modules.
Collection 4
Circadian–Neuroimmune Convergence
Purpose:
Support sleep and REM analyses.
Collection 5
Viragenesis and Viral Mimicry
Purpose:
Support viral-origin investigations.
Collection 6
Apoptosis–Neurodegeneration Convergence
Purpose:
Support cell-fate modeling.
Collection 7
Therapeutic Vulnerability Intelligence
Purpose:
Support PCR Blueprint development.
SECTION 9
REQUIRED DATABASE OUTPUTS
The Advanced Literature Intelligence Database continuously generates:
Disease Intelligence Reports
Knowledge Gap Reports
Biomarker Discovery Reports
Therapeutic Opportunity Reports
Multi-Omics Intelligence Reports
PNI Intelligence Reports
Trauma–Epigenomic Reports
Circadian–Neuroimmune Reports
Viragenesis Intelligence Reports
STRANDSHIFT Research Priority Reports
SECTION 10
ROLE WITHIN PROJECT STRANDSHIFT
The Advanced Literature Intelligence Database serves as the foundational evidence engine for the entire STRANDSHIFT program.
Every deliverable generated in:
- Disease Intelligence
- Disease Origin Discovery
- Fault Architecture
- Multi-Omics Reconstruction
- Pathogenesis Modeling
- Trauma Biology
- Psychoneuroimmunology
- Viragenesis
- Biomarker Discovery
- Therapeutic Vulnerability
- Advanced Medicine Translation
should be traceable back to literature records stored, classified, scored, and linked within the ALID system.
The ALID therefore functions as the master scientific memory architecture of PROJECT STRANDSHIFT, enabling evidence synthesis, hypothesis generation, biomarker prioritization, therapeutic target discovery, and translational decision support across the entire SCF Advanced Medicine Clinic research program.