BioMapper
PYPI · BIOMAPPER
Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs.
Available components
Last scanned (21 hours ago)
Scores higher than 55% of PyPI servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security50
- Malware scan not yet available for this package.Unverified
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs poetry.core.masonry.api at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 2 of 33 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency45
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Build provenance not yet verified. View diagnostics → Unverified
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 0 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability69
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 843 tokens (~84/item across 10 items; 10 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management0
- Stability not yet verified: not enough scan history yet (needs a 30-day window).Unverified
Tool Coverage71
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 0% of tool parameters carry a description.Fail
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 10 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 11 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
Unverified: 1 category
A category scored 0 because we could not verify it: a data source with nothing on this package, evidence we could not reach, or a check we could not run. We only credit what we can confirm.
Checks we ran (13)
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- License
- Maintenance
- Security disclosure
- Schema quality
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
Checks we could not complete (3)
These are gaps on our side, not findings about this package. We only credit what we can confirm, so a category made up entirely of them scores 0.
- Malware scan in Supply Chain SecurityMalware scan not yet available for this package.
- Provenance in Provenance & TransparencyBuild provenance not yet verified.
- Stability in Stability & Change Management (scores 0 for this)Stability not yet verified: not enough scan history yet (needs a 30-day window).
Does not apply to this package (2)
- Endpoint SecurityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
- Transport & ReachabilityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
The score does not measure everything. What the score does not measure →
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 5 Nov 26 52
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed pypi/biomapper@1.6.2
Provenance Inconclusive
We could not complete the check, so nothing is claimed either way. This is a gap on our side, not a finding about the package.
| Result | Inconclusive |
|---|---|
| Ecosystem | pypi |
| Reason | Attestation not fetched |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | Known build tool | poetry.core.masonry.api |
Background: Why install scripts are a supply-chain risk →
Dependencies 33 packages
| Packages resolved | 33 |
|---|---|
| Stale | 1 |
| No linked repository | 1 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
cancel_job ~43
Cancel a job. It stops after the current chunk; the partial output and cache are kept, so resume_job can continue it later.
| Name | Type | Req | Description |
|---|---|---|---|
| job_id | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| created_utc | string | yes | – |
| entities_done | integer | yes | – |
| entities_failed | integer | – | – |
| entities_total | integer | yes | Unique entities (duplicate rows are mapped once) |
| eta_s | – | – | Best-effort estimate, not a promise |
| input_path | string | yes | – |
| job_id | string | yes | – |
| kg_build | string | – | – |
| kg_verified | boolean | – | – |
| output_path | string | yes | – |
| owner | – | – | – |
| partial_path | string | yes | – |
| pass_index | integer | – | – |
| provenance_path | string | yes | – |
| reason | – | – | – |
| rows_total | integer | yes | – |
| state | string | yes | – |
| updated_utc | string | yes | – |
No examples provided.
job_status ~78
Status of one map_file job (job_id) or of all jobs in the current folders: state (queued, running, paused, stalled, expired, cancelled, complete, failed, owned_elsewhere), progress, ETA estimate, output path, and whether the KG build is verified. Makes no request to BioMapper.
| Name | Type | Req | Description |
|---|---|---|---|
| job_id | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| jobs | array | yes | – |
| note | – | – | – |
No examples provided.
list_annotators ~22
List the annotators the BioMapper mapping pipeline can use.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| annotators | array | yes | – |
No examples provided.
list_entity_types ~39
List the Biolink entity types BioMapper accepts, with aliases and default identifier prefixes. Call this first to choose entity_type for the mapping tools.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| entity_types | array | yes | – |
No examples provided.
list_vocabularies ~25
List the identifier vocabularies (CURIE prefixes) BioMapper knows.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| vocabularies | array | yes | – |
No examples provided.
map_batch ~81
Map up to 5 entities of one entity_type in a single request (about 4-5 s per entity, so up to ~25 s). More than 5 is refused: write them to a TSV/CSV and use map_file.
| Name | Type | Req | Description |
|---|---|---|---|
| annotation_mode | string | – | – |
| entities | array | yes | – |
| entity_type | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| provenance | – | yes | – |
| results | array | yes | – |
No examples provided.
map_entity ~117
Map ONE entity name to knowledge-graph identifiers. Takes about 4-5 s. Call list_entity_types first to choose entity_type (e.g. biolink:SmallMolecule for metabolites). Optional identifiers are hints, e.g. {"HMDB": "HMDB0000177"}. For more than 5 entities use map_file instead; repeated single calls are refused after a limit.
| Name | Type | Req | Description |
|---|---|---|---|
| annotation_mode | string | – | – |
| entity_type | string | yes | – |
| identifiers | – | – | – |
| name | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| provenance | – | yes | – |
| result | – | yes | – |
No examples provided.
map_file ~208
Map every row of a TSV/CSV file as a resumable BACKGROUND job and return immediately with a job_id and an ETA (about 4-5 s per unique entity). Use this for more than 5 entities. The file must be inside an allowed folder (the client's roots or BIOMAPPER_MCP_ROOTS). Writes <input>.biomapper.tsv next to the input (never overwrites) plus a provenance JSON. identifier_columns maps a column name to its vocabulary, e.g. {"hmdb_id": "HMDB"}. Re-submitting the same file and options returns the existing job; rerun=true starts over with a fresh cache. Poll job_status about once a minute.
| Name | Type | Req | Description |
|---|---|---|---|
| annotation_mode | string | – | – |
| entity_type | string | yes | – |
| identifier_columns | – | – | – |
| key_column | – | – | – |
| name_column | string | yes | – |
| output_path | – | – | – |
| path | string | yes | – |
| rerun | boolean | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| created_utc | string | yes | – |
| entities_done | integer | yes | – |
| entities_failed | integer | – | – |
| entities_total | integer | yes | Unique entities (duplicate rows are mapped once) |
| eta_s | – | – | Best-effort estimate, not a promise |
| input_path | string | yes | – |
| job_id | string | yes | – |
| kg_build | string | – | – |
| kg_verified | boolean | – | – |
| output_path | string | yes | – |
| owner | – | – | – |
| partial_path | string | yes | – |
| pass_index | integer | – | – |
| provenance_path | string | yes | – |
| reason | – | – | – |
| rows_total | integer | yes | – |
| state | string | yes | – |
| updated_utc | string | yes | – |
No examples provided.
resume_job ~42
Resume a stalled, expired, paused, or cancelled job after a fresh health check. Rows already mapped are not re-mapped.
| Name | Type | Req | Description |
|---|---|---|---|
| job_id | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| created_utc | string | yes | – |
| entities_done | integer | yes | – |
| entities_failed | integer | – | – |
| entities_total | integer | yes | Unique entities (duplicate rows are mapped once) |
| eta_s | – | – | Best-effort estimate, not a promise |
| input_path | string | yes | – |
| job_id | string | yes | – |
| kg_build | string | – | – |
| kg_verified | boolean | – | – |
| output_path | string | yes | – |
| owner | – | – | – |
| partial_path | string | yes | – |
| pass_index | integer | – | – |
| provenance_path | string | yes | – |
| reason | – | – | – |
| rows_total | integer | yes | – |
| state | string | yes | – |
| updated_utc | string | yes | – |
No examples provided.
server_info ~38
Server version, KG provenance (pending until the startup probe lands), limits, and the folders map_file may read. Makes no request to BioMapper.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| allowed_roots | array | yes | – |
| batch_cap | integer | yes | – |
| loop_limit | integer | yes | – |
| loop_window_s | number | yes | – |
| provenance | – | yes | – |
| server_version | string | yes | – |
No examples provided.
How do I install the BioMapper MCP server?
BioMapper runs locally as a PyPI package, launched with uvx biomapper. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · biomapper
claude mcp add trentleslie-biomapper -- uvx biomapper
What is the BioMapper MCP server?
BioMapper is an MCP server listed in the public MCP registry as io.github.trentleslie/biomapper. Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs. This page covers its PyPI package (biomapper).
Is the BioMapper MCP server safe to use?
BioMapper scores 52 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the BioMapper MCP server expose?
BioMapper exposes 10 tools: list_entity_types, list_vocabularies, list_annotators, server_info, map_entity, and 5 more. Their descriptions and schemas cost roughly 693 tokens of context every time the server is loaded.
Is the BioMapper MCP server still maintained?
BioMapper is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the BioMapper MCP server under?
BioMapper declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.
What did VerifyMCP test on the BioMapper MCP server?
VerifyMCP ran 13 checks on BioMapper, covering Known CVEs, Install scripts, Dependency health, Source repository and 9 more. 3 items could not be completed, a gap on our side rather than a finding about BioMapper: Malware scan, Provenance and Stability. One category scores 0 for that reason, because we only credit what we can confirm. Endpoint Security and Transport & Reachability do not apply to a PyPI package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.