# Phở Research Tools

> Checks AI-written references against Crossref, PubMed and OpenAlex. Formats citations, PRISMA.

- name: io.github.thaohienhomes/pho-research-tools
- version: 1.0.1
- connection class: R0 (autonomous)
- trust: 97/100
- quality: 80/100 (good)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.thaohienhomes%2Fpho-research-tools
- tools: https://api.protogrid.dev/v1/servers/io.github.thaohienhomes%2Fpho-research-tools/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "pho-research-tools": {
      "type": "http",
      "url": "https://mcp.pho.chat/mcp"
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: 100
- freshness: 100
- provenance: 90
- drivers: +repository +namespace-matches-repo +website +reachable +uptime-100% +updated-9d-ago
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality 80/100 (good)

### protocol: 75 (weight 25)

- warn `protocol.modern`: newest supported version is 2025-11-25; 2026-07-28 not supported, older versions are deprecated until 2027-07-28
- n/a `protocol.stateless`: only applies to 2026-07-28 servers
- pass `protocol.transport`: streamable HTTP
- n/a `protocol.list_ttl`: only applies to 2026-07-28 servers

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: 86 (weight 30)

- pass `tools.descriptions`: every tool has a description
- warn `tools.description_length`: 2 tools have descriptions over 1,024 characters, which crowds the context
- pass `tools.schemas`: every tool has an object input schema
- pass `tools.annotations`: 9 of 9 tools declare readOnlyHint or destructiveHint
- warn `tools.directory_hints`: 8 of 9 tools declare all four hints; missing: search_papers (idempotentHint)
- pass `tools.token_cost`: about 5,237 tokens to load every tool
- pass `tools.api_dump`: tools are not a one-to-one API dump

### stability: 75 (weight 15)

- warn `stability.changes`: 25 tool changes in 30 days
- pass `stability.rug_pull`: no tool changed its meaning under the same name

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: no npm or PyPI package

- tools: 9, about 5,237 tokens to load them all
- tool set hash: b04b143d98e98ffc3febd43b0796464a
- tools last changed: 2026-10-20T11:19:33.101Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.thaohienhomes/pho-research-tools.svg)](https://protogrid.dev/servers/io.github.thaohienhomes/pho-research-tools)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-20 `find_evidence` changed (description, outputSchema)
  - before: Find the strongest published evidence for and against a scientific or medical claim. Searches PubMed (including a pass limited to guidelines, meta-analyses, systematic reviews and randomized trials) and OpenAlex, and returns real papers, each with a PMID or DOI, ordered by level of evidence: guideline, meta-analysis, systematic review, RCT, other trial, observational study, narrative review, case report. Each paper comes with the conclusion copied verbatim from its abstract, so you can judge for yourself whether it supports the claim, contradicts it, or does not address it, and quote the sentence you rely on. The tool does not judge stance and does not summarise: count a paper as support or contradiction only when its conclusion says so. Pass `query` with English search keywords when the claim is long or not in English. Retracted papers and correction notices are left out. Preprints are included and marked (not peer reviewed).
  - after: Find the strongest published evidence for and against a scientific or medical claim. Searches PubMed (including a pass limited to guidelines, meta-analyses, systematic reviews and randomized trials) and OpenAlex, and returns real papers, each with a PMID or DOI, ordered by level of evidence: guideline, meta-analysis, systematic review, RCT, other trial, observational study, narrative review, case report, then study protocols that have not reported results yet. Each paper comes with the conclusion copied verbatim from its abstract, so you can judge for yourself whether it supports the claim, contradicts it, or does not address it, and quote the sentence you rely on. The tool does not judge stance and does not summarise: count a paper as support or contradiction only when its conclusion says so. Pass `query` with English search keywords when the claim is long or not in English. Retracted papers and correction notices are left out. Preprints are included and marked (not peer reviewed).
- 2026-10-20 `prisma_flow_diagram` changed (description, inputSchema)
  - before: Draw a PRISMA 2020 flow diagram for a new systematic review from the record counts, as a PNG image plus an SVG and download links. Give the counts you have; boxes that follow arithmetically from others are filled in and marked as derived. The tool checks that the numbers add up (records identified minus removed equals screened, and so on) and returns a warning naming each box that does not, with the value it should have. The diagram always shows the numbers exactly as given. Add `otherMethods` counts to draw the second column (websites, organisations, citation searching).
  - after: Draw a PRISMA 2020 flow diagram for a new systematic review from the record counts, as a PNG image plus an SVG and download links. Give the counts you have; screened, sought, assessed and reports-included boxes that follow from others are filled in and marked as derived. Studies included is never derived. The tool checks that the numbers add up (records identified minus removed equals screened, and so on) and returns a warning naming each box that does not, with the value it should have. The diagram always shows the numbers exactly as given. Add `otherMethods` counts to draw the second column (websites, organisations, citation searching).
- 2026-10-20 `check_retractions` changed (description)
  - before: Check DOIs for retractions, expressions of concern and corrections, using Crossref (which includes Retraction Watch data). Status per DOI: retracted, concern, corrected, other_notice, no_notice (nothing on record), not_in_crossref, invalid_doi, rate_limited or lookup_failed (the DOI could not be checked, which is not a clean result). Works for a single paper or a whole reference list. verify_references already includes this check, so use this tool for DOIs that have not just been through verify_references.
  - after: Check DOIs for retractions, expressions of concern and corrections, using Crossref (which includes Retraction Watch data). Status per DOI: retracted, concern, corrected, other_notice, no_notice (nothing on record), not_in_crossref, invalid_doi, rate_limited or lookup_failed (the DOI could not be checked, which is not a clean result). Works for a single paper or a whole reference list. verify_references already includes this check, so use this tool for DOIs that have not just been through verify_references. A DOI the same caller checked in the last hour is answered again at no cost to the allowance.
- 2026-10-19 `find_tools` changed (outputSchema)
- 2026-10-19 `find_datasets` changed (outputSchema)
- 2026-10-19 `check_retractions` changed (outputSchema)
- 2026-10-19 `format_citations` changed (outputSchema)
- 2026-10-19 `verify_references` changed (outputSchema)
- 2026-10-19 `find_tools` added
  - Find research software for a task from the bio.tools registry (ELIXIR), check each tool's licence, verify the paper behind it (DOI, retractions, corrections), label whether it is still maintained, and give the install line. Describe the task (e.g. "cluster single-cell RNA-seq data") and optionally the file format the data is in (e.g. H5AD, FASTQ, VCF); tools that list that format as an input are favoured. Each result has a match level, a plain-language licence verdict, the paper and whether it checks out, a maintenance label (active, idle, stale, archived) read from the linked GitHub repository, and an install line built from a PyPI, Bioconda, Bioconductor, CRAN or GitHub link the registry lists. Every identifier and command comes from the registry's own records; nothing is generated. The `why` field lists the facts behind the match: explain the fit in your own words from those facts, and say plainly when no tool matched. Pass `keywords` with English words when the task is long or not in English. Licence verdicts come from registry and repository metadata and are not legal advice.
- 2026-10-19 `find_datasets` added
  - Find open scientific datasets (and optionally models) that fit a research question, check their licences, verify the source papers (DOI, retractions, corrections), and return a citable Research Data Brief with a public share link. Searches DataCite (Zenodo, Figshare, Dryad and other data repositories), the Hugging Face Hub boosted by the Hugging Science curated index, and, for life-science questions, NCBI GEO, CZ CELLxGENE Discover (curated single-cell data) and the CZ CryoET Data Portal (cryo-electron tomography). Each result has a match level, a plain-language licence verdict, the source paper and whether it checks out, a citation for the data, and a line of code to load it. Every identifier comes from the repositories' own metadata; nothing is generated. The `why` field lists the facts behind the match: explain the fit to the user in your own words from those facts, and say plainly when the brief is empty. Pass `keywords` with English search words when the question is long or not in English. Licence verdicts come from repository metadata and are not legal advice.

Full history: https://api.protogrid.dev/v1/servers/io.github.thaohienhomes%2Fpho-research-tools/changes

## Remotes

- https://mcp.pho.chat/mcp (streamable-http, auth none, reachable true, uptime30d 1)

## Packages

_none_

## Tools (9)

- `check_retractions`: Check DOIs for retractions, expressions of concern and corrections, using Crossref (which includes Retraction Watch data). Status per DOI: retracted, concern, corrected, other_notice, no_notice (nothing on record), not_in_crossref, invalid_doi, rate_limited or lookup_failed (the DOI could not be checked, which is not a clean result). Works for a single paper or a whole reference list. verify_references already includes this check, so use this tool for DOIs that have not just been through verify_references. A DOI the same caller checked in the last hour is answered again at no cost to the allowance.
- `find_datasets`: Find open scientific datasets (and optionally models) that fit a research question, check their licences, verify the source papers (DOI, retractions, corrections), and return a citable Research Data Brief with a public share link. Searches DataCite (Zenodo, Figshare, Dryad and other data repositories), the Hugging Face Hub boosted by the Hugging Science curated index, and, for life-science questions, NCBI GEO, CZ CELLxGENE Discover (curated single-cell data) and the CZ CryoET Data Portal (cryo-electron tomography). Each result has a match level, a plain-language licence verdict, the source paper and whether it checks out, a citation for the data, and a line of code to load it. Every identifier comes from the repositories' own metadata; nothing is generated. The `why` field lists the facts behind the match: explain the fit to the user in your own words from those facts, and say plainly when the brief is empty. Pass `keywords` with English search words when the question is long or not in English. Licence verdicts come from repository metadata and are not legal advice.
- `find_evidence`: Find the strongest published evidence for and against a scientific or medical claim. Searches PubMed (including a pass limited to guidelines, meta-analyses, systematic reviews and randomized trials) and OpenAlex, and returns real papers, each with a PMID or DOI, ordered by level of evidence: guideline, meta-analysis, systematic review, RCT, other trial, observational study, narrative review, case report, then study protocols that have not reported results yet. Each paper comes with the conclusion copied verbatim from its abstract, so you can judge for yourself whether it supports the claim, contradicts it, or does not address it, and quote the sentence you rely on. The tool does not judge stance and does not summarise: count a paper as support or contradiction only when its conclusion says so. Pass `query` with English search keywords when the claim is long or not in English. Retracted papers and correction notices are left out. Preprints are included and marked (not peer reviewed).
- `find_tools`: Find research software for a task from the bio.tools registry (ELIXIR), check each tool's licence, verify the paper behind it (DOI, retractions, corrections), label whether it is still maintained, and give the install line. Describe the task (e.g. "cluster single-cell RNA-seq data") and optionally the file format the data is in (e.g. H5AD, FASTQ, VCF); tools that list that format as an input are favoured. Each result has a match level, a plain-language licence verdict, the paper and whether it checks out, a maintenance label (active, idle, stale, archived) read from the linked GitHub repository, and an install line built from a PyPI, Bioconda, Bioconductor, CRAN or GitHub link the registry lists. Every identifier and command comes from the registry's own records; nothing is generated. The `why` field lists the facts behind the match: explain the fit in your own words from those facts, and say plainly when no tool matched. Pass `keywords` with English words when the task is long or not in English. Licence verdicts come from registry and repository metadata and are not legal advice.
- `format_citations`: Format references in a citation style (APA 7, MLA 9, Chicago author-date, Harvard, Vancouver, IEEE, AMA) or export them as BibTeX, RIS or CSL-JSON. By default every reference is first verified against Crossref, PubMed and OpenAlex, and verified references are formatted from the database record, so wrong years, pages or author names in the input are corrected. References that could not be verified are formatted exactly as written and flagged in `entries[].warnings`. Returns the bibliography and, for text and html output, the matching in-text citation for each reference.
- `prisma_flow_diagram`: Draw a PRISMA 2020 flow diagram for a new systematic review from the record counts, as a PNG image plus an SVG and download links. Give the counts you have; screened, sought, assessed and reports-included boxes that follow from others are filled in and marked as derived. Studies included is never derived. The tool checks that the numbers add up (records identified minus removed equals screened, and so on) and returns a warning naming each box that does not, with the value it should have. The diagram always shows the numbers exactly as given. Add `otherMethods` counts to draw the second column (websites, organisations, citation searching).
- `screening_log`: Turn the screening decisions of a systematic review into its PRISMA 2020 counts, flow diagram and screening log. Give one row per record: its title/abstract decision (include or exclude), its full-text decision for records that passed (include, exclude or not_retrieved), and the reason for each exclusion. Every box from "records screened" down is counted from the rows, so the diagram always matches the decisions; full-text exclusions are grouped by reason. Returns the diagram (PNG, SVG, links), the counts, a CSV of every decision for the review appendix, and the problems a reviewer would catch: full-text exclusions without a reason, records still waiting for a full-text decision, and duplicate ids. Add the identification counts (records from databases, duplicates removed) to complete the top of the diagram. At most 5000 records per call.
- `search_papers`: Search PubMed and OpenAlex for real papers. Every result carries a DOI or PubMed ID that resolves, so nothing returned can be fabricated. Finds sources for a claim or a topic. Filters: publication year range, open-access only, study types, and the number of results. Retracted papers are left out by default. Preprints are included and marked `preprint: true` (not peer reviewed). Results are ranked by the databases' relevance, alternating between the two sources.
- `verify_references`: Check every reference in a list against Crossref, PubMed and OpenAlex and report, for each one, whether the paper really exists and whether the details are right. Works on lists written by a person or generated by an AI model. Input: a pasted reference list in any common style (APA, Vancouver, numbered, mixed), BibTeX, RIS, CSL-JSON, or one DOI per line. Each reference gets exactly one status: verified, verified_with_corrections (real paper, some details wrong; corrected metadata included), likely_fabricated (no such paper exists), not_found (could not be confirmed either way), retracted, or ambiguous (several papers fit). likely_fabricated, not_found and ambiguous mean the reference could not be confirmed as a real paper; retracted means the paper exists but has been withdrawn. Retractions, expressions of concern and corrections are already checked here, so there is no need to call check_retractions on the same references afterwards. At most 50 references per call.