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Glama

Server Details

Biotech intelligence for AI agents: drugs, targets, diagnostics, PoS estimates, and writeups.

Status
Healthy
Last Tested
Transport
Streamable HTTP
URL

Glama MCP Gateway

Connect through Glama MCP Gateway for full control over tool access and complete visibility into every call.

MCP client
Glama
MCP server

Full call logging

Every tool call is logged with complete inputs and outputs, so you can debug issues and audit what your agents are doing.

Tool access control

Enable or disable individual tools per connector, so you decide what your agents can and cannot do.

Managed credentials

Glama handles OAuth flows, token storage, and automatic rotation, so credentials never expire on your clients.

Usage analytics

See which tools your agents call, how often, and when, so you can understand usage patterns and catch anomalies.

100% free. Your data is private.
Tool DescriptionsA

Average 3.8/5 across 13 of 13 tools scored. Lowest: 3.2/5.

Server CoherenceA
Disambiguation4/5

Tools have mostly distinct purposes, though get_node and get_pos_score both provide probability-of-success data (get_node includes a summary, get_pos_score gives detailed factors). Descriptions clarify the difference, so confusion is minimal.

Naming Consistency4/5

Naming follows a verb_noun pattern but mixes verbs: 'find', 'get', 'list', 'search'. Within the 'get' group, all are consistent. The mix is not chaotic and remains predictable.

Tool Count5/5

13 tools cover the biomedical domain well without being excessive. Each tool has a clear purpose, from searching and listing to fetching detailed node data, statistics, and specialized reports.

Completeness5/5

For a read-only database, the tool set is complete. It supports search, filtered queries, detailed node retrieval, specialized data (PoS, freshness, staleness), and statistics. No obvious gaps for typical query needs.

Available Tools

13 tools
find_by_phaseAInspect

List drugs/diagnostics at a specific clinical phase.

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum results (default 100, max 500)
phaseYesOne of "approved", "on_market", "phase3", "phase2", "phase1", "in_development", "cleared", "ldt", "ruo"
node_typeNoOptional filter — "drug", "pipeline", "diagnostic", "target"

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior3/5

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

No annotations are provided, so the description carries full burden. It states the tool 'lists' items (implying read-only), but does not disclose pagination behavior, sorting, or whether results include full node details. The output schema covers return format, but behavioral traits like rate limits or data freshness are absent.

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

Conciseness4/5

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

The description is a single sentence with no wasted words. It efficiently conveys the core purpose. However, it is extremely minimal and could include additional context without becoming verbose.

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

Completeness3/5

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

Given the rich input schema (100% coverage, 3 parameters) and presence of an output schema, the description is adequate. However, it lacks usage guidelines and behavioral transparency, which reduces completeness for an AI agent selecting the 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 description coverage is 100%, so the baseline is 3. The description adds no meaning beyond the schema: 'at a specific clinical phase' echoes the phase parameter description. No extra context is provided for 'limit' or 'node_type'.

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 verb 'List' and the resource 'drugs/diagnostics' with a specific filtering criterion ('at a specific clinical phase'). It distinguishes from sibling tools like 'find_by_target' or 'list_by_therapeutic_area' by specifying the phase focus.

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?

The description implies usage when filtering by clinical phase, but provides no explicit guidance on when to use this tool versus alternatives (e.g., 'find_by_target'), nor does it state when not to use it. No exclusions or prerequisites are mentioned.

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

find_by_targetBInspect

Find all drugs that target a specific gene/protein.

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum results (default 50, max 200)
target_geneYesGene symbol or target name (e.g. "EGFR", "KRAS", "PD-1")

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior2/5

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

No annotations are provided, so the description carries full burden. It does not disclose whether the operation is read-only, any rate limits, pagination behavior, or the maximum number of results (though the input schema indicates a limit parameter). This lack of transparency could lead to incorrect usage.

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 a single, concise sentence that front-loads the purpose. Every word is necessary, and there is no fluff or redundancy.

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

Completeness3/5

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

The description covers the core purpose but lacks details on limits, sorting, or result format. While the output schema exists, the description could provide more context for effective use, especially given the number of sibling tools.

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% (both parameters have descriptions). The tool description adds no new information beyond the schema. Per rule, baseline is 3 when coverage is high.

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 verb 'Find', the resource 'drugs', and the criterion 'target a specific gene/protein'. It is concise and distinct from sibling tools like 'find_by_phase' which filters by clinical phase.

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. It does not mention when not to use it or suggest any alternatives, despite the presence of 13 sibling tools with overlapping functionality.

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

get_company_portfolioBInspect

Get a company's full drug/diagnostic portfolio from BioCosm.

ParametersJSON Schema
NameRequiredDescriptionDefault
company_nameYesCompany name (e.g. "Merck", "Roche", "Illumina")

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior2/5

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

With no annotations provided, the description must disclose behavioral traits. It only states 'Get a company's full drug/diagnostic portfolio' but does not mention whether the operation is read-only, what data is returned (e.g., pipeline includes preclinical? approved?), or if any side effects occur. The lack of detail limits transparency.

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

Conciseness4/5

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

The description is a single, efficient sentence that gets straight to the point. However, it is so brief that it omits potentially useful context, which would not harm length. It earns a high score for lack of redundancy but could be slightly more informative without losing conciseness.

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

Completeness3/5

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

Given the tool's simplicity (one parameter, output schema exists), the description is minimally adequate. The output schema likely provides structure, but the description does not clarify the scope of 'full portfolio' (e.g., including diagnostics? all phases?). This ambiguity slightly lowers completeness.

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% (one parameter with a clear example). The tool description adds no extra meaning beyond the schema's own description of 'company_name.' Per the scoring rule, a baseline of 3 is appropriate when coverage is high and description doesn't enhance it.

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 verb and resource: 'Get a company's full drug/diagnostic portfolio.' It is specific and distinct from sibling tools like 'find_by_phase' or 'find_by_target' which focus on more granular queries. The name also reinforces the purpose.

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?

No guidance on when to use this tool vs alternatives (e.g., when to use 'search_nodes' or 'get_coverage'). The description lacks any context about prerequisites, exclusions, or typical use cases, leaving the agent to infer solely from the command name.

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

get_coverageAInspect

Report BioCosm's actual data coverage so you never mistake missing data for a real-world zero. An empty or absent field on a node means "not in BioCosm's data," never a true zero. BioCosm is AI-generated and may contain errors.

ParametersJSON Schema
NameRequiredDescriptionDefault

No parameters

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

Behavior3/5

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

No annotations are provided, so the description must carry the behavioral transparency burden. It adds the caveat that BioCosm is AI-generated and may contain errors, but does not elaborate on the tool's behavior beyond reporting coverage, such as whether it is read-only or the scope of coverage.

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 extremely concise with two sentences. The first sentence delivers the purpose and benefit, and the second adds a necessary caveat. Every word earns its place, with no wasted text.

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 is fairly complete given the tool's simplicity and the existence of an output schema. It explains the critical interpretation of coverage data, though it could be slightly more explicit about what the coverage report contains (e.g., per field or per node).

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?

The tool has no parameters, and schema coverage is 100% (trivially). According to the rubric, the baseline for 0 parameters is 4, and the description adds no further parameter information since none are needed.

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's purpose: 'Report BioCosm's actual data coverage'. It uses a specific verb and resource, and distinguishes itself from sibling tools like get_node or get_stats by focusing on coverage rather than node content or statistics.

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 explains when to use the tool implicitly: 'so you never mistake missing data for a real-world zero'. This provides clear context on the tool's utility, but it does not explicitly state when not to use it or mention alternatives among siblings.

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

get_nodeAInspect

Get full details for a single BioCosm node: identity and all name aliases, classification, gene targets and mechanism, therapeutic areas, companies, revenue history where available (sparse: ~100 drugs, mostly blockbusters, as annualized quarterly estimates; source links when present), probability-of- success predictions for pipeline drugs (with confidence intervals and contributing factors), structured clinical trial outcomes, external cross-references, and writeup availability. Empty fields mean "not in BioCosm's coverage," NOT zero or absent in reality.

ParametersJSON Schema
NameRequiredDescriptionDefault
node_idYesThe node identifier (e.g. "pembrolizumab", "trastuzumab")

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior5/5

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

With no annotations, the description fully carries behavioral disclosure. It details all returned fields, notes sparsity of revenue data, explains that empty fields mean not in coverage rather than zero, and mentions source links and writeup availability. No destructive side effects implied.

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

Conciseness4/5

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

The description is well-structured with a clear overview followed by a detailed list and a usage note. While slightly long, every sentence adds value and there is no redundancy.

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

Completeness5/5

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

Given the simple input (one parameter) and presence of an output schema, the description is complete. It explains what the tool returns in detail, leaving no obvious gaps for an agent to understand its functionality.

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?

The only parameter (node_id) is fully described in the schema with 100% coverage. The description adds context that the node is a 'single BioCosm node' but no extra syntax or semantics beyond the schema, warranting baseline 3.

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 retrieves full details for a single BioCosm node, listing specific data fields like aliases, classifications, revenue history, etc. It distinguishes from sibling tools by being comprehensive and node-specific.

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?

The description implies usage for retrieving all details of a specific node, but does not explicitly state when to use versus alternatives like search_nodes or get_pos_score. The note about empty fields provides some guidance but lacks explicit when-to/not-to-use instructions.

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

get_node_freshnessAInspect

Get freshness details for a single node: writeup age, enrichment hash match, staleness score, validation score.

ParametersJSON Schema
NameRequiredDescriptionDefault
node_idYesThe node identifier (e.g. "pembrolizumab")

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior2/5

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

No annotations provided, so the description must disclose behavioral traits. It lists output fields but does not mention read/write safety, authentication needs, rate limits, or behavior on invalid input (e.g., missing node). The output schema exists but the description adds no behavioral context.

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?

Single sentence, front-loaded with key purpose and output details. Every word is relevant and there is no wasted text.

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

Completeness3/5

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

For a simple 1-param tool with output schema, the description is mostly adequate but lacks usage guidelines and behavioral transparency. Could be improved by specifying when to use this vs siblings and any side effects.

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%, baseline of 3. The description does not add additional meaning beyond what the schema provides; the schema already describes node_id with example 'pembrolizumab'. No enrichment.

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's action ('Get freshness details for a single node') and lists the specific fields returned (writeup age, enrichment hash match, staleness score, validation score). This distinguishes it from siblings like 'get_node' (node info) and 'get_staleness_report' (broader report).

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?

No explicit guidance on when to use this tool versus alternatives. Usage is implied by the description, but there is no mention of exclusions or when to prefer it over similar tools like 'get_node' or 'get_coverage'.

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

get_pos_scoreAInspect

Get the Probability of Success estimate for a node, including the base rate, adjustment factors with reasoning, confidence interval, and model version.

Returns None for nodes without a PoS score (typically only late-stage pipeline drugs are scored).

ParametersJSON Schema
NameRequiredDescriptionDefault
node_idYesNode identifier

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior4/5

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

Without annotations, the description fully discloses the return value details (components of PoS) and the None case. It provides transparency about what the tool does beyond a simple read 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?

Two sentences, no redundant information. Every part adds value: first sentence states purpose and output contents, second covers the edge case.

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 single required parameter and existing output schema, the description covers the tool's behavior sufficiently. It could mention the expected node type, but it's adequate for selection and invocation.

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% for node_id, and the description adds no additional semantic information about the parameter. The baseline of 3 is appropriate as the schema already describes the parameter.

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 retrieves the Probability of Success estimate for a node, listing specific components (base rate, adjustment factors, etc.) and mentioning when it returns None. This distinguishes it from sibling tools like 'get_node' or 'get_writeup'.

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?

It explicitly notes that nodes without a PoS score return None, typically for early-stage drugs, implying when the tool is not useful. No explicit alternatives are given, but the context is clear.

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

get_staleness_reportAInspect

Get writeup staleness report: overall stats, top stale nodes, data source freshness.

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNoNumber of top stale nodes to return (default 20)

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

Behavior3/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It mentions the output includes overall stats, top stale nodes, and data source freshness, but does not specify side effects, idempotency, or access requirements. The presence of an output schema partially compensates, making this minimal but 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 a single compact sentence with no redundancy. It efficiently conveys the tool's function and main outputs, earning its place without filler.

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 low complexity (1 optional parameter, output schema exists), the description adequately covers the tool's purpose and output categories. However, it lacks any usage context relative to sibling tools, which slightly reduces completeness.

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?

The single parameter 'limit' is fully documented in the input schema with description and default. The description adds no additional semantics beyond that, so baseline 3 is appropriate given 100% schema coverage.

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 explicitly states the tool retrieves a writeup staleness report with overall stats, top stale nodes, and data source freshness. The verb 'Get' and resource 'writeup staleness report' are clear, and the scope is well-defined, distinguishing it from sibling tools like find_by_phase or get_node_freshness.

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. It does not mention prerequisites, conditions, or contrast with related tools such as get_stats, get_node_freshness, or find_related, leaving the agent to infer usage context.

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

get_statsAInspect

Get a high-level overview of the BioCosm database: total nodes, writeups, companies, breakdowns by type/status/domain, validation scores, and recent pipeline runs.

ParametersJSON Schema
NameRequiredDescriptionDefault

No parameters

Output Schema

ParametersJSON Schema
NameRequiredDescription

No output parameters

Behavior3/5

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

While the description lists output contents, it lacks details on authorization, caching, or data freshness. Without annotations, more behavioral disclosure is expected.

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?

A single, information-dense sentence with no redundancy. The structure is efficient and front-loaded.

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

Completeness5/5

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

With zero parameters and an output schema present, the description adequately covers the tool's function and return data, leaving no gaps.

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?

No parameters exist, so the description does not need to add parameter meaning. Baseline 4 is appropriate.

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 retrieves a 'high-level overview' listing specific data elements (total nodes, writeups, companies, etc.), distinguishing it from sibling tools that handle individual entities.

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?

The description implies usage for aggregate overviews but does not explicitly state when to avoid this tool in favor of siblings like get_node or search_nodes.

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

get_writeupAInspect

Get the full writeup for a BioCosm node, including all sections, citations, structured data, and validation score.

ParametersJSON Schema
NameRequiredDescriptionDefault
node_idYesThe node identifier (e.g. "pembrolizumab")

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior2/5

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

No annotations are provided, so the description must carry behavioral disclosure. It does not mention any side effects, authentication needs, rate limits, or whether the operation is read-only. The read nature is implied but not explicit.

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 a single, well-structured sentence with no redundancy. Every word adds value, making it highly concise.

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 presence of an output schema and high schema coverage, the description is fairly complete. It explains what the tool returns but could mention prerequisites (e.g., existence of node) or error handling. Still very good.

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%, and the parameter 'node_id' is described in the schema. The tool description does not add additional meaning or usage tips beyond the schema, so it meets 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 specifies the action ('Get') and the resource ('full writeup'), and details what is included (sections, citations, structured data, validation score). It effectively distinguishes from siblings like 'get_node' and 'get_pos_score' by focusing on the full writeup.

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?

The description does not explicitly state when to use this tool versus alternatives like 'get_node' or 'search_nodes'. While it implies usage for obtaining the full writeup, it lacks explicit exclusions or comparative guidance.

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

list_by_therapeutic_areaBInspect

List all nodes in a given therapeutic area.

ParametersJSON Schema
NameRequiredDescriptionDefault
areaYesTherapeutic area to search (e.g. "breast cancer", "non-small cell lung cancer")
limitNoMaximum results (default 50)

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior2/5

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

The description implies a read operation ('list') but does not disclose any behavioral traits such as authentication requirements, rate limits, or pagination behavior. Since no annotations are provided, the description should carry this burden but falls short.

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

Conciseness4/5

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

The description is a single, clear sentence that front-loads the purpose. While concise, it could include more detail without being verbose, but it is not wasteful.

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

Completeness3/5

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

Given the tool's simplicity and the presence of an output schema, the description is minimally adequate. However, it lacks context about what 'nodes' are or how they relate to therapeutic areas, which could help an agent better understand the tool's role among many siblings.

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?

Input schema covers both parameters (area and limit) with descriptions and an example for area. Schema description coverage is 100%, so the description adds no value beyond the schema, yielding a baseline score of 3.

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 'List all nodes in a given therapeutic area', using a specific verb and resource, and distinguishes from sibling tools like find_by_phase and search_nodes.

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?

No explicit guidance on when to use this tool versus alternatives. The description only mentions a therapeutic area parameter without indicating when not to use it or providing context for selection among siblings.

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

search_nodesAInspect

Search BioCosm nodes by name, gene symbol, target, therapeutic area, or company.

Results are ranked: exact name/brand matches first, then partial name matches, with a node-type prior (canonical drug/diagnostic nodes rank above gene-target nodes, which rank above ChEMBL salt-form duplicates). Nodes matched only via description/company/area rank last. Each result includes a name field for disambiguation.

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum results to return (default 20, max 100)
queryYesSearch term (e.g. "breast cancer", "pembrolizumab", "Merck")

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes
Behavior4/5

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

With no annotations provided, the description effectively discloses the ranking algorithm (exact matches first, then partial, with node-type priors) and confirms the presence of a 'name' field. It stops short of mentioning rate limits or authentication, but covers the most critical behavioral aspects.

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 concise with two clear paragraphs: the first states purpose, the second details ranking. Every sentence adds value, and there is no redundant or filler content.

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

Completeness5/5

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

Given the presence of an output schema, the description covers all essential aspects: search scope, ranking behavior, and the existence of a 'name' field for disambiguation. No important gaps remain for a search tool of this complexity.

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 is 100%, so the baseline is 3. The description adds concrete examples for the query parameter (e.g., 'breast cancer', 'pembrolizumab', 'Merck') and explains the fields searched, providing meaningful context beyond the schema's generic 'Search term'.

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 BioCosm nodes by multiple fields (name, gene symbol, target, therapeutic area, or company), matching a specific verb+resource pattern. It distinguishes itself from siblings like find_by_target by offering a broad, combined 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?

No explicit guidance is provided about when to use this tool versus its siblings (find_by_target, find_by_phase, etc.). The description implies it's a general search but fails to state alternatives or when not to use it.

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

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