Biomedical Data
Server Details
Biomedical data: compounds, drug info, and molecular targets
- Status
- Healthy
- Last Tested
- Transport
- Streamable HTTP
- URL
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Tool Definition Quality
Average 3.5/5 across 3 of 3 tools scored.
Each tool targets a distinct data source and type: PubChem for compound data, OpenFDA for drug safety/label info, and ChEMBL for target and bioactivity data. No overlap in purpose.
All tools follow a consistent 'get_' prefix followed by a descriptive noun ('compound_data', 'drug_info', 'drug_targets'), forming a clear pattern.
Three tools is a well-scoped number for a specialized biomedical data server, each providing a distinct and valuable function without unnecessary bloat.
The server covers compound data, drug safety/label, and targets, which are core aspects. Minor gaps exist, such as lack of clinical trial or interaction data, but the essential retrieval needs are met.
Available Tools
3 toolsget_compound_dataAInspect
Get drug/compound data from PubChem (NIH). Returns CID, IUPAC name, molecular formula, molecular weight, canonical SMILES, InChI, description, and synonyms.
| Name | Required | Description | Default |
|---|---|---|---|
| cid | No | PubChem CID number (alternative to name) | |
| name | No | Drug or compound name (e.g. aspirin, caffeine, ibuprofen) | aspirin |
Tool Definition Quality
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries full burden. It mentions the data source (PubChem) but does not disclose behavioral traits such as network dependency, rate limits, or that it is a read-only operation. This lack of transparency could lead to misuse.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence that is succinct and front-loaded with the purpose. Every word adds value, with no fluff or repetition.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description lists the return fields comprehensively, but lacks details on how parameters interact (e.g., is one required?) and does not mention response format or ambiguity handling. However, given low complexity and complete schema, it is mostly adequate.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%; both parameters (cid and name) have clear descriptions in the schema. The tool description adds no additional parameter semantics beyond what the schema already provides, so the baseline score of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the verb 'Get' and resource 'drug/compound data from PubChem (NIH)', and lists specific return fields. This distinguishes it from sibling tools like get_drug_info and get_drug_targets, which likely serve different purposes.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage for retrieving compound data, but does not explicitly state when to use this tool versus alternatives like get_drug_info or get_drug_targets. 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.
get_drug_infoBInspect
Get drug label, safety info, adverse events, or recall data from OpenFDA. Returns brand names, generic name, indications, warnings, dosage, interactions.
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | Drug name (e.g. metformin, aspirin, lisinopril) | metformin |
| type | No | label (default), adverse_events, or recalls | label |
Tool Definition Quality
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description must disclose behavioral traits. It indicates the tool is read-only (returns data) and lists return types, which is useful. However, it does not mention rate limits, auth requirements, or potential limitations of the OpenFDA source.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence that efficiently conveys the tool's purpose and return content. No wasted words.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a tool with two simple parameters and no output schema, the description is fairly complete. It identifies the external source (OpenFDA) and enumerates return fields. It could mention that results are from an API or briefly note limitations, but overall sufficient.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% with clear descriptions for both parameters (name and type). The description adds no additional parameter meaning beyond what the schema already provides, so baseline of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool retrieves drug label, safety info, adverse events, or recall data from OpenFDA. It uses a specific verb ('Get') and resource ('drug info'). However, it does not explicitly differentiate from sibling tools (get_compound_data, get_drug_targets), though the mention of OpenFDA and specific data types provides implicit distinction.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
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, such as the siblings get_compound_data or get_drug_targets. It does not state prerequisites, exclusions, or context-specific usage.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
get_drug_targetsAInspect
Get drug target and bioactivity data from ChEMBL (EMBL-EBI). Returns ChEMBL ID, max clinical phase, molecule type, molecular properties, and indication class.
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | Drug or compound name (e.g. ibuprofen, atorvastatin) | ibuprofen |
| type | No | molecule (default) or activity | molecule |
| chembl_id | No | ChEMBL ID for activity lookup (e.g. CHEMBL521) |
Tool Definition Quality
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations exist, so description carries full burden. It indicates a read-only operation ('Get') and specifies the data source (ChEMBL) and return fields. It lacks details on rate limits, authentication, or potential side effects, but does not contradict any annotations since none are provided.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single sentence that is front-loaded with the main purpose. No wasted words; every part adds value. Concise and efficient.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description lists return fields partially compensating for missing output schema. However, it does not clarify how parameters (name, type, chembl_id) interact or affect results. With 3 optional parameters and moderate complexity, more detail on parameter usage would improve completeness.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, so parameters are well-documented there. The description adds minimal extra meaning beyond the schema, mentioning 'indication class' in return but not explaining parameter behavior or relationships. Baseline 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the verb 'Get' and resource 'drug target and bioactivity data' from ChEMBL, listing specific return fields. However, it does not differentiate from sibling tools 'get_compound_data' and 'get_drug_info', leaving the agent to infer differences from names.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies use for obtaining target and bioactivity data, but offers no explicit guidance on when to use this tool versus alternatives or when not to use it. No exclusions or prerequisites mentioned.
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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