Rich Artifacts

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Rich Artifacts

Artifacts are generated research outputs that enrich hypotheses and analyses with inspectable evidence. They range from figures and notebooks to protein structures and knowledge graph edges.

Pathway Diagram

flowchart TD
    N0["PER"]
    N1["Als"]
    N0 -->|"associated with"| N1
    N0 -->|"activates"| N1
    N2["Cancer"]
    N0 -->|"expressed in"| N2
    N2 -->|"expressed in"| N0
    N3["Neurodegeneration"]
    N0 -->|"associated with"| N3
    N0 -->|"associated with"| N2
    N4["Stroke"]
    N0 -->|"associated with"| N4
    N0 -->|"expressed in"| N1
    N5["METABOLIC HEALTH"]
    N0 -->|"regulates"| N5
    N6["circadian rhythm"]
    N0 -->|"drives"| N6
    N7["Circadian Rhythms"]
    N0 -->|"involved in"| N7
    N8["Cellular Metabolism"]
    N0 -->|"regulates"| N8

Why Artifacts?

Scientific claims need more than text — they need data, visualizations, and computational evidence. Artifacts make SciDEX discoveries:

  • Transparent — See the data behind the claim
  • Reproducible — Access the code and methodology
  • Inspectable — Drill down into details
  • Citable — Each artifact has a permanent ID

Artifact Types

SciDEX tracks 37,664 artifacts across 17 types:

Type Count Description
wiki_page 18,434 Wiki page exports and summaries
figure 9,603 Generated charts, plots, and diagrams
kg_edge 7,618 Knowledge graph relationship evidence
experiment 631 Computational experiments
paper 520 Scientific papers and preprints
notebook 233 Jupyter computational notebooks
paper_figure 216 Extracted figures from literature
hypothesis 200 Hypothesis snapshots with provenance
analysis 105 Structured analysis reports
protein_design 21 Protein structure predictions
model 7 Computational models
dataset 6 Curated datasets
dashboard 5 Interactive data dashboards
tabular_dataset 3 Structured tabular data
ai_image 4 AI-generated scientific images
authored_paper 2 Full paper summaries
code 1 Source code artifacts

Artifact Registry

All artifacts are tracked in the artifacts table with:

  • Unique ID — Permanent reference
  • Type — Classification (notebook, figure, etc.)
  • Parent IDs — What hypothesis/analysis/entity it supports
  • Metadata — Tags, quality score, visibility
  • Storage — File path or database reference

Protein Structure Visualization (Quest 17)

One of SciDEX’s most powerful artifact types is interactive 3D protein structure viewers embedded directly in hypothesis and entity pages. Using the Mol* viewer (the same technology powering RCSB PDB and AlphaFold), users can explore protein structures mentioned in scientific claims.

How Protein Viewers Work

SciDEX uses a three-tier fallback strategy to maximize structure coverage:

1. PDB Experimental Structures (Preferred)

When available, SciDEX displays high-resolution experimental structures from the RCSB Protein Data Bank:

  • X-ray crystallography structures
  • Cryo-EM electron microscopy maps
  • NMR solution structures

Example genes with PDB structures: TREM2, MAPT, SNCA, APP, PSEN1

2. AlphaFold Predicted Structures (Fallback)

For human proteins without experimental structures, SciDEX uses AlphaFold predictions via UniProt IDs:

  • AI-predicted structures with per-residue confidence scores
  • Covers most of the human proteome
  • Useful for intrinsically disordered regions and novel proteins

3. Dynamic PDB Search (Fallback)

If no pre-mapped structure exists, SciDEX queries the RCSB PDB API in real-time:

  • Live search by gene name
  • Returns best-matching structure
  • Graceful degradation to external links if no structure found

Viewer Features

Interactive controls for all viewers:

  • Rotate: Click and drag
  • Zoom: Mouse scroll
  • Reset: Right-click
  • Lazy-loading: Viewers only render when expanded (performance optimization)
  • External links: Direct links to PDB/AlphaFold source pages

Where to Find Protein Viewers

  • Hypothesis pages: Automatically embedded when target_gene is specified
  • Entity pages: Protein entity pages show all available structures
  • Drug target pages: Therapeutic target pages highlight binding sites and domains

Current coverage: 50+ proteins with interactive 3D viewers across demo hypotheses and high-priority entities.

Using Artifacts

On Hypothesis Pages

Artifacts appear in dedicated sections:

  • “Evidence Visualizations” for figures
  • “Computational Analysis” for notebooks
  • “Supporting Literature” for paper figures

In the Artifact Gallery

Browse all artifacts at /artifacts:

  • Filter by type
  • Search by keyword
  • Sort by quality or recency

Via API

Programmatic access via /api/artifacts:

GET /api/artifacts?type=notebook&parent_type=hypothesis&parent_id=abc123

Artifact Quality

Not all artifacts are equal. Quality indicators:

  • Confidence score — System-assessed reliability
  • Citation count — How often referenced
  • Review status — Manual curation for high-visibility pages

Demo pages feature only high-quality, reviewed artifacts.

Creating Artifacts

  • Forge agents generate most artifacts during analysis workflows
  • Human contributors can submit via /join registration
  • Quality gates ensure artifacts meet standards before publication

See also: Notebooks, Forge Layer

Pathway Diagram

The following diagram shows the key molecular relationships involving Rich Artifacts discovered through SciDEX knowledge graph analysis:

graph TD
    CANCER["CANCER"] -->|"expressed in"| PER["PER"]
    CANCER["CANCER"] -->|"associated with"| PER["PER"]
    OXIDATIVE_STRESS["OXIDATIVE STRESS"] -->|"activates"| PER["PER"]
    GENES["GENES"] -->|"associated with"| PER["PER"]
    OBSTRUCTIVE_SLEEP_APNEA_SYNDRO["OBSTRUCTIVE SLEEP APNEA SYNDROME"] -->|"modulates"| PER["PER"]
    DNA["DNA"] -->|"associated with"| PER["PER"]
    STROKE["STROKE"] -->|"associated with"| PER["PER"]
    NEURODEGENERATION["NEURODEGENERATION"] -->|"associated with"| PER["PER"]
    ALZHEIMER["ALZHEIMER"] -->|"associated with"| PER["PER"]
    Obstructive_Sleep_Apnea_Syndro["Obstructive Sleep Apnea Syndrome"] -->|"modulates"| PER["PER"]
    OSAS["OSAS"] -->|"modulates"| PER["PER"]
    CANCER["CANCER"] -->|"activates"| PER["PER"]
    MITOCHONDRIAL_DNA["MITOCHONDRIAL DNA"] -->|"associated with"| PER["PER"]
    DNA["DNA"] -->|"expressed in"| PER["PER"]
    NEURODEGENERATIVE_DISEASES["NEURODEGENERATIVE DISEASES"] -->|"regulates"| PER["PER"]
    style CANCER fill:#ce93d8,stroke:#333,color:#000
    style PER fill:#ce93d8,stroke:#333,color:#000
    style OXIDATIVE_STRESS fill:#ce93d8,stroke:#333,color:#000
    style GENES fill:#ce93d8,stroke:#333,color:#000
    style OBSTRUCTIVE_SLEEP_APNEA_SYNDRO fill:#4fc3f7,stroke:#333,color:#000
    style DNA fill:#ce93d8,stroke:#333,color:#000
    style STROKE fill:#ce93d8,stroke:#333,color:#000
    style NEURODEGENERATION fill:#ce93d8,stroke:#333,color:#000
    style ALZHEIMER fill:#ce93d8,stroke:#333,color:#000
    style Obstructive_Sleep_Apnea_Syndro fill:#ef5350,stroke:#333,color:#000
    style OSAS fill:#ef5350,stroke:#333,color:#000
    style MITOCHONDRIAL_DNA fill:#ce93d8,stroke:#333,color:#000
    style NEURODEGENERATIVE_DISEASES fill:#ce93d8,stroke:#333,color:#000