GeneForgeLang Ontology
Version: 0.1 Maintainer: Fundación de Neurociencias License: MIT Purpose: Provide a unified ontological foundation for symbolic reasoning in molecular design, reconciling biological logic and philosophical logic through GeneForgeLang (GFL).
1. Ontological Premises
| Domain | Description |
|---|---|
| Philosophical Logic | Reasoning based on causality, implication, modality, and consequence |
| Biological Logic | Reasoning constrained by molecular pathways, structural feasibility, species |
This ontology enables deductive, inductive, and abductive reasoning over biological syntax encoded in GFL.
2. Core Concepts
2.1 Entities
| Entity | GFL Representation | Ontological Role |
|---|---|---|
| Gene | ~d:[TSS]... |
Instructional template |
| Transcript | :r:Cap5'-Ex1-Intr1-Ex2-UTR3' |
Intermediate expression unit |
| Protein | ^p:Dom(...) |
Functional effector |
| Enhancer | Ctrl{Enh} |
Regulatory controller |
| Pathway | → sequences of events |
Causal chains |
| Edit | [MUT:...], [INS:...] |
Change agent |
2.2 Relations
| Relation | Syntax | Meaning |
|---|---|---|
| Causes | A → B |
A triggers or enables B |
| Requires | A ∧ B |
B is necessary for A |
| Equivalent | A ≡ B |
Semantic equivalence (e.g., isoforms) |
| Conditional | if A then B |
Logic gate for downstream events |
| Annotates | A [note: "..."] |
Optional human annotation |
3. Logical Operators and GFL Syntax Mapping
| Logic Concept | GFL Representation | Example |
|---|---|---|
| AND (∧) | Dom(X)-Mot(Y) |
Kinase domain AND nuclear localization motif |
| OR (∨) | Mot(X)/Mot(Y) |
Either motif X OR motif Y |
| NOT (¬) | !Mot(X) (planned) |
Absence of motif X |
| IMPLIES (→) | X = Y |
X implies Y (e.g., Mot(PEST) = Deg) |
| CONDITIONAL | if PTM(X) → Y |
If PTM, then downstream localization |
4. Reasoning Framework
4.1 Deductive Reasoning
From a general GFL rule to a specific output:
Rule: Mot(PEST) = Deg
Input: ^p:Dom(Kin)-Mot(PEST)
→ Inferred: Degradation likely
4.2 Inductive Reasoning
From observed patterns to a generalized rule:
Observed: MUT@42 → Functional loss
→ Inferred: All variants at position 42 likely deleterious
4.3 Abductive Reasoning
From observed effects to probable cause:
Phenotype: Loss of enzyme activity
→ Candidate phrase: ^p:Dom(Hyd)-[MUT:G>A@123]
5. Layers and Domains
| Layer | Ontological Implication |
|---|---|
| DNA | Blueprint; supports edit operations |
| RNA | Structural intermediates; supports splicing logic |
| Protein | Functional targets; supports PTMs and complex logic |
6. Species-Aware Reasoning
Species, organ specificity, and delivery mechanisms can be integrated as structured metadata:
target:
gene: "CPS1"
mutation: "[MUT:G>A@1001]"
species: "Homo sapiens"
delivery: "mRNA-nanoparticles"
edit_type: "Adenine base editor (ABE)"
7. Commentary and Meta-Logic
- Comments allowed via
#(ignored by parser) - Meta-level statements prefixed with
//for human-readable explanation - Reserved terms allowed in ontology-aware extensions:
causes,restores,requires,localizes
8. Roadmap
- ✅ Integration with GFL Transformer for symbolic → causal simulation
- ✅ Export support to OWL and RDF for use in semantic web agents
- ✅ Syntax-to-logic validator for consistency enforcement
- 🔜 Ontology-driven therapeutic reasoning engine
- 🔜 Multi-organism cross-mapping for translational models
End of Ontology Specification