pubmed-stream
PYPI · PUBMED-STREAM
Search PubMed and PMC, read full texts, map evidence and build Obsidian knowledge graphs
Available components
Last scanned (5 hours ago)
Scores higher than 59% 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 setuptools.build_meta at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 0 of 5 dependencies flagged as unhealthy. View diagnostics → Pass
Provenance & Transparency45
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Provenance check failed: no build-provenance attestation is published. See how to fix → View diagnostics → Fail
- 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 Usability63
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 1326 tokens (~147/item across 9 items; 9 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- 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 Coverage89
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 66% of tool parameters carry a description.Partial
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 9 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 10 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 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.
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.
- 23 Oct 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 23 Oct 2026 · Analysed pypi/pubmed-stream@0.4.4
Provenance No attestation
The registry publishes no build provenance for this version, so there is nothing to verify.
| Result | No attestation |
|---|---|
| Ecosystem | pypi |
| Reason | No attestation published |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | setuptools.build_meta |
Background: Why install scripts are a supply-chain risk →
Dependencies 5 packages
| Packages resolved | 5 |
|---|---|
| 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 →
build_knowledge_graph Build or refresh a knowledge graph ~143
Link a study's searches and key papers into an Obsidian vault, kg_<topic>, with notes for papers, MeSH concepts and searches. Later calls with the same topic add to it; refresh reruns every recorded search and key paper.
| Name | Type | Req | Description |
|---|---|---|---|
| abstracts | boolean | – | Also save PubMed abstracts, so articles without free full text join |
| max_per_relation | integer | – | – |
| max_results | integer | – | – |
| queries | array | – | – |
| refresh | boolean | – | – |
| seeds | array | – | PubMed IDs of key papers |
| topic | string | yes | Short study name, e.g. gut microbiome parkinson |
No output schema declared.
No examples provided.
download Download full texts ~89
Download the newest matches of a PMC search as JSON files, one per article, into <output_dir>/<folder named after the search>. Existing files are skipped. Articles whose publishers forbid downloading are counted as unavailable.
| Name | Type | Req | Description |
|---|---|---|---|
| max_results | integer | – | – |
| output_dir | string | – | Folder of downloads, relative to the project |
| query | string | yes | PMC search, checked first with search_pmc |
No output schema declared.
No examples provided.
export_citations Export citations ~100
Write the downloaded articles, or chosen ones, as a BibTeX or RIS file that Zotero, EndNote or Mendeley imports. Give the researcher the file's path.
| Name | Type | Req | Description |
|---|---|---|---|
| file | string | – | File to write, relative to the project |
| format | string | – | – |
| ids | array | – | PubMed or PMC IDs; all articles when omitted |
| path | string | – | Folder of downloads, relative to the project |
No output schema declared.
No examples provided.
fetch_abstracts Save PubMed abstracts ~108
Save the abstracts of a PubMed search's newest matches, including articles whose full text is not free in PMC, into the same folder download uses. list_articles then shows them marked [abstract only]. Use it when search_pmc reports many more articles in PubMed than in PMC.
| Name | Type | Req | Description |
|---|---|---|---|
| max_results | integer | – | – |
| output_dir | string | – | Folder of downloads, relative to the project |
| query | string | yes | The same search as for search_pmc and download |
No output schema declared.
No examples provided.
list_articles List downloaded articles ~106
Downloaded articles, newest first, each once: identifiers, year, journal, title and length. With ids, only those articles; with abstracts, their abstracts too. Scan titles first, then read the abstracts of the articles that bear on the question.
| Name | Type | Req | Description |
|---|---|---|---|
| abstracts | boolean | – | – |
| ids | array | – | PubMed IDs or PMC IDs |
| limit | integer | – | Only the newest N articles |
| path | string | – | Folder of downloads, relative to the project |
No output schema declared.
No examples provided.
most_cited Most cited works ~53
The works the downloaded articles cite most: the field's foundations, and good key papers for the neighborhood tool.
| Name | Type | Req | Description |
|---|---|---|---|
| n | integer | – | – |
| path | string | – | Folder of downloads, relative to the project |
No output schema declared.
No examples provided.
neighborhood Evidence around one paper ~94
Similar, citing and cited papers of one PubMed article, with counts of reviews, retractions and NIH funding, and the retracted papers named. Saved as <output_dir>/neighborhood_<pmid>/neighborhood.json.
| Name | Type | Req | Description |
|---|---|---|---|
| max_per_relation | integer | – | – |
| output_dir | string | – | Folder of downloads, relative to the project |
| pmid | string | yes | PubMed ID, not a PMC ID |
No output schema declared.
No examples provided.
read_article Read one article's full text ~99
The full text of one downloaded article. With find, only the paragraphs that contain the term, numbered, which is usually enough; without it, the text up to max_chars.
| Name | Type | Req | Description |
|---|---|---|---|
| find | string | – | Term to search for, case-insensitive |
| id | string | yes | PubMed ID or PMC ID of a downloaded article |
| max_chars | integer | – | – |
| path | string | – | Folder of downloads, relative to the project |
No output schema declared.
No examples provided.
search_pmc Size a PMC search ~112
Count a PubMed Central search and list its newest matches, without downloading. Use PubMed field tags: [Title], [Title/Abstract], [mh] for MeSH, "open access"[filter]. Plain words match anywhere in the full text, so most results are off topic.
| Name | Type | Req | Description |
|---|---|---|---|
| query | string | yes | PMC search, e.g. "gut microbiota"[Title] AND parkinson[Title] |
| show | integer | – | How many of the newest matches to list (0 for the count) |
No output schema declared.
No examples provided.
How do I install the pubmed-stream MCP server?
pubmed-stream runs locally as a PyPI package, launched with uvx pubmed-stream. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · pubmed-stream
claude mcp add melhzy-pubmed-stream -- uvx pubmed-stream
What is the pubmed-stream MCP server?
pubmed-stream is an MCP server listed in the public MCP registry as io.github.melhzy/pubmed-stream. Search PubMed and PMC, read full texts, map evidence and build Obsidian knowledge graphs. This page covers its PyPI package (pubmed-stream).
Is the pubmed-stream MCP server safe to use?
pubmed-stream scores 52 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 23 October 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 pubmed-stream MCP server expose?
pubmed-stream exposes 9 tools: search_pmc, download, fetch_abstracts, list_articles, most_cited, and 4 more. Their descriptions and schemas cost roughly 904 tokens of context every time the server is loaded.
Is the pubmed-stream MCP server still maintained?
pubmed-stream is still listed as active in the MCP registry. We last reached this channel on 23 October 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 pubmed-stream MCP server under?
pubmed-stream declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.