Skip to main content
Glama
ncbo

bioportal-mcp

by ncbo
OverviewSchemaRelated ServersScoreDiscussions
Python

Server Quality Checklist

58%
Profile completionA complete profile improves this server's visibility in search results.

  • Latest release: v0.1.1

  • Disambiguation5/5

    Each tool targets a different aspect of BioPortal: analytics for usage data, properties search for ontology properties, and term search for ontology terms. There is no overlap in functionality.

    Naming Consistency5/5

    All tool names follow a consistent verb_noun (snake_case) pattern: get_ontology_analytics, search_ontology_properties, search_ontology_terms.

    Tool Count4/5

    Three tools is on the lower end but reasonable for a focused search and analytics server. The number is appropriate given the scope, though additional tools could be justified.

    Completeness2/5

    The server lacks essential operations for ontology management: no tool to list or retrieve ontologies, no term details beyond search, no mappings or annotations. This leaves significant gaps for typical BioPortal use cases.

  • Average 3.7/5 across 3 of 3 tools scored.

    See the Tool Scores section below for per-tool breakdowns.

    • 0 of 1 community issues answered or closed in the last 6 months
    • 0 commits in the last 12 weeks
    • Last stable release on
    • No critical vulnerability alerts
    • No high-severity vulnerability alerts
    • No code scanning findings
    • CI status not available

  • Add a LICENSE file by following GitHub's guide. Once GitHub recognizes the license, the system will automatically detect it within a few hours.

    If the license does not appear after some time, you can manually trigger a new scan using the MCP server admin interface.

    MCP servers without a LICENSE cannot be installed.

  • This repository includes a README.md file.

  • No tool usage detected in the last 30 days. Usage tracking helps demonstrate server value.

    Tip: use the "Try in Browser" feature on the server page to seed initial usage.

  • Add a glama.json file to provide metadata about your server.

  • If you are the author, simply .

    If the server belongs to an organization, first add glama.json to the root of your repository:

    {
  "$schema": "https://glama.ai/mcp/schemas/server.json",
  "maintainers": [
    "your-github-username"
  ]
}

    Then . Browse examples.

  • Add related servers to improve discoverability.

How to sync the server with GitHub?

Servers are automatically synced at least once per day, but you can also sync manually at any time to instantly update the server profile.

To manually sync the server, click the "Sync Server" button in the MCP server admin interface.

How is the quality score calculated?

The overall quality score combines two components: Tool Definition Quality (70%) and Server Coherence (30%).

Tool Definition Quality measures how well each tool describes itself to AI agents. Every tool is scored 1–5 across six dimensions: Purpose Clarity (25%), Usage Guidelines (20%), Behavioral Transparency (20%), Parameter Semantics (15%), Conciseness & Structure (10%), and Contextual Completeness (10%). The server-level definition quality score is calculated as 60% mean TDQS + 40% minimum TDQS, so a single poorly described tool pulls the score down.

Server Coherence evaluates how well the tools work together as a set, scoring four dimensions equally: Disambiguation (can agents tell tools apart?), Naming Consistency, Tool Count Appropriateness, and Completeness (are there gaps in the tool surface?).

Tiers are derived from the overall score: A (≥3.5), B (≥3.0), C (≥2.0), D (≥1.0), F (<1.0). B and above is considered passing.

Tool Scores

  • Behavior2/5

    Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

    With no annotations, the description carries full burden. It does not disclose any behavioral traits like case sensitivity, pagination, performance implications, or side effects. The schema provides some details but the description adds little beyond the basic search operation.

    Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

    Conciseness5/5

    Is the description appropriately sized, front-loaded, and free of redundancy?

    The description is two sentences, concise, and front-loaded with the purpose. Every sentence adds value without redundancy.

    Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

    Completeness2/5

    Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

    Given the absence of annotations and the presence of an output schema, the description should provide more contextual completeness about usage and behavior. It lacks guidelines and behavioral details, making it insufficient for full understanding.

    Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

    Parameters3/5

    Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

    Schema description coverage is 100%, so baseline is 3. The description does not add any additional meaning beyond the schema; it only mentions the return format. No extra parameter context.

    Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

    Purpose5/5

    Does the description clearly state what the tool does and how it differs from similar tools?

    The description clearly states the tool searches for ontology terms in BioPortal and specifies the return format (list of tuples with term ID, label, ontology, URL). It distinguishes from siblings like get_ontology_analytics and search_ontology_properties by focusing on term search.

    Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

    Usage Guidelines2/5

    Does the description explain when to use this tool, when not to, or what alternatives exist?

    The description provides no guidance on when to use this tool versus alternatives, no exclusions, and no context about prerequisites or limitations. It only describes the basic function.

    Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

  • Behavior3/5

    Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

    With no annotations, the description must disclose behavior fully. It describes that it retrieves analytics data but does not mention authentication, rate limits, or side effects. However, the tool is read-only and the API key parameter is in the schema, so basic transparency is adequate.

    Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

    Conciseness5/5

    Is the description appropriately sized, front-loaded, and free of redundancy?

    The description is two sentences with no redundant words. The first sentence states the purpose, and the second elaborates on usage, making it front-loaded and efficient.

    Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

    Completeness4/5

    Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

    The description covers the main functionalities: retrieving analytics for all or specific ontologies with optional time filters. An output schema exists, so return values are documented separately. No missing critical aspects for this simple tool.

    Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

    Parameters3/5

    Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

    Schema coverage is 100%, so the baseline is 3. The description summarizes parameter usage (filter by month/year, specific ontology) but adds no new details beyond the schema descriptions. Thus, it does not exceed the baseline.

    Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

    Purpose5/5

    Does the description clearly state what the tool does and how it differs from similar tools?

    The description clearly states it gets visitor analytics for BioPortal ontologies. It specifies three modes: all ontologies, filtered by month/year, or for a specific ontology. This distinguishes it from sibling tools which search properties and terms.

    Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

    Usage Guidelines4/5

    Does the description explain when to use this tool, when not to, or what alternatives exist?

    The description provides clear usage context: it can retrieve analytics for all ontologies, filter by month/year, or get detailed analytics for a specific ontology. However, it does not explicitly state when not to use it or compare with alternatives, though the alternatives are unrelated.

    Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

  • Behavior3/5

    Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

    No annotations provided, so description bears full burden. It states it searches by labels and IDs but lacks details on idempotency, side effects, or expected response specifics. Output schema exists, reducing need to explain return values, but behavioral traits like rate limits or necessary permissions are omitted.

    Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

    Conciseness5/5

    Is the description appropriately sized, front-loaded, and free of redundancy?

    Two sentences, no redundant information, clear and direct.

    Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

    Completeness4/5

    Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

    Given the tool's complexity (7 parameters, output schema), the description covers the core purpose and adds context on property types and scope. Could mention relationship to sibling tool for differentiation, but overall adequate.

    Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

    Parameters4/5

    Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

    Schema coverage 100% with detailed parameter descriptions. Description adds value by specifying that search is by labels and IDs, which is not in schema. This clarifies the search mechanism.

    Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

    Purpose5/5

    Does the description clearly state what the tool does and how it differs from similar tools?

    Description clearly states it searches for ontology properties, lists types (object, annotation, datatype), and mentions operation across BioPortal ontologies. Distinguishes from sibling tools which are analytics and term search.

    Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

    Usage Guidelines3/5

    Does the description explain when to use this tool, when not to, or what alternatives exist?

    Description gives context but does not provide explicit guidance on when to use this tool over siblings, nor does it mention conditions where it should not be used.

    Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

GitHub Badge

Glama performs regular codebase and documentation scans to:

  • Confirm that the MCP server is working as expected.
  • Confirm that there are no obvious security issues.
  • Evaluate tool definition quality.

Our badge communicates server capabilities, safety, and installation instructions.

Card Badge

bioportal-mcp MCP server

Copy to your README.md:

Score Badge

bioportal-mcp MCP server

Copy to your README.md:

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/ncbo/bioportal-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server