BioMCP

1---
2name: biomcp
3description: Search and retrieve biomedical data — genes, variants, clinical trials, articles, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, and phenotype-disease matching. 15 sources including PubMed, ClinicalTrials.gov, ClinVar, OncoKB, Reactome, UniProt, PharmGKB, OpenFDA, Monarch. Use when asked about gene function, variant pathogenicity, trial matching, drug safety, resistance mechanisms, hereditary syndromes, or literature evidence.
4---
5 
6# BioMCP CLI
7 
8BioMCP is a biomedical command-line tool plus an embedded workflow catalog for agents. The CLI supports direct lookup/search tasks, while skills provide reusable multi-step investigation patterns.
9 
10## Quick Start
11 
12Run these three commands first in every new session:
13 
14```bash
15biomcp health
16biomcp list
17biomcp list gene
18```
19 
20What each command gives you:
21- `biomcp health`: verifies source/API connectivity.
22- `biomcp list`: shows all entities, patterns, and helper families.
23- `biomcp list <entity>`: shows detailed per-entity filters, IDs, and examples.
24 
25## Command Model
26 
27BioMCP follows a small command grammar:
28 
29- `biomcp search <entity> [filters]`
30- `biomcp get <entity> <id> [section...]`
31- `biomcp <entity-family> <helper> <id-or-name>`
32 
33Examples:
34 
35```bash
36biomcp get gene BRAF pathways
37biomcp get variant rs113488022 clinvar
38biomcp get article 22663011 annotations
39biomcp get trial NCT02576665 eligibility
40biomcp get drug carboplatin shortage
41```
42 
43## Search Patterns
44 
45Free-text searches:
46- `gene`, `disease`, `drug`, `pathway`, `protein` support `-q` (and positional query input).
47- `article` supports `-k/--keyword` and `-q/--query` aliases (and positional query input).
48 
49Structured/filter-first searches:
50- `variant` uses structured filters (for example: gene, significance, consequence, protein change).
51- `trial` uses structured filters (for example: condition, intervention, mutation, phase, status).
52 
53Query examples:
54 
55```bash
56biomcp search disease "lung cancer"
57biomcp search gene -q BRAF --limit 5
58biomcp search article -q "immunotherapy resistance" --limit 5
59biomcp search variant -g BRAF --significance pathogenic --limit 5
60biomcp search trial -c melanoma --mutation "BRAF V600E" --status recruiting --limit 5
61```
62 
63## Cross-Entity Helpers
64 
65Helpers let you pivot quickly between related entities without manually rebuilding filters.
66 
67```bash
68biomcp variant trials "BRAF V600E"
69biomcp variant articles "BRAF V600E"
70biomcp drug adverse-events pembrolizumab
71biomcp disease trials melanoma
72biomcp gene articles BRCA1
73biomcp pathway drugs R-HSA-5673001
74biomcp protein structures P15056 --limit 25
75```
76 
77## Per-Entity Guides
78 
79Use `biomcp list <entity>` for the full reference page of an entity.
80 
81Each page includes:
82- supported command forms (`search`, `get`, helpers)
83- ID formats and section names
84- filter vocabulary
85- practical examples
86 
87Common entries:
88 
89```bash
90biomcp list gene
91biomcp list variant
92biomcp list article
93biomcp list trial
94biomcp list protein
95```
96 
97## Skills
98 
99Skills are step-by-step investigation workflows. Each skill chains multiple BioMCP commands into a validated research pattern.
100 
101Use skills when you need a structured investigation, not just a single lookup.
102 
103```bash
104biomcp skill list
105biomcp skill 03
106biomcp skill gene-set-analysis
107```
108 
109| # | Slug | Focus |
110|---|------|-------|
111| 01 | `variant-to-treatment` | Variant to treatment/evidence workflow |
112| 02 | `drug-investigation` | Drug mechanism, safety, alternatives |
113| 03 | `trial-searching` | Trial discovery + patient matching |
114| 04 | `rare-disease` | Rare disease evidence and trial strategy |
115| 05 | `drug-shortages` | Shortage monitoring and alternatives |
116| 06 | `advanced-therapies` | CAR-T/checkpoint therapy workflows |
117| 07 | `hereditary-cancer` | Hereditary syndrome workflows |
118| 08 | `resistance` | Resistance and next-line options |
119| 09 | `gene-function-lookup` | Gene-centric function and context lookup |
120| 10 | `gene-set-analysis` | Enrichment + pathway + interaction synthesis |
121| 11 | `literature-synthesis` | Evidence synthesis with cross-entity checks |
122| 12 | `pharmacogenomics` | PGx gene-drug interactions and dosing |
123| 13 | `phenotype-triage` | Symptom-first rare disease workup |
124| 14 | `protein-pathway` | Protein structure and pathway deep dive |
125 
126## Common Pitfalls
127 
128- Variant IDs with shell metacharacters must be quoted:
129 
130```bash
131biomcp get variant "chr7:g.140453136A>T"
132```
133 
134- Variant `search` vs `get`:
135  - `search variant` is filter-based.
136  - `get variant` accepts rsID, HGVS, or `GENE CHANGE` formats.
137 
138- Best-effort helpers search free-text fields (for example, eligibility criteria or abstracts). Results depend on source document wording.
139 
140- If zero results:
141  - broaden to a higher-level entity (for example, `gene` before `variant`),
142  - try alternate wording/synonyms,
143  - try a different source option where supported (for example, `--source nci` for trial workflows).
144