Pubchem MCP Server vs Medical Terminologies MCP
A side-by-side look at the Pubchem MCP Server 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 Pubchem MCP Server for biology & bioinformatics work; 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 Pubchem MCP Server when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- Its auth model fits you: No auth required.
- You want tools like
pubchem_search_compounds, pubchem_get_compound_details, pubchem_get_compound_image.
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 | 55/100 · Good | 68/100 · Great |
| Install command | Not confirmed yet | Confirmed |
| Transport | — | Local subprocess (stdio) |
| Auth | No auth required | API key required |
| Pricing | Free | Free |
| Required env vars | None listed | WHO_CLIENT_IDWHO_CLIENT_SECRETWHO_ICD11_RELEASE_ID |
| Verified owner | Community listing | Community listing |
| GitHub stars | 10 | 15 |
| Directory activity | 2 views 0 installs 0 upvotes | 4 views 0 installs 0 upvotes |
| Tools | 10 | 33 |
| Full listing | View Pubchem MCP Server | View Medical Terminologies MCP |
Tools & capabilities
Pubchem MCP Server tools 10
pubchem_search_compoundsSearch for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity, or list the compounds a bioassay found active.pubchem_get_compound_detailsGet physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.pubchem_get_compound_imageFetch a 2D structure diagram (PNG) for a compound by CID.pubchem_get_compound_3d_structureFetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.pubchem_get_compound_xrefsGet external database cross-references (PubMed, patents, genes, proteins, etc.).pubchem_get_compound_safetyGet GHS hazard classification and safety data for one or more compounds by CID (batch).pubchem_get_bioactivityGet a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.pubchem_get_compound_interactionsGet drug-drug, drug-food, and chemical-target interactions for a compound by CID.pubchem_search_assaysFind bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).pubchem_get_summaryGet summaries for PubChem entities: assays, genes, proteins, taxonomy.
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.
Pubchem MCP Server
No confirmed install command for Pubchem MCP Server yet — follow the setup steps linked from its listing page rather than a guessed package name.
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
Pubchem MCP Server is categorized under Biology & Bioinformatics and uses an install path we have not confirmed yet. Medical Terminologies MCP belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Pubchem MCP Server 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. Pubchem MCP Server has no confirmed install command yet — follow its own setup instructions.
Pubchem MCP Server is listed as free. Auth: no auth required. 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 pubchem-mcp-server and sidneybissoli-medical-terminologies-mcp as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Pubchem MCP Server has a quality signal of 55/100 (Good) with 2 views, 0 installs and 10 GitHub stars. Medical Terminologies MCP has 68/100 (Great) with 4 views, 0 installs and 15 GitHub stars.