Bioportal vs Hpo Api
A side-by-side look at the Bioportal and Hpo Api MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Bioportal for biology, medicine and bioinformatics work as a local process; choose Hpo Api for biology, medicine and bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Bioportal when
- You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
- You prefer a local stdio subprocess transport.
Choose Hpo Api when
- You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
term, search, term_children.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 41/100 · Fair | 60/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner |
Tools & capabilities
Bioportal tools
No tool names declared yet. Check the project README from the listing page.
Hpo Api tools 7
term"What does HP:[N] mean" / "look up HPO phenotype [ID]" — fetch a single Human Phenotype Ontology (HPO) term by ID. HPO is the standard ontology for clinical phenotypes used in rare-disease research. Returns label, definition, synonyms, cross-references. Example ID: HP:0001250 (Seizure).search"HPO term for [symptom]" / "phenotype code for [clinical sign]" / "find HPO IDs about [feature]" / "what's the HPO for seizures / autism / short stature" — text search the Human Phenotype Ontology (HPO). Returns ranked terms with HP: IDs. Use to map clinical descriptions to standard ontology terms for rare-disease workups, genomics, or clinical phenotype databases.term_children"More specific HPO phenotypes under [HP:N]" / "child terms of [phenotype]" — direct children of an HPO term in the ontology graph. Use to narrow from a general phenotype (e.g. "Abnormality of the nervous system") to specifics (seizures, ataxia, etc).term_parents"What broader phenotype is [HP:N] under" / "parent term of [HPO ID]" — direct parents of an HPO term in the ontology graph. Use to walk up to a more general phenotype class.term_descendants"All phenotypes under [HP:N]" / "full subtree of [HPO term]" — transitive descendants (children, grandchildren, …) of an HPO term. Use for exhaustive coverage (e.g. "every cardiac phenotype" via descendants of HP:0001626).gene_diseases"What diseases is gene [NCBIGene:N] associated with" / "diseases linked to gene [X]" / "TP53 disease associations" — fetch diseases associated with a gene ID (NCBIGene:N format). Use for gene-to-disease lookups in rare-disease research, variant prioritization. Example ID: NCBIGene:7157 (TP53).disease_phenotypes"What symptoms / clinical features does [disease] cause" / "HPO phenotypes for [OMIM N]" / "clinical signs of [rare disease]" — list HPO phenotype terms for a disease ID (OMIM:N, ORPHA:N, or MONDO:N format). Use to enumerate clinical features of rare diseases. Example ID: OMIM:154700 (Marfan syndrome).
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.
Bioportal
{
"mcpServers": {
"bioportal": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-bioportal"
]
}
}
}
Hpo Api
{
"mcpServers": {
"hpo-api": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-hpo-api"
]
}
}
}
Frequently asked questions
Bioportal is categorized under Biology, Medicine and Bioinformatics and uses a local stdio subprocess. Hpo Api belongs to Biology, Medicine and Bioinformatics and uses a local stdio subprocess. Pick Bioportal for biology, medicine and bioinformatics work and Hpo Api for biology, medicine and 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.
Bioportal has no declared pricing — check the project's own site. Hpo Api has no declared pricing — check the project's own site. 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 bioportal and hpo-api as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Bioportal has a quality signal of 41/100 (Fair) with 1 views, 0 installs and 0 GitHub stars. Hpo Api has 60/100 (Good) with 3 views, 0 installs and 0 GitHub stars.