Retrieve reproducible, complete, verifiable records from 26 public biomedical sources (PDB, UniProt, NCBI Protein/Virus/Datasets, ClinVar, Ensembl, gnomAD, PubChem, AlphaFold, ClinicalTrials, openFDA, Open Targets, Reactome, GTEx, GWAS Catalog, and more — run `catalog` for the full list) via Pinakes — the same 8 verbs over an MCP server (pinakes_<verb> tools) or the identical pinakes CLI. Use when an agent must pull biomedical data that has to be reproducible, deterministic, byte-identical, complete-or-fail, or independently verifiable; when a record count, cited fact, or dataset must carry provenance a reviewer can re-derive offline; when pinning a content-addressed snapshot; reading a manifest's completeness or reproducible flag; verifying before citing; or self-correcting a rejected filter. Teaches the judgement the tool schemas do not: pin-or-no-determinism, complete vs best_effort, and verify-before-cite.
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Retrieve reproducible, complete, verifiable records from 26 public biomedical sources (PDB, UniProt, NCBI Protein/Virus/Datasets, ClinVar, Ensembl, gnomAD, PubChem, AlphaFold, ClinicalTrials, openFDA, Open Targets, Reactome, GTEx, GWAS Catalog, and more — run `catalog` for the full list) via Pinakes — the same 8 verbs over an MCP server (pinakes_<verb> tools) or the identical pinakes CLI. Use when an agent must pull biomedical data that has to be reproducible, deterministic, byte-identical, complete-or-fail, or independently verifiable; when a record count, cited fact, or dataset must carry provenance a reviewer can re-derive offline; when pinning a content-addressed snapshot; reading a manifest's completeness or reproducible flag; verifying before citing; or self-correcting a rejected filter. Teaches the judgement the tool schemas do not: pin-or-no-determinism, complete vs best_effort, and verify-before-cite.
short-description
Retrieve reproducible, complete, verifiable biomedical records via Pinakes (MCP pinakes_<verb> tools or the identical CLI) over 26 public sources. Use when data must be deterministic, byte-identical, complete-or-fail, snapshot-pinned, or carry provenance a reviewer can re-derive offline — and when reading a manifest, verifying before citing, or self-correcting a rejected filter.
Pinakes is a deterministic, verifiable input layer for AI agents over 26
public biomedical sources, shipped as one static Go binary that exposes the same
8 verbs over an MCP server (pinakes_<verb> tools), an identical CLI
(pinakes <verb>), and a loopback REST server. Its value is invisible from the
tool schemas, which is why this skill exists: every result pins a
content-addressed snapshot (byte-reproducible forever), retrieval is
complete-or-fail (reconciled against the source's authoritative total — never
a silent partial), and every result ships a re-runnable manifest that
verify re-derives offline. This skill teaches the judgement layer — pin or
you get no determinism, read completeness honestly, verify before you cite — not
the schemas (tools/list and pinakes catalog already carry field names,
operators, and enums; do not duplicate them here).
Boundary. Pinakes fixes the input only. It does not run analysis, does
not build evolutionary trees, and never claims a source is wrong — the public
databases are authoritative. It fixes naive client retrieval (no imposed order,
no reconciliation, no provenance). It covers public sources only. The arXiv
literature corpus is not yet shipped — do not assume it. Hand the verified
manifest to a domain skill for the actual science.
When to Use This Skill
✅ Use when:
An agent must pull biomedical data that has to be reproducible /
deterministic / byte-identical across runs.
You need a record count that goes in a methods section and must reproduce
next month.
You need a cited fact a reviewer can independently re-fetch and check.
You are handed a manifest and must confirm it reproduces before building on
it (verify-before-cite).
A query was rejected (UNKNOWN_FIELD, BAD_ENUM, INVALID_FILTER,
UNSATISFIABLE_QUERY) and the agent must self-correct rather than retry blind.
You must know whether a result is complete vs best_effort vs partial, or
whether it is reproducible at all.
You are pulling from PDB, UniProt, NCBI Protein, NCBI Virus, ClinVar, Ensembl,
gnomAD, PubChem, AlphaFold, ChEMBL, ClinicalTrials, openFDA, cBioPortal, or
NCBI Datasets and want provenance, not just bytes.
❌ Do not use when:
The task is analysis (differential expression, alignment, tree-building,
modeling). Use this to fetch the verified input, then a domain skill.
You want to assert a source is wrong or compute a "true eternal count" —
Pinakes does neither; a count is a property of a pin, not of all time.
The source is private/internal or behind a login — Pinakes serves public
databases only.
You need the arXiv corpus — not shipped yet.
A raw, throwaway lookup where reproducibility genuinely does not matter (rare —
if it will be cited or re-run, it matters).
Clarification Questions
1. ⚠️ CRITICAL: ASK THIS FIRST — Will this result be reported, cited, or re-run?
If yes, you MUST pin a concrete snapshot_version (sha256:…, never empty,
never latest) and verify the manifest before citing. An unpinned result is
served from latest ⇒ reproducible:false, and a re-run next month silently
returns a different set — so a bare count or fact with no pin is not a fact you can
cite. If the answer is genuinely no (a throwaway lookup nobody will repeat),
you may skip the pin — but confirm that explicitly, because this is rare.
2. Which source, and is it materializable?
Which of the 26 sources answers the question (run catalog to confirm the id
and its filter schema)?
Is that source L2+ and HostServe? A copyleft source (ChEMBL, served
live) can never be reproducible:true — if the task demands reproducibility,
route to a materializable source instead (see Picking a Connector).
3. Does the answer have to be complete, or is best-effort acceptable?
If it must be the whole answer, do not pass a limit — a cap below the
authoritative total downgrades the result to best_effort (it cannot be
reconciled). Let complete-or-fail reconcile.
If a sample is fine, label it best_effort honestly — never present a capped or
best-effort set as "all matching records".
Setup & Surface Detection
Pinakes is client-neutral: the same 8 verbs are an MCP tool and a CLI
subcommand. Detect the surface and degrade gracefully.
Rule:use the MCP pinakes_<verb> tool if it is present in your tools; else
shell out to the identical pinakes <verb> CLI. Every recipe below is shown in
both forms — they are interchangeable.
MCP present (tools named pinakes_catalog, pinakes_search, …): call them
directly. Generic stdio registration is just:
No token, no Docker, no env. If a GUI client can't find pinakes on its
PATH, replace "command": "pinakes" with the absolute path from
which pinakes.
CLI only (no MCP tools, but which pinakes resolves): run pinakes <verb>
with the same arguments. Pass a manifest as --manifest @manifest.json.
Neither (which pinakes is empty): you cannot fetch. Say so plainly and
stop — do not fabricate records or a manifest. Point the user at install (depth
→ references/setup.md).
Confirm wiring with pinakes catalog (CLI) or pinakes_catalog (MCP) before the
first real query. Depth: references/setup.md.
The Core Loop (1–8)
Run this loop for any retrieval that will be reported, cited, or re-run. The
hinge steps are 4 (pin a snapshot), 5 (read the manifest), and 7
(verify) — skip any one and the determinism guarantee silently evaporates.
Catalog.pinakes_catalog / pinakes catalog to list sources (id,
maturity, license); scope to one source to get its filter schema (fields,
operators, enums). This is how you learn what is queryable.
Validate locally. Check every filter field/operator/value against that
schema before any network call. A bad one is rejected locally with a precise
code (UNKNOWN_FIELD / BAD_ENUM / INVALID_FILTER) — fix it here, cheaply.
Estimate (optional).pinakes_estimate / pinakes estimate for a dry-run
record/byte/call count. An estimate never substitutes for reconciliation —
it is a cost preview, not a completeness claim.
Retrieve WITH a pinned snapshot_version.search / get / resolve,
always passing a concrete snapshot_version (sha256:…). Empty or
latest ⇒ not reproducible. This is the #1 footgun (see below).
Read Completeness + reproducible. Inspect the manifest: is
completeness.statecomplete? Is reproducibletrue? Do not report until
you have read these — the records alone don't tell you.
Export (optional).pinakes_export / pinakes export to materialize to
parquet/json/fasta/vcf/mmcif. The reproducibility anchor stays the canonical
NDJSON logical_record_hash, not the export bytes.
Verify.pinakes_verify / pinakes verify --manifest @manifest.json
re-derives the count and record hash from the pinned snapshot offline.
Exit 0 / verified:true ⇒ it reproduces. A refusal ⇒ stop, do not cite.
Cite the manifest. The citation is the manifest: source_id, pinned
snapshot_version, logical_record_hash, completeness.state, and per-source
license/attribution. Hand this to the next skill.
Copy-able checklist:
[ ] 1. catalog → confirmed source + read filter schema
[ ] 2. filters validated locally (no UNKNOWN_FIELD / BAD_ENUM / INVALID_FILTER)
[ ] 3. (estimate, if cost matters — not a completeness claim)
[ ] 4. snapshot_version pinned (concrete sha256:… — NOT empty, NOT "latest")
[ ] 5. manifest read: completeness.state == complete? reproducible == true?
[ ] 6. (export, if a file is needed — hash is over NDJSON, not export bytes)
[ ] 7. verify → exit 0 / verified:true (offline)
[ ] 8. cited the manifest (source_id + snapshot_version + logical_record_hash
+ completeness + license/attribution)
Pin or no determinism (the #1 footgun)
This is the single most common failure. The snapshot_version is what makes a
result reproducible. No pin ⇒ the engine serves latest ⇒
reproducible:false, and a re-run next month silently returns a different set.
A bare count or fact with no pin is not a fact you can cite.
A manifest is reproducible:trueonly when ALL of these hold (the engine's
SetReproducible enforces every one — you cannot bypass it):
#
Condition
Source of truth
1
Served from a pinned snapshot (served_from = snapshot@…)
ServedFrom.DeterminismClaimable()
2
Completeness is complete and reconciled (count == authoritative)
Completeness.Reconciled()
3
At least one source, and every source is L2+ (any L0/L1 ⇒ false)
MaturityLevel.DeterminismClaimable()
4
Every source pins a concrete snapshot — not empty, not latest
SetReproducible
If any row fails, reproducible is false — honestly. The fix is almost always
row 1/4: pass a snapshot_version. Full table:
references/manifest-and-completeness.md.
Reading the Manifest
The manifest is the product. Read it; never infer from the record list.
Completeness decision table (completeness.state):
State
Means
What you may say
Action
complete
Retrieved count reconciled against the source's authoritative total and they match
"the whole answer (N/N)"
Safe to cite as complete
best_effort
No trustworthy authoritative total exists (carries a mandatory reason)
"a best-effort set, completeness unproven" — never "all"
Report the reason; do not claim complete
partial
A multi-source query where ≥1 upstream failed (has reason + resume_cursor)
"partial; some upstream failed"
Resume via cursor or report the gap
The limit footgun. A limit below the source's authoritative total cannot
be reconciled, so the engine downgrades the result to best_effort — not
complete. If you need a complete answer, drop the cap and let
complete-or-fail reconcile, or report honestly that the set is best_effort.
Treating a limit-capped set as "all matching records" is a classic error.
Key manifest fields to cite: manifest_schema_version, engine_version, per-
source snapshot_version + maturity + license, logical_record_hash (the
SHA-256 over canonical NDJSON — the anchor), completeness, served_from, and
reproducible. Depth:
references/manifest-and-completeness.md.
Picking a Connector
Short routing table (26 sources). L0 = catalog-only (not queryable); L1 =
queryable but never reproducible (live proxy); L2+ = reproducible against
a pinned snapshot. All 26 shipped connectors are L2. catalog is the live
source of truth; this table is the at-a-glance version, the full one with SPDX and
attribution flags lives in references/sources.md.
Source id
Domain
Maturity
License posture
pdb
structures
L2
public-domain → materializable
uniprot
proteins
L2
attribution (CC-BY-4.0) → materializable
ncbi-protein
sequences
L2
public-domain → materializable
ncbi-virus
viruses
L2
public-domain → materializable
ncbi-datasets
genes
L2
public-domain → materializable
clinvar
variants
L2
public-domain → materializable
ensembl
genomics
L2
no-restrictions → materializable
gnomad
variants
L2
public-domain → materializable
pubchem
compounds
L2
public-domain → materializable
alphafold
structures
L2
attribution (CC-BY-4.0) → materializable
clinicaltrials
clinical_trials
L2
public-domain → materializable
openfda
drug_labels
L2
public-domain → materializable
opentargets
target-disease
L2
public-domain → materializable
reactome
pathways
L2
public-domain → materializable
interpro
protein_families
L2
public-domain → materializable
complex-portal
protein_complexes
L2
public-domain → materializable
rhea
reactions
L2
attribution (CC-BY-4.0) → materializable
gene-ontology
ontology
L2
attribution (CC-BY-4.0) → materializable
gtex
expression
L2
IndexProxy (redistribute:false) — see note
gwas-catalog
gwas
L2
IndexProxy (redistribute:false) — see note
jaspar
tf_motifs
L2
IndexProxy (redistribute:false) — see note
monarch
phenotypes
L2
IndexProxy (redistribute:false) — see note
hpo
phenotypes
L2
IndexProxy (redistribute:false) — see note
cbioportal
cancer_genomics
L2
IndexProxy (redistribute:false) — see note
chembl
drugs
L2
copyleft (share-alike) → served LIVE, reproducible:false
guide-to-pharmacology
pharmacology
L2
copyleft (share-alike) → served LIVE, reproducible:false
⚠️ Copyleft caveat (ChEMBL, Guide to PHARMACOLOGY). These two are
Creative Commons Attribution-ShareAlike (copyleft / share-alike). The engine
refuses to materialize a share-alike source, so every result from them is
served live and is reproducible:false by construction — no pin makes it
reproducible. Carry the attribution string; for a reproducible drug-data answer,
prefer a materializable source. Full routing, license postures, and attribution
rules: references/sources.md.
Worked Recipe A — Ebola, reproduced (flagship)
Goal: the complete-genome records for Zaire ebolavirus in NCBI Virus,
pinned, complete, and offline-verified. Exact values from the repo case study.
Result (this pin): 32 records, completeness.state = complete (32 == 32
authoritative), logical_record_hash = sha256:01fffd0c…, NCBI datasets version
18.30.1, reproducible: true. verify re-derives the count and hash from the
snapshot offline — a shortened or altered snapshot is refused
(COMPLETENESS_DRIFT / HASH_MISMATCH).
Cite it like this: "NCBI Virus, complete-genome records for taxon 186538
released since 2023-01-01; snapshot sha256:b1983c09…; 32 records, Complete
(32/32); logical_record_hash sha256:01fffd0c…; verified offline." The "32" is a
property of this pin, not an eternal count — NCBI grows daily; the pin always
yields this set. More recipes (UniProt, resolve, export, multi-filter):
references/recipes.md.
Error Handling
Stable, surface-independent codes (identical across MCP/CLI/REST). Group them by
action, not by name:
Band
Codes
Action
Self-correct locally
UNKNOWN_FIELD, BAD_ENUM, INVALID_FILTER
Re-read the catalog filter schema; fix the field / value / operator before any network call
Self-correct the query
UNSATISFIABLE_QUERY
Caller-fixable (maps to 4xx/422); read the message, change the query (add a co-filter, shrink the window) — never retry unchanged
Stop and report the exact code. A drift refusal caught a real reproducibility problem; it is not a bug to retry around
Fallback
INTERNAL
Unexpected; report verbatim, do not paper over
A verify that returns a drift code is doing its job — refusing a result that
does not reproduce. Full ~28-code table grouped by recover-or-stop:
references/errors.md.
Decision Points
Decision
Default
Override when
Pin a snapshot_version?
Always
Never skip if the result is reported/cited/re-run
MCP tool vs CLI
MCP pinakes_<verb> if present
CLI pinakes <verb> when no MCP tool; same args
Apply a limit?
No (limit ⇒ best_effort)
Only for a deliberate sample you label non-complete
estimate before search?
Skip for small queries
Use when cost/size is unknown — not a completeness claim
Verify before citing?
Always
No exception — verify is the gate
Use ChEMBL for a reproducible answer
No (served live)
Use only when live drug data is acceptable; carry attribution
Accept best_effort
Only if labeled as such
Never present best_effort/partial as "all"
Common Issues
Issue
Cause
Solution
reproducible:false on a clean query
No snapshot_version (served latest)
Pass a concrete sha256:… pin
Count differs on re-run
Ran against latest; source grew
Pin a snapshot; report count as a property of the pin
Result marked best_effort unexpectedly
A limit below the authoritative total
Drop the limit; let complete-or-fail reconcile
IMMATURE_SOURCE on verify
Source is L0/L1 (not L2+)
Reproducibility is impossible below L2; pick an L2+ source
ChEMBL never reproducible
Copyleft (share-alike) → served live
Expected; carry attribution, prefer a materializable source for reproducibility
UNSATISFIABLE_QUERY loops
Retried identical filters
Read the message; change the query (co-filter, smaller window)
UNKNOWN_FIELD / BAD_ENUM
Filter not in the source schema
Re-read catalog --source-id <id>; fix locally before the call
SNAPSHOT_NOT_FOUND
Pinned a snapshot not in the store
Use a snapshot the catalog/case study actually pins
HASH_MISMATCH / COMPLETENESS_DRIFT on verify
Snapshot shortened/altered, or drift
Stop; do not cite — the refusal is correct
MCP client can't find pinakes
Not on the GUI app's PATH
Use the absolute path from which pinakes in the config
Export bytes differ but hash matches
Export format isn't the anchor
The anchor is the NDJSON logical_record_hash, not export bytes
Treating an estimate as the count
estimate is a dry run
Estimates never substitute for reconciliation; run search
Multi-source verify refused
MULTI_SOURCE_UNSUPPORTED (deferred)
Verify single-source manifests; split the query
Asked for arXiv / literature
Not shipped yet
Out of scope; use a literature tool, not Pinakes
resolve returns ambiguities
Many-to-many identifier mapping
Surfaced on purpose, not an error; read ambiguities, pick per authority
Suggested Next Steps
Pinakes produces the verified input; hand the manifest to a domain skill for
the science:
references/recipes.md — Recipes B–F (UniProt, resolve, export, …), each ending in cite-the-manifest, in both MCP + CLI forms.
Scripts:
scripts/verify_and_cite.sh — verify a manifest, and on pass print a paste-ready citation; degrades to a no-op message if pinakes is absent.
Self-describing surface:pinakes catalog and MCP tools/list carry the
live source list, filter schemas, and every verb's parameters — the contract is
in-band. This skill is the judgement layer on top.
