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fip-mcp

fip-mcp

by ScienceLiveHub
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Python
Hybrid

fip-mcp

DOI PyPI

An MCP server that turns community FAIR Implementation Profiles (FIPs) into guidance and deterministic compliance checks for AI agents such as Claude Code.

A FIP records a community's agreed FAIR choices: identifiers, repositories, formats, vocabularies, licences and provenance models. It is published as nanopublications by the FIP Wizard. Today FIPs are mostly filled in once and rarely read again. This server makes them operational. An agent helping a researcher asks the FIP what the community agreed before it suggests anything, and can check work against the FIP.

fip-mcp was developed in the OSCARS-funded FIESTA project (FAIR Image Data Workflows in Galaxy), and is maintained by the Science Live community.

Tools

Tool

What it does

communities

Known communities and their FIP nanopubs (any tool also accepts a FIP URI).

profile

The community's choices question by question, from the latest FIP version.

recommend

What the community agreed for a topic (format, repository, licence, …).

check

Checks a folder or Zenodo record against the FIP: pass / fail (+ fix) / manual / no-choice.

crosswalk

What changes when a workflow or dataset moves between two communities.

Design rules:

  • Verdicts are code, not LLM judgement. Each declared resource maps to a probe of facts read from the target. A resource with no probe is manual, so the agent asks the user instead of guessing.

  • A community gap stays a gap. no-choice is reported as a gap in the FIP, and the agent is told not to put its own preference in its place.

  • Latest version. The FIP Wizard republishes a FIP and its declaration index, and both supersede their predecessors. The resolver only follows successors that are themselves FIPs.

Related MCP server: ml-skills-mcp

Install and use

pipx install fip-mcp
claude mcp add fip -s user -- fip-mcp     # as an MCP server
fip-check check fiesta-eo 10.5281/zenodo.20960690   # same operations from the shell
fip-check crosswalk fiesta-bio fiesta-eo

Nanopubs are cached in ~/.cache/fip-mcp. They are immutable, so they are cached for good. Version lookups always go to the network.

For development: pip install -e '.[dev]' and python -m pytest -q (the tests need no network).

Status

Prototype. The short names in src/fip_mcp/data cover the Astronomy, Bioimaging and Earth Observation FIPs of the OSCARS-FIESTA community FAIR Image Data Workflows in Galaxy. Any tool also accepts the nanopublication URI of another FIP, but the check probes have so far only been exercised on FIESTA outputs.

Assistant test

eval/ tests whether an AI assistant follows a community's FIP, with and without fip-mcp. It asks 6 questions (repository, data format, licence, identifier, vocabulary, provenance) for each of the 3 FIESTA communities, 3 runs per condition. The expected answers are read from the published FIPs, not typed by hand. Results from 2026-10-20 (Claude Opus 5.5, web and file tools disabled) are in eval/results/:

Variant

Without fip-mcp

With fip-mcp

choice: "what has my community agreed?"

54 of 54 abstain

54 of 54 give the declared choice or report the gap

plain: "what do you recommend?", declared questions

30 of 45 on-profile, 15 off-profile

45 of 45 on-profile

plain: questions the community left open

9 of 9 recommend their own default, with a caveat

9 of 9 report the gap

python eval/run_eval.py --runs 3 --out eval/results/<name>     # needs Claude Code
python eval/score.py eval/results/<name>

Citation

Please cite fip-mcp with the metadata in CITATION.cff. The concept DOI 10.5281/zenodo.24155500 always resolves to the latest version; each release also has its own DOI (v0.1.0: 10.5281/zenodo.24155501).

Funding

fip-mcp was developed within FIESTA, a project funded by OSCARS (Open Science Clusters' Action for Research and Society). OSCARS is funded by the European Union's Horizon Europe programme under grant agreement No 101129751. Views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them.

Science Live is a community-driven, unfunded initiative. Further funders will be listed here as they support the work.

Available Tools

5 tools
checkA

Check a folder or a Zenodo record against the community's FIP.

target: a local folder path, a Zenodo record URL or id, or a Zenodo DOI.

The verdicts are deterministic: each declared resource is matched to a probe of facts read from the target (DOIs, licence, repository, file formats, RO-Crate). Statuses: pass, fail (with fix), manual (no automatic probe — ask the user, do not guess), no-choice (the community left it open), planned-only. offProfileFormats lists data formats present in the target that the community did not declare. Report results as given; do not upgrade a manual to pass.

Inputs: target (required), community (required).

communitiesC

Known communities and the FIP each one has published. Any tool below also accepts a FIP nanopub URI in place of a short name.

Inputs: no named parameters.

crosswalkC

What changes when a workflow or dataset moves from the source community's practices to the target community's: per FIP question, same / overlap / differs / only one side chose / neither chose, with conversion notes for data formats. Use it when reusing a method across disciplines.

Inputs: source (required), target (required).

profileA

The community's FAIR choices, question by question, from the LATEST version of its FIP (the supersedes chain is followed and returned as versionChain).

noChoice: true means the community left that question open. Treat it as a gap in the profile, not as permission to pick something yourself.

Inputs: community (required).

recommendA

What the community has agreed for one topic, with each resource's URL and description. Call this BEFORE suggesting a repository, file format, licence, vocabulary or identifier scheme to a researcher in this community.

topic: identifier, metadata-schema, linking, repository, protocol, access, longevity, format, vocabulary, references, licence, provenance, standards — or a FAIR principle such as "I1".

Inputs: topic (required), community (required).

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

Loading tool schema changelog…

    Deploy Server
    One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

    TDQS

    A3.5/5.0

    Scored across 5 tools

    Disambiguation5/5

    Each tool has a distinct role: listing communities, retrieving a community profile, giving a topic recommendation, checking a target, and comparing two communities. The boundaries between profile, recommend, check, and crosswalk are clear from their descriptions, and the shared FIP URI input convention does not create selection ambiguity.

    Naming Consistency4/5

    All tool names are single lowercase words, which is a readable and consistent surface style. However, they mix nouns and verbs (communities/profile vs recommend/check), so they do not follow a strict action-oriented verb_noun pattern.

    Tool Count5/5

    Five tools is well scoped for an FIP advisory/checking server: discovery, profile inspection, topic recommendation, compliance checking, and cross-community comparison. Each tool has a clear place, with no obvious redundancy or missing scale.

    Completeness4/5

    The surface covers the core read-only FIP workflows: finding communities, reading their latest profile choices, recommending agreed resources, checking targets, and crosswalking between communities. Minor gaps include no explicit topic/question listing tool and no broader FIP-authoring lifecycle, but these are not required for the apparent advisory purpose.

    Maintenance

    ActivityMaintained
    ResponsivenessNo recent community issues

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