IDC MCP Server Guide

IDC operates a hosted Model Context Protocol server that exposes IDC discovery and metadata as agent tools. This guide covers how to recognize it, how to divide work between it and idc-index, and what to hand off across that boundary.

The server is optional. Everything in SKILL.md works without it.

Endpoint

Identifying the server

Tool names and resource URIs are defined by the server, so they are the same on every host. Use them, not host-specific naming conventions, to decide whether the server is present.

Strongest signal — resource URIs. The server publishes two resources under an idc:// scheme:

If the host can enumerate MCP resources, a resource with URI idc://guide identifies the server unambiguously.

Fallback — tool-name fingerprint. Require three or more of build_cohort, get_cohort_urls, list_analysis_results, and get_idc_version. Do not treat run_sql, get_stats, list_tables, or get_citations as evidence on their own; those names are generic enough that another server could expose them.

This is disambiguation, not authentication. No runtime check can prove the server on the other end is operated by NCI — a hostile server could serve idc://guide and name its tools anything. The trust anchor is the URL the user configured plus TLS, which is established when the server is added, not when the skill runs. That is sufficient for routing: the check only has to distinguish IDC from the user's other installed servers.

Fail soft. If identification is ambiguous, or a tool call fails, fall back rather than reporting an error — to the REST API (rest_api_guide.md) for read-only metadata, which is the same service with no configuration, or to idc-index when it is already installed or the task needs downloads or local analysis. Tool names may change as the server matures.

Tool inventory

Live initialize, tools/list, and resources/list verified on 2026-09-30 against server 3.0.0b3. Treat this as a snapshot, not a contract — call the server's own listing rather than assuming this list is current.

The server ships its own usage instructions, which most hosts inject automatically. Follow those instructions for tool sequencing (ground with list_attributes / get_attribute_values before filtering; check list_tables before writing SQL). Do not re-derive that workflow from SKILL.md — the two would drift apart on the server's next release.

Cohort results report their own filters. build_cohort and get_cohort_urls require at least one filter predicate and fail cleanly without one, rather than returning the whole archive; results echo the filters actually applied along with warnings (inside counts for build_cohort) for any predicate that was dropped or any value whose casing did not match. Read those warnings before reporting a count — a zero with no warning means the filter matched nothing, which is a real answer. Same contract as the REST endpoints they wrap; see rest_api_guide.md.

Division of labor

The server and idc-index overlap on metadata queries and diverge everywhere else.

Two rules resolve the overlap:

• Prefer the server for discovery. It is hosted against a current IDC release, so it does not depend on the idc-index version pinned in SKILL.md.
• **Prefer idc-index when the result must become a Python object.** Round-tripping a DataFrame through tool output wastes context and loses types.

Handing off from the server to idc-index

The boundary artifact is a list of SeriesInstanceUID values.

# UIDs obtained from the MCP server's build_cohort / run_sql output
series_uids = [
    "1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463",
    # ...
]

from idc_index import IDCClient
client = IDCClient()

# Confirm size before downloading — the server reports size_TB, but re-check locally
selected = client.index[client.index["SeriesInstanceUID"].isin(series_uids)]
missing = set(series_uids) - set(selected["SeriesInstanceUID"])
if missing:
    raise ValueError(f"{len(missing)} requested series absent from local index; reconcile versions")
print({"series": len(selected), "size_GB": selected["series_size_MB"].sum() / 1000})

client.download_from_selection(
    downloadDir="./data",
    seriesInstanceUID=series_uids,       # a list, not a DataFrame
    dirTemplate="%collection_id/%PatientID/%Modality",
)

Run python scripts/check_version.py before the first idc-index call in a session, even if discovery happened server-side — the two components version independently.

get_cohort_urls also returns ready-made idc CLI commands. Those are the better handoff when the user wants a shell command they can re-run outside the session, after validating the CLI syntax: the reviewed server omits required --manifest-file in its download-from-manifest suggestion. Add it; see references/cli_guide.md.

build_cohort uses zero-based page/page_size; collect all pages until the returned series count matches total_series. get_cohort_urls defaults to only 100 URLs; inspect truncated and increase its bounded limit or partition the cohort before download.

Going the other direction, idc-index results are already local, so there is rarely a reason to send them back to the server.

Version authority

When the server is present, it is the authority on the IDC data version: call get_idc_version rather than quoting the idc-data-version value in the SKILL.md frontmatter, which records the release the skill was last verified against.

If the server and a locally installed idc-index report different versions, say so and name both. The mismatch is real — the hosted server tracks IDC releases independently of the user's installed package — and it changes which answers about "what's new" are correct.

Host-specific notes

Everything above is portable. The items below are not, and apply only to specific agent environments.

Claude Code

Reviewed against the official MCP and permissions documentation; connector naming and discovery surfaces still depend on the installed host version.

• Tool naming. MCP tools are exposed as mcp__<server>__<tool>, where <server> is the configured server name with every character outside A-Za-z0-9_- replaced by _. A CLI install named idc yields mcp__idc__build_cohort; a claude.ai connector named IDC MCP prod yields mcp__claude_ai_IDC_MCP_prod__build_cohort.
• Enumerating resources. ListMcpResourcesTool returns each resource with a server field, which is how to find the idc://guide resource and the owning server name in one call.
• Adding the server. claude mcp add --transport http idc https://api.imaging.datacommons.cancer.gov/mcp
• Permission rules. Allow rules need a literal, glob-free server segment: mcp__idc__* works, mcp__* does not. Connector installs need their own mcp__claude_ai_<name>__* rule, so the rule differs by install path.
• Detecting via the CLI does not work. claude mcp list reads only file-based configuration (~/.claude.json, .mcp.json). It reports "No MCP servers configured" for a claude.ai connector that is connected and working in the same session, so it cannot be used as a presence check.

Other hosts

Any agent that supports MCP over streamable HTTP can use the server. Consult that agent's documentation for how servers are registered and how tool names are namespaced; the endpoint URL and the absence of authentication are all the configuration it needs.