Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation

- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization.
- Added a script for running RNA velocity analysis with customizable parameters and output options.
- Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation.
- Included references for velocity models and their mathematical framework, along with a comparison of different models.
- Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.

scientific-skills/monarch-database/references/phenotype_ontology.md

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+# HPO and Disease Ontology Reference for Monarch
+
+## Human Phenotype Ontology (HPO)
+
+### HPO Structure
+
+HPO is organized hierarchically:
+- **Root**: HP:0000001 (All)
+  - HP:0000118 (Phenotypic abnormality)
+    - HP:0000478 (Abnormality of the eye)
+    - HP:0000707 (Abnormality of the nervous system)
+    - HP:0001507 (Growth abnormality)
+    - HP:0001626 (Abnormality of the cardiovascular system)
+    - etc.
+
+### Top-Level HPO Categories
+
+| HPO ID | Name |
+|--------|------|
+| HP:0000924 | Abnormality of the skeletal system |
+| HP:0000707 | Abnormality of the nervous system |
+| HP:0000478 | Abnormality of the eye |
+| HP:0000598 | Abnormality of the ear |
+| HP:0001507 | Growth abnormality |
+| HP:0001626 | Abnormality of the cardiovascular system |
+| HP:0002086 | Abnormality of the respiratory system |
+| HP:0001939 | Abnormality of metabolism/homeostasis |
+| HP:0002664 | Neoplasm |
+| HP:0000818 | Abnormality of the endocrine system |
+| HP:0000119 | Abnormality of the genitourinary system |
+| HP:0001197 | Abnormality of prenatal development/birth |
+
+### Common HPO Terms in Rare Disease Genetics
+
+#### Neurological
+| HPO ID | Term |
+|--------|------|
+| HP:0001250 | Seizures |
+| HP:0001251 | Ataxia |
+| HP:0001252 | Muscular hypotonia |
+| HP:0001263 | Global developmental delay |
+| HP:0001270 | Motor delay |
+| HP:0002167 | Neurological speech impairment |
+| HP:0000716 | Depressivity |
+| HP:0000729 | Autistic behavior |
+| HP:0001332 | Dystonia |
+| HP:0002071 | Abnormality of extrapyramidal motor function |
+
+#### Growth/Morphology
+| HPO ID | Term |
+|--------|------|
+| HP:0004322 | Short stature |
+| HP:0001508 | Failure to thrive |
+| HP:0000252 | Microcephaly |
+| HP:0000256 | Macrocephaly |
+| HP:0001511 | Intrauterine growth retardation |
+
+#### Facial Features
+| HPO ID | Term |
+|--------|------|
+| HP:0000324 | Facial asymmetry |
+| HP:0001249 | Intellectual disability |
+| HP:0000219 | Thin upper lip vermilion |
+| HP:0000303 | Mandibular prognathia |
+| HP:0000463 | Anteverted nares |
+
+#### Metabolic
+| HPO ID | Term |
+|--------|------|
+| HP:0001943 | Hypoglycemia |
+| HP:0001944 | Hyperglycemia (Diabetes mellitus) |
+| HP:0000822 | Hypertension |
+| HP:0001712 | Left ventricular hypertrophy |
+
+## MONDO Disease Ontology
+
+MONDO integrates disease classifications from multiple sources:
+- OMIM (Mendelian diseases)
+- ORPHANET (rare diseases)
+- MeSH (medical subject headings)
+- SNOMED CT
+- DOID (Disease Ontology)
+- EFO (Experimental Factor Ontology)
+
+### Key MONDO IDs for Common Rare Diseases
+
+| MONDO ID | Disease | OMIM |
+|----------|---------|------|
+| MONDO:0007739 | Huntington disease | OMIM:143100 |
+| MONDO:0009061 | Cystic fibrosis | OMIM:219700 |
+| MONDO:0008608 | Down syndrome | OMIM:190685 |
+| MONDO:0019391 | Fragile X syndrome | OMIM:300624 |
+| MONDO:0010726 | Rett syndrome | OMIM:312750 |
+| MONDO:0014517 | Dravet syndrome | OMIM:607208 |
+| MONDO:0024522 | SCN1A-related epilepsy | — |
+| MONDO:0014817 | CHARGE syndrome | OMIM:214800 |
+| MONDO:0009764 | Marfan syndrome | OMIM:154700 |
+| MONDO:0013282 | Alpha-1-antitrypsin deficiency | OMIM:613490 |
+
+### OMIM ID Patterns
+
+- **Phenotype only**: OMIM number alone (e.g., OMIM:104300)
+- **Gene and phenotype**: Same gene, multiple phenotype entries
+- **Phenotype series**: Grouped phenotypes at a locus
+
+```python
+import requests
+
+def omim_to_mondo(omim_id):
+    """Convert OMIM ID to MONDO ID via Monarch API."""
+    search_id = f"OMIM:{omim_id}" if not omim_id.startswith("OMIM:") else omim_id
+    data = requests.get(
+        f"https://api-v3.monarchinitiative.org/v3/entity/{search_id}"
+    ).json()
+    # Check for same_as/equivalent_id links to MONDO
+    return data
+```
+
+## Association Evidence Codes
+
+Monarch associations include evidence types:
+
+| Code | Evidence Type |
+|------|--------------|
+| `IEA` | Inferred from electronic annotation |
+| `TAS` | Traceable author statement |
+| `IMP` | Inferred from mutant phenotype |
+| `IGI` | Inferred from genetic interaction |
+| `IDA` | Inferred from direct assay |
+| `ISS` | Inferred from sequence or structural similarity |
+| `IBA` | Inferred from biological aspect of ancestor |
+
+Higher-quality evidence: IDA > TAS > IMP > IEA
+
+## Semantic Similarity Metrics
+
+Monarch supports multiple similarity metrics:
+
+| Metric | Description | Use case |
+|--------|-------------|---------|
+| `ancestor_information_content` | IC of most informative common ancestor (MICA) | Disease similarity |
+| `jaccard_similarity` | Overlap coefficient | Simple set comparison |
+| `cosine` | Cosine similarity of IC vectors | Large-scale comparisons |
+| `phenodigm` | Combined MICA + Jaccard | Model organism matching |
+
+```python
+import requests
+
+def compute_disease_similarity(disease_ids_1, disease_ids_2, metric="ancestor_information_content"):
+    """Compute semantic similarity between two sets of disease phenotypes."""
+    # Get phenotype sets for each disease
+    url = "https://api-v3.monarchinitiative.org/v3/semsim/compare"
+    params = {
+        "subjects": disease_ids_1,
+        "objects": disease_ids_2,
+        "metric": metric
+    }
+    response = requests.get(url, params=params)
+    return response.json()
+```