docs: update gitignore to track report results, add README cross-links

- Revised .gitignore to ignore raw data/cache but track data/report/
  (candidates TSV/Parquet, plots, reproducibility metadata)
- Added zh↔en cross-links between README.md and README.en.md

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.gitignore

@@ -1,11 +1,24 @@
-# Data files
+# === Raw data & intermediate files ===
-data/
+data/cache/
+data/gnomad/
+data/annotation/
+data/expression/
+data/localization/
+data/animal_models/
+data/scoring/
 
-# DuckDB
+# DuckDB database (large, regeneratable)
 *.duckdb
 *.duckdb.wal
 
-# Python
+# Provenance JSON (regenerated on each run)
+*.provenance.json
+*.provenance.provenance.json
+
+# === Keep report results ===
+# data/report/ is NOT ignored — candidates.tsv, parquet, plots are tracked
+
+# === Python ===
 __pycache__/
 *.pyc
 *.pyo
@@ -18,23 +31,27 @@ dist/
 build/
 .eggs/
 
-# Testing
+# === Testing ===
 .pytest_cache/
 .coverage
 htmlcov/
 .tox/
 
-# IDE
+# === IDE ===
 .vscode/
 .idea/
 *.swp
 *.swo
 *~
 
-# Provenance files (not in data/)
+# === Virtual environment ===
-/*.provenance.json
-
-# Virtual environment
 .venv/
 venv/
 env/
+
+# === OS ===
+.DS_Store
+Thumbs.db
+
+# === Planning (internal) ===
+.planning/

README.en.md

@@ -1,5 +1,7 @@
 # Usher Cilia Candidate Gene Discovery Pipeline
 
+> **[中文版 (README.md)](README.md)**
+
 A reproducible bioinformatics pipeline for systematic screening of candidate genes associated with Usher syndrome and ciliopathies.
 
 This pipeline evaluates approximately 22,600 human protein-coding genes across six independent evidence layers, producing weighted composite scores and tiered candidate gene lists for downstream experimental validation.

README.md

@@ -1,5 +1,7 @@
 # Usher Cilia Candidate Gene Discovery Pipeline
 
+> **[English version (README.en.md)](README.en.md)**
+
 一套可重現的生物資訊分析管線，用於系統性篩選與 Usher 症候群及纖毛病變（ciliopathies）相關的候選基因。
 
 本管線對人類約 22,600 個蛋白質編碼基因，透過六個獨立的證據層面進行評分與排序，最終產出分層候選基因清單，供後續實驗驗證參考。

data/report/candidates.provenance.yaml

@@ -0,0 +1,33 @@
+generated_at: '2026-02-12T18:42:59.932245+00:00'
+output_files:
+- candidates.tsv
+- candidates.parquet
+statistics:
+  total_candidates: 18116
+  high_count: 0
+  medium_count: 2151
+  low_count: 15965
+column_count: 22
+column_names:
+- gene_id
+- gene_symbol
+- gnomad_score
+- expression_score
+- annotation_score
+- localization_score
+- animal_model_score
+- literature_score
+- evidence_count
+- available_weight
+- weighted_sum
+- composite_score
+- quality_flag
+- gnomad_contribution
+- expression_contribution
+- annotation_contribution
+- localization_contribution
+- animal_model_contribution
+- literature_contribution
+- confidence_tier
+- supporting_layers
+- evidence_gaps

data/report/reproducibility.json

@@ -0,0 +1,57 @@
+{
+  "run_id": "5f00f9da-e548-4a58-b1b3-028d05c94d32",
+  "timestamp": "2026-02-12T18:43:00.223842+00:00",
+  "pipeline_version": "0.1.0",
+  "parameters": {
+    "gnomad": 0.2,
+    "expression": 0.2,
+    "annotation": 0.15,
+    "localization": 0.15,
+    "animal_model": 0.15,
+    "literature": 0.15
+  },
+  "data_versions": {
+    "ensembl_release": 113,
+    "gnomad_version": "v4.1",
+    "gtex_version": "v8",
+    "hpa_version": "23.0"
+  },
+  "software_environment": {
+    "python": "3.14.3",
+    "polars": "1.38.1",
+    "duckdb": "1.4.4"
+  },
+  "filtering_steps": [
+    {
+      "step_name": "load_scored_genes",
+      "input_count": 0,
+      "output_count": 0,
+      "criteria": ""
+    },
+    {
+      "step_name": "apply_tier_classification",
+      "input_count": 0,
+      "output_count": 0,
+      "criteria": ""
+    },
+    {
+      "step_name": "write_candidate_output",
+      "input_count": 0,
+      "output_count": 0,
+      "criteria": ""
+    },
+    {
+      "step_name": "generate_visualizations",
+      "input_count": 0,
+      "output_count": 0,
+      "criteria": ""
+    }
+  ],
+  "validation_metrics": {},
+  "tier_statistics": {
+    "total": 18116,
+    "high": 0,
+    "medium": 2151,
+    "low": 15965
+  }
+}

data/report/reproducibility.md

@@ -0,0 +1,45 @@
+# Pipeline Reproducibility Report
+
+**Run ID:** `5f00f9da-e548-4a58-b1b3-028d05c94d32`
+**Timestamp:** 2026-02-12T18:43:00.223842+00:00
+**Pipeline Version:** 0.1.0
+
+## Parameters
+
+**Scoring Weights:**
+
+- gnomAD: 0.20
+- Expression: 0.20
+- Annotation: 0.15
+- Localization: 0.15
+- Animal Model: 0.15
+- Literature: 0.15
+
+## Data Versions
+
+- **ensembl_release:** 113
+- **gnomad_version:** v4.1
+- **gtex_version:** v8
+- **hpa_version:** 23.0
+
+## Software Environment
+
+- **python:** 3.14.3
+- **polars:** 1.38.1
+- **duckdb:** 1.4.4
+
+## Filtering Steps
+
+| Step | Input Count | Output Count | Criteria |
+|------|-------------|--------------|----------|
+| load_scored_genes | 0 | 0 |  |
+| apply_tier_classification | 0 | 0 |  |
+| write_candidate_output | 0 | 0 |  |
+| generate_visualizations | 0 | 0 |  |
+
+## Tier Statistics
+
+- **Total Candidates:** 18116
+- **HIGH:** 0
+- **MEDIUM:** 2151
+- **LOW:** 15965