| # PRD: Phylogenetic Relationship Metadata for Cognate Pairs |
|
|
| **Status**: In Progress |
| **Date**: 2026-03-14 |
| **Author**: Alvin (assisted by Claude) |
|
|
| --- |
|
|
| ## Problem |
|
|
| The cognate pair dataset (23.4M pairs) currently has NO metadata about the phylogenetic relationship between language pairs — no distinction between mother-daughter (Latin→Spanish), close sisters (Spanish~Italian), or distant sisters (Spanish~Hindi). Every pair should indicate its degree of cognacy. |
|
|
| ## Solution |
|
|
| A post-processing enrichment pipeline that cross-references cognate pairs against an authoritative phylogenetic tree (Glottolog CLDF v5.x) to classify each unique language pair. |
|
|
| --- |
|
|
| ## Data Source |
|
|
| **Primary**: Glottolog CLDF v5.x (Hammarström, Forkel, Haspelmath & Bank) |
| - Repository: `https://github.com/glottolog/glottolog-cldf` |
| - Archive: Zenodo DOI: 10.5281/zenodo.15640174 |
| - License: CC BY 4.0 |
| - Key files: `cldf/languages.csv` (27,177 languoids with ISO mapping), `cldf/classification.nex` (NEXUS with Newick trees per family) |
| - 8,184 languoids have ISO 639-3 codes |
| - Trees are topological (no branch lengths) |
|
|
| **Download method**: `scripts/ingest_glottolog.py` — downloads the CLDF CSV and NEXUS files from GitHub raw content into `data/training/raw/glottolog_cldf/`. Follows the same pattern as `ingest_acd.py`. |
|
|
| **Supplementary** (Phase 2, not in scope): Phlorest Bayesian phylogenies for calibrated branch lengths (years of divergence). |
|
|
| --- |
|
|
| ## Output |
|
|
| **File**: `data/training/metadata/phylo_pairs.tsv` |
|
|
| A lookup table keyed on canonically-ordered `(Lang_A, Lang_B)` pairs. NOT inline columns in the 23M-row cognate pair files — that would add massive redundancy since the same language pair always has the same phylo classification. |
|
|
| ### Schema (9 columns) |
|
|
| | Column | Type | Description | |
| |--------|------|-------------| |
| | `Lang_A` | str | ISO 639-3 code (alphabetically first) | |
| | `Lang_B` | str | ISO 639-3 code (alphabetically second) | |
| | `Phylo_Relation` | enum | `near_ancestral`, `close_sister`, `distant_sister`, `cross_family`, `unclassified` | |
| | `Tree_Distance` | int | Edge count through MRCA (0 = same leaf group, 99 = unclassified/cross-family) | |
| | `MRCA_Clade` | str | Glottocode or name of MRCA node (e.g., `roma1334`, `germ1287`) | |
| | `MRCA_Depth` | int | Depth of MRCA in tree (0 = root, higher = more specific) | |
| | `Ancestor_Lang` | str | For `near_ancestral`: ISO of the ancestor. `-` otherwise | |
| | `Family_A` | str | Top-level Glottolog family of Lang_A | |
| | `Family_B` | str | Top-level Glottolog family of Lang_B | |
| |
| ### Classification Taxonomy |
| |
| | Relation | Definition | Example | |
| |----------|-----------|---------| |
| | `near_ancestral` | One language is an attested ancestor of the other's clade (from curated NEAR_ANCESTOR_MAP) | Latin↔Spanish, Old English↔English, Sanskrit↔Hindi | |
| | `close_sister` | MRCA depth ≥ 3 (share a specific sub-branch) | Spanish↔Italian (both under Romance), Swedish↔Danish (both under North Germanic) | |
| | `distant_sister` | MRCA depth = 1 or 2 (share family or major branch only) | English↔Hindi (both IE, but Germanic vs Indo-Iranian) | |
| | `cross_family` | Different top-level families | English↔Japanese | |
| | `unclassified` | One or both languages not in Glottolog tree | Undeciphered/isolate languages without Glottocode | |
|
|
| **Depth thresholds**: The boundary between close and distant is at MRCA depth 3+. This means: |
| - Depth 0: root (should not occur for same-family pairs) |
| - Depth 1: top-level family (e.g., `indo1319` = Indo-European) → `distant_sister` |
| - Depth 2: major branch (e.g., `germ1287` = Germanic) → `distant_sister` |
| - Depth 3+: sub-branch (e.g., `west2793` = West Germanic) → `close_sister` |
|
|
| ### Near-Ancestral Detection |
|
|
| A curated `NEAR_ANCESTOR_MAP` lists ~25 attested ancient/medieval languages and the Glottolog clades they are historically ancestral to: |
|
|
| ```python |
| NEAR_ANCESTOR_MAP = { |
| "lat": ["roma1334"], # Latin → Romance |
| "grc": ["mode1248", "medi1251"], # Ancient Greek → Modern Greek clades |
| "san": ["indo1321"], # Sanskrit → Indic |
| "ang": ["angl1265"], # Old English → Anglian/English |
| "enm": ["angl1265"], # Middle English → English |
| "fro": ["oilf1242"], # Old French → Oïl French |
| "osp": ["cast1243"], # Old Spanish → Castilian |
| "non": ["nort3160"], # Old Norse → North Germanic modern |
| "goh": ["high1289"], # Old High German → High German |
| "dum": ["mode1258"], # Middle Dutch → Modern Dutch |
| "sga": ["goid1240"], # Old Irish → Goidelic modern |
| "mga": ["goid1240"], # Middle Irish → Goidelic modern |
| "wlm": ["bryt1239"], # Middle Welsh → Brythonic modern |
| "chu": ["sout3147"], # Old Church Slavonic → South Slavic |
| "orv": ["east1426"], # Old East Slavic → East Slavic modern |
| "och": ["sini1245"], # Old Chinese → Sinitic modern |
| "ota": ["oghu1243"], # Ottoman Turkish → Oghuz modern |
| "okm": ["kore1284"], # Middle Korean → Korean modern |
| } |
| ``` |
|
|
| Logic: |
| 1. If either language is in `NEAR_ANCESTOR_MAP` |
| 2. AND the other language's ancestry path in Glottolog passes through one of the listed descendant clades |
| 3. AND the other language is NOT itself an ancient/medieval language (to avoid classifying Latin↔Oscan as near_ancestral) |
| 4. THEN classify as `near_ancestral` with `Ancestor_Lang` = the ancient language's ISO |
| |
| **Gothic (`got`) edge case**: Gothic is ancient but has NO modern descendants (East Germanic is extinct). Gothic↔Swedish should be `distant_sister`, not `near_ancestral`. The map correctly handles this by only listing clades with living descendants. |
| |
| --- |
| |
| ## Scripts |
| |
| ### Script 1: `scripts/ingest_glottolog.py` |
| Downloads Glottolog CLDF data from GitHub. |
|
|
| ### Script 2: `scripts/build_glottolog_tree.py` |
| Parses the Glottolog NEXUS file into a usable Python tree structure. |
|
|
| ### Script 3: `scripts/build_phylo_pairs.py` |
| The main enrichment script that generates the lookup table. |
|
|
| ### Script 4: `scripts/validate_phylo_pairs.py` |
| Validation script with known-answer checks. |
|
|
| --- |
|
|
| ## Execution Order |
|
|
| 1. Write PRD → push to `docs/prd/PRD_PHYLO_ENRICHMENT.md` |
| 2. Write `scripts/ingest_glottolog.py` → download Glottolog CLDF |
| 3. Write `scripts/build_glottolog_tree.py` → parse NEXUS, build tree index |
| 4. Adversarial audit: Verify tree covers ≥95% of ISO codes in cognate pairs |
| 5. Write `scripts/build_phylo_pairs.py` → generate lookup table |
| 6. Adversarial audit: Verify 20 random pairs trace back to Glottolog tree |
| 7. Write `scripts/validate_phylo_pairs.py` → automated known-answer tests |
| 8. Update `docs/DATABASE_REFERENCE.md` with phylo_pairs documentation |
| 9. Commit + push to GitHub + HuggingFace |
| |
| --- |
| |
| ## Critical Design Decisions |
| |
| ### Why a separate lookup table (not inline columns)? |
| - The 22.9M inherited pairs reference ~385K unique language pairs. Adding 7 columns to 22.9M rows = 160M+ redundant cells. |
| - Downstream consumers join at query time: `pair_key = (min(a,b), max(a,b))`; lookup is O(1) with a dict. |
| - The phylo classification is orthogonal to the cognate data — it can be updated independently when Glottolog releases new versions. |
|
|
| ### Why Glottolog (not the existing phylo_tree.json)? |
| - `phylo_tree.json` has 755 Austronesian languages in ONE flat list — zero sub-classification for 90% of the dataset |
| - Glottolog has deep sub-classification for ALL families including Austronesian |
| - Glottolog is the authoritative academic reference (Hammarström et al.) |
|
|
| ### Why curated near-ancestor map (not purely algorithmic)? |
| - Glottolog classifies ALL attested languages as leaf nodes (siblings), never as parent nodes |
| - Even Latin is a sibling of Romance under "Imperial Latin" in Glottolog — not a parent |
| - Algorithmic detection from tree topology alone would classify ALL pairs as sister-sister |
| - The curated map (~25 entries) is linguistically defensible and small enough to verify exhaustively |
|
|
| ### Why not branch-length / time-calibrated distances? |
| - Phase 1 focuses on topological classification |
| - Branch-length data requires Phlorest Bayesian phylogenies (separate download per family, inconsistent coverage) |
| - Branch lengths can be added in Phase 2 as a `Divergence_Years` column |
|
|
| --- |
|
|
| ## Honest Limitations |
|
|
| 1. **"Near-ancestral" is approximate**: Latin is not literally the ancestor of French — Vulgar Latin (unattested) is. We use "near-ancestral" to mean "the attested language is historically ancestral to the clade containing the other language." |
| 2. **Topological distance ≠ temporal distance**: Two languages with tree_distance=4 in Austronesian may have diverged 1,000 years ago, while two with tree_distance=4 in Indo-European may have diverged 5,000 years ago. |
| 3. **Glottolog is a single hypothesis**: Disputed affiliations are not represented. The tree reflects Glottolog's conservative consensus classification. |
| 4. **The similarity file (465K pairs) may contain cross-family pairs** that are correctly labeled `cross_family` — these are algorithmic similarity matches, not genetic relationships. |
| 5. **Proto-language codes (ine-pro, gem-pro, etc.) are NOT in Glottolog** — any cognate pairs involving proto-languages will be `unclassified`. (Currently zero such pairs exist in the dataset.) |
|
|
| --- |
|
|
| ## Verification |
|
|
| 1. `python scripts/validate_phylo_pairs.py` — all known-answer checks PASS |
| 2. Coverage: ≥95% of ISO codes in cognate pairs have a Glottolog classification |
| 3. Distribution: `close_sister` should be majority (most pairs are intra-family from ABVD/ACD) |
| 4. Adversarial audit: 20 random pairs traced back to Glottolog NEXUS tree |
| 5. No `unclassified` for any language that has a Glottocode in `languages.tsv` |
|
|
