Epic: Disease Research Workspace (Initial Focus: Akathisia)

[andytriboletti]

Epic: Disease Research Workspace (Initial Focus: Akathisia)

Summary

Add a Disease Research Workspace to BioNeighbor that allows users to select any disease and explore it in a dedicated tab within the app. The workspace is designed for mechanism-level bioinformatics research, hypothesis generation, and target/ligand exploration — not diagnosis or treatment.

The first supported disease will be Akathisia, serving as a reference implementation for future disease research workflows.

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Goals

• Enable structured, repeatable disease-focused research
• Integrate drugs, targets, ligands, assays, and pathways into a single view
• Support hypothesis generation via similarity and network analysis
• Maintain strict non-clinical, research-only positioning

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Non-Goals

• Medical advice or treatment recommendations
• Patient-facing clinical guidance
• Dosage, prescribing, or outcome prediction

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UI / UX Design

Primary Design

• New in-app tab: Disease Research
• Disease selector at top (searchable)
• Each disease opens its own internal workspace
• State persists per disease (filters, selections)

Rationale

• Keeps BioNeighbor context intact
• Allows fast switching between diseases
• Scales cleanly as disease count grows

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Disease Workspace Sections

1. Disease Overview

• Name
• Short mechanistic summary
• Known affected systems (e.g. motor, CNS)
• Key symptoms (research descriptors only)

Data Sources

• OMIM
• Orphanet
• MeSH
• PubMed review articles

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2. Associated Drugs

Categorized lists:

• Drugs known to induce or worsen the disease
• Drugs reported to reduce or alleviate symptoms (research-only)

Fields

• Drug name
• Primary targets
• Secondary/off-target effects
• Source references

Data Sources

• DrugBank
• ChEMBL (when reachable)
• FDA labels (FAERS summaries, non-diagnostic)
• Literature curation

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3. Targets & Mechanisms

Structured target map:

• Receptors
• Transporters
• Enzymes
• Ion channels

Each target includes:

• Functional role
• Agonist / antagonist / inhibitor relationships
• Known disease relevance

Data Sources

• UniProt
• IUPHAR / Guide to Pharmacology
• ChEMBL
• Literature-derived annotations

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4. Ligands & Similarity Analysis

• View ligands associated with disease-relevant targets
• Compare ligands by:
  • Bond structure
  • Functional groups
  • Target binding profiles

Features

• “Similar ligands” clustering
• Inverse-effect ligand discovery (similar structure, opposite effect)

Data Sources

• ChEMBL
• PubChem
• Open Babel / RDKit descriptors
• SMILES-based similarity metrics

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5. Pathway & Network View

Interactive graph showing:

• Drug → Target → Pathway → Symptom relationships
• Highlight imbalance patterns (e.g. inhibitory vs excitatory)

Data Sources

• Reactome
• KEGG
• Literature-derived pathway mappings

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6. Assay & Simulation Hooks (Research Mode)

Not real wet-lab simulation, but computational assay modeling:

Three abstraction levels:

1. Target-level: receptor activation/inhibition balance
2. Pathway-level: signaling flow shifts
3. System-level: motor vs inhibitory tone estimation

Purpose

• Compare compounds
• Identify imbalance signatures
• Generate hypotheses for further study

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Initial Disease Focus: Akathisia

Rationale

• Clear drug-induced mechanism patterns
• Strong receptor-level involvement
• Significant unmet understanding
• Well-suited to network analysis

Known Mechanistic Themes

• Dopamine D2 receptor blockade
• Serotonin (5-HT2A / 5-HT2C) modulation
• Adrenergic signaling imbalance
• GABAergic inhibitory tone disruption

Example Research Questions

• What receptor combinations correlate most strongly with akathisia induction?
• Are there ligands structurally similar to causative drugs but lacking restlessness signatures?
• What target imbalances distinguish akathisia from anxiety or agitation?

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Safety & Ethics

• Explicit “Research Only” labeling in UI
• No treatment suggestions or rankings
• No clinical scoring or outcome prediction
• All outputs framed as hypotheses

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Acceptance Criteria

• User can open Disease Research tab
• User can select Akathisia
• Workspace loads all defined sections
• Data sources are cited per section
• Similarity and target analysis functional at a basic level

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Future Extensions

• Save/share disease workspaces
• Cross-disease comparison
• User-curated disease annotations
• Import custom datasets
• Optional new-window mode for advanced users

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Notes

This epic establishes a general disease research framework with Akathisia as the first implementation, ensuring scalability to future conditions without redesign.