YB Translator

Translate programming/CS concepts to biological parallels. Must use real ontology IDs from EBI OLS.

Required Output Format

CONCEPT: [programming concept]
BIOLOGY: [biological parallel]
ONTOLOGY: [Ontology Name] - [Term Name] ([ID])
EXAMPLE: [specific instance from ontology]
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/[ont]/classes/[encoded-iri]

Ontologies to Use

Bionty Integration

For programmatic access to biological ontologies, use Bionty:

import bionty as bt

# Lookup GO terms
go = bt.Gene()
go.lookup("RNA polymerase")

# Cell ontology
cl = bt.CellType()
cl.search("T cell")

Bionty provides versioned, validated access to CL, GO, MONDO, UBERON, and more.

Fetch Live Data

bb ~/.claude/skills/yb-translator/scripts/fetch_ontology.clj verify <ID>

Example:

bb ~/.claude/skills/yb-translator/scripts/fetch_ontology.clj verify CL:0000084

Translation Examples

Immutability

CONCEPT: Immutable data structures
BIOLOGY: DNA template strand
ONTOLOGY: Gene Ontology - DNA replication (GO:0006260)
EXAMPLE: Template strand unchanged during replication; new strand synthesized
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0006260

Inheritance/Subtyping

CONCEPT: Class inheritance
BIOLOGY: Cell differentiation hierarchy
ONTOLOGY: Cell Ontology - T cell (CL:0000084)
EXAMPLE: T cell → CD4+ T cell (CL:0000624), CD8+ T cell (CL:0000625)
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000084

Interface/Protocol

CONCEPT: Interface contract
BIOLOGY: Enzyme classification by function
ONTOLOGY: Gene Ontology - kinase activity (GO:0016301)
EXAMPLE: All kinases transfer phosphate; different substrates
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0016301

Garbage Collection

CONCEPT: Automatic memory management
BIOLOGY: Autophagy
ONTOLOGY: Gene Ontology - autophagy (GO:0006914)
EXAMPLE: Lysosomal degradation of cytoplasmic components
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0006914

Static Type Checking

CONCEPT: Compile-time type verification
BIOLOGY: Receptor-ligand specificity
ONTOLOGY: Gene Ontology - receptor binding (GO:0005102)
EXAMPLE: Insulin receptor (INSR) only binds insulin; shape verified before signal
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0005102

Recursion

CONCEPT: Self-referential function
BIOLOGY: Fractal branching morphogenesis
ONTOLOGY: Gene Ontology - branching morphogenesis (GO:0001763)
EXAMPLE: Lung bronchi: branch → branches → branches (same pattern each level)
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0001763

Concurrency

CONCEPT: Parallel execution
BIOLOGY: Parallel metabolic pathways
ONTOLOGY: Gene Ontology - metabolic process (GO:0008152)
EXAMPLE: Glycolysis and beta-oxidation run simultaneously in cytoplasm/mitochondria
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0008152

Preconditions (Dafny requires)

CONCEPT: Function precondition
BIOLOGY: Enzyme substrate specificity
ONTOLOGY: Gene Ontology - substrate-specific channel activity (GO:0022838)
EXAMPLE: Lactase only accepts lactose; wrong substrate = no reaction
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0022838

Postconditions (Dafny ensures)

CONCEPT: Function postcondition
BIOLOGY: Enzyme product guarantee
ONTOLOGY: Gene Ontology - catalytic activity (GO:0003824)
EXAMPLE: Lactase guarantees galactose + glucose output from lactose input
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0003824

Formal Verification (Dafny)

CONCEPT: Compile-time proof of correctness
BIOLOGY: Immune checkpoint verification
ONTOLOGY: Gene Ontology - T cell activation (GO:0042110)
EXAMPLE: T cell requires MHC presentation + costimulation; verified before response
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0042110

REPL (Clojure)

CONCEPT: Interactive evaluation loop
BIOLOGY: Adaptive immune response
ONTOLOGY: Gene Ontology - adaptive immune response (GO:0002250)
EXAMPLE: Encounter antigen → test response → remember successful patterns
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0002250

Homoiconicity (Clojure)

CONCEPT: Code as data
BIOLOGY: Self-replicating RNA polymerase ribozymes
ONTOLOGY: Gene Ontology - RNA polymerase activity (GO:0097747)
EXAMPLE: Ribozymes catalyze synthesis of copies of themselves—RNA is simultaneously 
         catalyst (program) and template (data). E.g., R3C ligase (Joyce 2002).
SOURCE: https://www.ebi.ac.uk/ols4/ontologies/go/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0097747

Rules

1. Always include ontology ID (e.g., CL:0000084, GO:0006914)
2. Always include SOURCE URL to EBI OLS
3. Use real terms – verify they exist at ebi.ac.uk/ols4
4. One parallel per concept – no tables, no frills
5. Run fetch script when uncertain about term existence

Related Skills (Random Walk r=3)

Cross-comparison: All three skills explore the code↔chemistry↔life boundary that yb-translator maps via ontologies.

SDF Interleaving

This skill connects to Software Design for Flexibility (Hanson & Sussman, 2021):

Primary Chapter: 7. Propagators

Concepts: propagator, cell, constraint, bidirectional, TMS

GF(3) Balanced Triad

yb-translator (○) + SDF.Ch7 (○) + [balancer] (○) = 0

Skill Trit: 0 (ERGODIC – coordination)

Secondary Chapters

• Ch5: Evaluation
• Ch4: Pattern Matching

Connection Pattern

Propagators flow constraints bidirectionally. This skill propagates information.