Automated Foundation Stock

Automated Foundation Stock Relations

Extract has foundation stock (VBO:0300019) relations from kennel club registry breed pages and cross-reference across sources for confidence scoring.

Axiom Definition

Foundation stock is a directional ancestor relationship: the subject breed is the descendant, the foundation stock breed is the ancestor used in its creation. A breed merely mentioned on a page is NOT foundation stock. See: https://monarch-initiative.github.io/vertebrate-breed-ontology/ontologymodeling/axioms/

Process

Step 1: Identify Sources

For $ARGUMENTS, identify the relevant breed registry websites. Known sources for dogs:

• UKC (United Kennel Club): https://www.ukcdogs.com/ - breed history sections
• RKC (Royal Kennel Club, UK): https://www.royalkennelclub.com/search/breeds-a-to-z/ - "About this breed" sections
• CKC (Canadian Kennel Club): https://www.ckc.ca/en/Choosing-a-Dog/Choosing-a-Breed/All-Dogs - "Origin" sections

For other species, the user will provide source URLs.

Step 2: Fetch Breed Directory

For each source:

1. Fetch the breed directory/index page to get all breed URLs
2. Organize breeds into batches of ~20-25 for parallel fetching

Step 3: Extract Foundation Stock Data

For each breed page, extract:

• Breed name as stated on the page
• Foundation stock breeds - ONLY breeds explicitly described as ancestors, crossed to create, or used in developing the breed
• Exact quote from the source text
• Confidence of language - distinguish between:
  • High: "was created by crossing X and Y", "descended from X"
  • Medium: "it is thought that X was used", "may have X in its background"
  • Low: "resembles X", "related to X" (these are NOT foundation stock)

Critical filtering rules:

• Do NOT include breeds that are merely mentioned, compared to, or listed as descendants
• Do NOT include generic types without a specific breed name (e.g., "terrier types", "local dogs")
• Do NOT include breeds described as descendants OF the subject breed (reverse direction)
• DO flag hedging language with REVIEW notes

Step 4: Map to VBO IDs

Look up VBO identifiers for each breed name using src/ontology/vbo-edit.obo:

# Parse OBO file for breed name -> VBO ID mapping
# Match on name field, case-insensitive, stripping " (Species)" suffix

Common name aliases to handle:

• "Old English Mastiff" = "English Mastiff"
• "German Wolfspitz" = "Keeshond"
• "St. Hubert Hound" = "Bloodhound"
• "Wavy-coated Retriever" = "Flat-Coated Retriever"

Step 5: Create Per-Source TSV Files

One TSV per source with columns:

VBO ID | VBO label | foundation stock VBO ID | foundation stock VBO label | source URL | review_flag

Flag entries for:

• REVIEW: circular - A lists B as foundation stock AND B lists A
• REVIEW: "hedging language" - source uses uncertain language (quote it)
• REVIEW: VBO ID needed - could not map to a VBO identifier
• REVIEW: reverse relationship - the listed "ancestor" is actually a descendant
• REVIEW: generic type - source names a broad category, not a specific breed

Step 6: Cross-Reference and Combine

Merge all source TSVs into a combined file with confidence tiers:

VBO ID | VBO label | foundation stock VBO ID | foundation stock VBO label | confidence tier | sources | source count | review flags | source URLs

Confidence tiers:

Sort by tier (highest first), then alphabetically by breed.

Step 7: Summary

Report:

• Total unique relations found
• Breakdown by confidence tier
• Count of flagged entries by flag type
• Any breeds with no foundation stock data across all sources

Output Files

Place all output in src/ontology/:

• {species}_foundation_stock.tsv - primary source data (retain existing if updating)
• {species}_foundation_stock_{source}.tsv - per additional source
• {species}_foundation_stock_combined.tsv - cross-referenced combined file
• {species}_foundation_stock_README.md - documentation

Parallelization

Use background agents to fetch breed pages in parallel batches of ~20-25 URLs each. Launch multiple agents covering different letter ranges simultaneously. Compile results after all agents complete.