Galaxy MCP vs Medical Terminologies MCP
A side-by-side look at the Galaxy MCP and Medical Terminologies MCP MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Galaxy MCP for biology & bioinformatics work as a local process; choose Medical Terminologies MCP for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Galaxy MCP when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
connect, search_tools_by_name, get_tool_details.
Choose Medical Terminologies MCP when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: API key required.
- You have the keys it needs:
WHO_CLIENT_ID, WHO_CLIENT_SECRET, WHO_ICD11_RELEASE_ID. - You want tools like
icd11_search, icd11_lookup, icd11_hierarchy.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 61/100 · Good | 68/100 · Great |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | API key required |
| Pricing | Not declared | Free |
| Required env vars | None listed | WHO_CLIENT_IDWHO_CLIENT_SECRETWHO_ICD11_RELEASE_ID |
| Verified owner | Community listing | Community listing |
| GitHub stars | 39 | 15 |
| Directory activity | 1 views 0 installs 0 upvotes | 4 views 0 installs 0 upvotes |
| Tools | 48 | 33 |
| Full listing | View Galaxy MCP | View Medical Terminologies MCP |
Tools & capabilities
Galaxy MCP tools 48
connectConnect to Galaxy serversearch_tools_by_nameSearch Galaxy tools whose name, ID, or description contains the given query (substring match). Results are paginated. pagination.total_items is how many tools matched in total; pagination.next_offset is where the next page starts (None on the last page). RECOMMENDED WORKFLOW: 1. Use this function to find tools by name/keyword 2. Review the returned tool IDs and names 3. Call get_tool_details(tool_id) for full input parameters 4. Call run_tool() with the correct inputsget_tool_detailsGet detailed information about a specific tool including its input parameters. RECOMMENDED WORKFLOW: 1. First find tools using search_tools_by_name() or get_tool_panel() 2. Call this function with io_details=True to see all input parameters 3. Use the inputs schema to construct the inputs dict for run_tool()get_tool_run_examplesReturn the exact XML test definitions (inputs, outputs, assertions, required files) for a Galaxy tool so an LLM can study real, working run configurations.get_tool_input_templateReturn a ready-to-fill ``inputs`` skeleton for a tool, plus a compact schema. Call this before run_tool when you are unsure how to shape ``inputs``. Replace placeholders (e.g. ``<dataset_id>``) with real values. Repeats show one instance (``name_0|...``); duplicate with ``name_1|...`` to add more. The flattened-key convention is ``section|param``, ``cond|selector``, ``repeat_0|param``.get_tool_citationsGet citation information for a specific toolrun_toolRun a Galaxy tool on datasets in a history. RECOMMENDED WORKFLOW: 1. Create or select a history: create_history() or get_histories() 2. Upload data: upload_file() or upload_file_from_url() 3. Get tool parameters: get_tool_details(tool_id, io_details=True) 4. Call this function with properly formatted inputs 5. Monitor job: get_job_details() or check history contentsget_tool_panelBrowse the Galaxy tool panel (toolbox) one level at a time. The whole panel is megabytes on a production server, so it is never returned whole. Called with no arguments this lists the top-level entries - each section with the number of tools in it, plus any tools that sit outside a section. Pass section_id to list the tools in one section.create_historyCreate a new history to organize datasets and analyses. A history is the primary workspace in Galaxy. Create a new history for each distinct project or analysis to keep your work organized. RECOMMENDED WORKFLOW: 1. Create a history with a descriptive name 2. Upload your input data: upload_file() or upload_file_from_url() 3. Run tools on the data: run_tool() 4. View results: get_history_contents()update_historyUpdate an existing Galaxy history's metadata. Any combination of name, annotation, tags, deleted, and published can be updated in a single call. Fields left as None are not modified.search_tools_by_keywordsRecommend Galaxy tools based on a list of keywords. Matches on name and description first, then on accepted input formats, and keeps that order so paging is stable. Results are paginated: pagination.total_items is the full match count, pagination.next_offset is where the next page starts. Expensive: finding the format matches costs one detail lookup per tool that did not match by name, and every page repeats the whole scan. Prefer search_tools_by_name when a name or description substring will do.get_server_infoGet Galaxy server information including version, URL, and configuration details Also reports which tools this server is too old to run, in `unsupported_tools`, and whether its version could be read at all, in `version_known` -- an empty `unsupported_tools` means nothing is ruled out only when `version_known` is true. Returns: GalaxyResult with server information in data field- +36 more on the listing page
Medical Terminologies MCP tools 33
icd11_searchSearch for medical conditions, diseases, and health problems in ICD-11 (International Classification of Diseases, 11th Revision). Use this tool to: - Find ICD-11 codes for diagnoses - Search for diseases by name or keyword - Look up conditions in multiple languages Set `language` for WHO's official translations — e.g. `language: "pt"` searches and returns the official Portuguese (pt-BR) ICD-11 labels. Never machine-translated. Returns matching entities with codes, titles, and relevance scores.icd11_lookupGet detailed information about a specific ICD-11 entity by code or URI. Use this tool to: - Get the full definition of a disease - Retrieve coding notes and exclusions - Get the official title and synonyms Provide either an ICD-11 code (e.g., "BA00") or a full foundation URI. Set `language` for WHO's official translations (e.g. `language: "pt"` for official Portuguese).icd11_hierarchyNavigate the ICD-11 hierarchy to find parent or child entities. Use this tool to: - Find broader categories (parents) of a condition - Find specific subtypes (children) of a condition - Understand the classification structure Name the entity by `code` (a leaf code like "5A11", or a block range like "5A10-5A2Y" — blocks come back from 'parents' with an empty code and a code_range) or by `uri` (the URI any previous answer returned). Direction 'parents' returns ancestor categories, 'children' returns subcategories. ICD-10 codes (like "E11") are not ICD-11 codes: convert them first with map_icd10_to_icd11.icd11_chaptersList all ICD-11 chapters (top-level categories). Use this tool to: - Get an overview of ICD-11 structure - Find which chapter covers a body system or condition type - Navigate to specific disease categories ICD-11 has 28 chapters covering all areas of medicine.icd11_postcoordinationGet postcoordination information for an ICD-11 code. Use this tool to: - Find available axes for building composite codes - Check required vs optional postcoordination - Understand code extension possibilities Postcoordination allows adding severity, laterality, anatomy, etc.loinc_searchSearch for laboratory tests, clinical observations, and measurements in LOINC (Logical Observation Identifiers Names and Codes). Use this tool to: - Find LOINC codes for lab tests (e.g., "glucose", "hemoglobin") - Search for clinical measurements and vital signs - Look up diagnostic observations Returns matching LOINC codes with names, components, and properties.loinc_detailsGet detailed information about a specific LOINC code. Use this tool to: - Get the full name and description of a LOINC code - Find the component, property, timing, and system - Check the scale type and method Provide a LOINC number in format "XXXXX-X" (e.g., "2339-0" for Glucose).loinc_answersGet the list of valid answers for a LOINC questionnaire item. Use this tool to: - Find valid response options for survey questions - Get answer codes for data entry validation - Look up standardized answer lists Only applicable to LOINC codes that represent questions with defined answer sets.loinc_panelsGet the structure of a LOINC panel or form. Use this tool to: - See all tests included in a panel (e.g., CBC, metabolic panel) - Get the structure of assessment forms - Find related observations grouped together Returns the list of LOINC codes that make up the panel.rxnorm_searchSearch for drugs in RxNorm (Normalized names for clinical drugs). Use this tool to: - Find drug concepts by brand or generic name - Look up medications for prescribing - Search for drug formulations Returns matching drugs with RxCUI identifiers, names, and term types.rxnorm_conceptGet detailed information about a specific RxNorm concept by RxCUI. Use this tool to: - Get the full name and synonyms for a drug - Check the concept status (active, remapped, etc.) - View related concepts (ingredients, brands, forms) Provide an RxCUI (RxNorm Concept Unique Identifier) like "161".rxnorm_ingredientsGet active ingredients for a drug by RxCUI. Use this tool to: - Find the active ingredients in a medication - Check for single vs. multiple ingredient products - Identify the generic components of brand drugs Returns ingredient RxCUIs and names.- +21 more on the listing page
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Galaxy MCP
{
"mcpServers": {
"galaxy-mcp": {
"command": "uvx",
"args": [
"galaxy-mcp"
]
}
}
}
Medical Terminologies MCP
{
"mcpServers": {
"sidneybissoli-medical-terminologies-mcp": {
"command": "npx",
"args": [
"-y",
"medical-terminologies-mcp"
],
"env": {
"WHO_CLIENT_ID": "YOUR_WHO_CLIENT_ID_HERE",
"WHO_CLIENT_SECRET": "YOUR_WHO_CLIENT_SECRET_HERE",
"WHO_ICD11_RELEASE_ID": "YOUR_WHO_ICD11_RELEASE_ID_HERE"
}
}
}
}
Frequently asked questions
Galaxy MCP is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Medical Terminologies MCP belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Galaxy MCP for biology & bioinformatics work and Medical Terminologies MCP for biology & bioinformatics.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Galaxy MCP has no declared pricing — check the project's own site. Medical Terminologies MCP is listed as free. Auth: api key required. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add galaxy-mcp and sidneybissoli-medical-terminologies-mcp as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Galaxy MCP has a quality signal of 61/100 (Good) with 1 views, 0 installs and 39 GitHub stars. Medical Terminologies MCP has 68/100 (Great) with 4 views, 0 installs and 15 GitHub stars.