biomcp

Name: biomcp
Author: genomoncology

2.8kinstalls/mo · pypi554stars109forks

How to install biomcp?

genomoncology/biomcp

$git clone https://github.com/genomoncology/biomcp

Installs into the current project.

Summary

One binary. One grammar. Evidence from the biomedical sources you already trust.

Files · 1

View on GitHub

README.md

1	# BioMCP
2
3	One binary. One grammar. Evidence from the biomedical sources you already trust.
4
5	## What is BioMCP?
6
7	BioMCP is one CLI binary over a single command grammar that reaches ~30 trusted
8	biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, and
9	more). It is also an MCP (Model Context Protocol) server, so the same tools are
10	available to AI agents such as Claude Code, Codex, and Claude Desktop.
11
12	BioMCP cuts through the usual biomedical data maze: one query reaches the
13	sources that normally live behind different APIs, identifiers, and search
14	habits. Researchers, clinicians, and agents use the same command grammar to
15	search, focus, and pivot without rebuilding the workflow for each source. You
16	get compact, evidence-oriented results across live public data plus local study analytics.
17
18	## Features
19
20	- Search the literature: `search article` fans out across PubTator3 and
21	Europe PMC, deduplicates PMID/PMCID/DOI identifiers, and can add a Semantic
22	Scholar leg when your filters support it.
23	- Pivot without rework: move from a gene, variant, drug, disease, pathway,
24	protein, or article straight into the next built-in view instead of
25	rebuilding filters by hand.
26	- Choose a playbook: `biomcp skill list` shows shipped worked examples
27	so you can open the matching `biomcp skill <slug>` workflow.
28	- Analyze studies locally: `study` commands cover local query, cohort, survival,
29	compare, and co-occurrence workflows with native terminal, SVG, and PNG
30	charts for downloaded cBioPortal-style datasets.
31	- Follow the paper trail: `article citations`, `article references`,
32	`article recommendations`, and `article entities` turn one known paper into a
33	broader evidence map.
34	- Enrich and batch: use `biomcp enrich` for top-level g:Profiler
35	enrichment and `biomcp batch` for up to 10 focused `get` calls in one
36	command.
37
38	## Quick start
39
40	First useful query in under 30 seconds:
41
42	```bash
43	uv tool install biomcp-cli
44	biomcp health --apis-only
45	biomcp skill list
46	biomcp list gene
47	biomcp search all --gene BRAF --disease melanoma # unified cross-entity discovery
48	biomcp get gene BRAF pathways hpa
49	```
50
51	## Installation
52
53	### Binary install
54
55	```bash
56	curl -fsSL https://biomcp.org/install.sh \| bash
57	```
58
59	### PyPI tool install
60
61	```bash
62	uv tool install biomcp-cli
63	# or: pip install biomcp-cli
64	```
65
66	> PyPI package warning: install `biomcp-cli`, not `biomcp`. The `biomcp`
67	> PyPI package is unrelated to this project.
68
69	MCP Registry ownership marker: `mcp-name: io.github.genomoncology/biomcp`.
70
71	This installs the `biomcp` binary on your PATH.
72
73	### Homebrew
74
75	```bash
76	brew tap genomoncology/biomcp
77	brew install biomcp
78	```
79
80	The separate `genomoncology/homebrew-biomcp` tap repository must exist before these commands can work.
81
82	### Docker
83
84	```bash
85	docker run --rm ghcr.io/genomoncology/biomcp --version
86	docker run --rm ghcr.io/genomoncology/biomcp list
87	docker run --rm -i ghcr.io/genomoncology/biomcp serve
88	```
89
90	Use the GHCR image for quick CLI checks or stdio MCP clients without a local install.
91
92	### Claude Code plugin
93
94	Install the `biomcp` binary first, then add the hosted plugin marketplace and
95	install the BioMCP plugin in Claude Code:
96
97	```text
98	/plugin marketplace add genomoncology/biomcp
99	/plugin install biomcp@biomcp
100	```
101
102	The plugin wires Claude Code to the local stdio MCP server with `biomcp serve`.
103	For guided BioMCP workflows, also install the skill assets below.
104
105	### Codex MCP server
106
107	Install the `biomcp` binary first, then register the same stdio MCP server with
108	Codex:
109
110	```bash
111	codex mcp add biomcp -- biomcp serve
112	```
113
114	### Claude Desktop extension (.mcpb)
115
116	Install BioMCP from the Anthropic Directory in Claude Desktop when that path is
117	available for your environment. For local/manual setups, use the JSON MCP
118	config below.
119
120	### Install skills
121
122	Install guided investigation workflows into your agent directory:
123
124	```bash
125	biomcp skill install ~/.claude --force
126	```
127
128	### MCP clients
129
130	```json
131	{
132	"mcpServers": {
133	"biomcp": {

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biomcp

2.8kinstalls/mo · pypi554stars109forks

View on GitHub

How to install biomcp?

genomoncology/biomcp

$git clone https://github.com/genomoncology/biomcp

Installs into the current project.

Summary

One binary. One grammar. Evidence from the biomedical sources you already trust.

Files · 1

View on GitHub

README.md

1	# BioMCP
2
3	One binary. One grammar. Evidence from the biomedical sources you already trust.
4
5	## What is BioMCP?
6
7	BioMCP is one CLI binary over a single command grammar that reaches ~30 trusted
8	biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, and
9	more). It is also an MCP (Model Context Protocol) server, so the same tools are
10	available to AI agents such as Claude Code, Codex, and Claude Desktop.
11
12	BioMCP cuts through the usual biomedical data maze: one query reaches the
13	sources that normally live behind different APIs, identifiers, and search
14	habits. Researchers, clinicians, and agents use the same command grammar to
15	search, focus, and pivot without rebuilding the workflow for each source. You
16	get compact, evidence-oriented results across live public data plus local study analytics.
17
18	## Features
19
20	- Search the literature: `search article` fans out across PubTator3 and
21	Europe PMC, deduplicates PMID/PMCID/DOI identifiers, and can add a Semantic
22	Scholar leg when your filters support it.
23	- Pivot without rework: move from a gene, variant, drug, disease, pathway,
24	protein, or article straight into the next built-in view instead of
25	rebuilding filters by hand.
26	- Choose a playbook: `biomcp skill list` shows shipped worked examples
27	so you can open the matching `biomcp skill <slug>` workflow.
28	- Analyze studies locally: `study` commands cover local query, cohort, survival,
29	compare, and co-occurrence workflows with native terminal, SVG, and PNG
30	charts for downloaded cBioPortal-style datasets.
31	- Follow the paper trail: `article citations`, `article references`,
32	`article recommendations`, and `article entities` turn one known paper into a
33	broader evidence map.
34	- Enrich and batch: use `biomcp enrich` for top-level g:Profiler
35	enrichment and `biomcp batch` for up to 10 focused `get` calls in one
36	command.
37
38	## Quick start
39
40	First useful query in under 30 seconds:
41
42	```bash
43	uv tool install biomcp-cli
44	biomcp health --apis-only
45	biomcp skill list
46	biomcp list gene
47	biomcp search all --gene BRAF --disease melanoma # unified cross-entity discovery
48	biomcp get gene BRAF pathways hpa
49	```
50
51	## Installation
52
53	### Binary install
54
55	```bash
56	curl -fsSL https://biomcp.org/install.sh \| bash
57	```
58
59	### PyPI tool install
60
61	```bash
62	uv tool install biomcp-cli
63	# or: pip install biomcp-cli
64	```
65
66	> PyPI package warning: install `biomcp-cli`, not `biomcp`. The `biomcp`
67	> PyPI package is unrelated to this project.
68
69	MCP Registry ownership marker: `mcp-name: io.github.genomoncology/biomcp`.
70
71	This installs the `biomcp` binary on your PATH.
72
73	### Homebrew
74
75	```bash
76	brew tap genomoncology/biomcp
77	brew install biomcp
78	```
79
80	The separate `genomoncology/homebrew-biomcp` tap repository must exist before these commands can work.
81
82	### Docker
83
84	```bash
85	docker run --rm ghcr.io/genomoncology/biomcp --version
86	docker run --rm ghcr.io/genomoncology/biomcp list
87	docker run --rm -i ghcr.io/genomoncology/biomcp serve
88	```
89
90	Use the GHCR image for quick CLI checks or stdio MCP clients without a local install.
91
92	### Claude Code plugin
93
94	Install the `biomcp` binary first, then add the hosted plugin marketplace and
95	install the BioMCP plugin in Claude Code:
96
97	```text
98	/plugin marketplace add genomoncology/biomcp
99	/plugin install biomcp@biomcp
100	```
101
102	The plugin wires Claude Code to the local stdio MCP server with `biomcp serve`.
103	For guided BioMCP workflows, also install the skill assets below.
104
105	### Codex MCP server
106
107	Install the `biomcp` binary first, then register the same stdio MCP server with
108	Codex:
109
110	```bash
111	codex mcp add biomcp -- biomcp serve
112	```
113
114	### Claude Desktop extension (.mcpb)
115
116	Install BioMCP from the Anthropic Directory in Claude Desktop when that path is
117	available for your environment. For local/manual setups, use the JSON MCP
118	config below.
119
120	### Install skills
121
122	Install guided investigation workflows into your agent directory:
123
124	```bash
125	biomcp skill install ~/.claude --force
126	```
127
128	### MCP clients
129
130	```json
131	{
132	"mcpServers": {
133	"biomcp": {

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