@pipeworx/herb-tcm

Connect: https://gateway.pipeworx.io/herb-tcm/mcp · Install: one-click buttons

Tools: 7

HERB 2.0’s Traditional Chinese Medicine knowledge base — herbs, ingredients, gene targets, diseases, PubMed-cited papers and GEO transcriptomic experiments — proxied live from herb.ac.cn, with every relationship row tagged an evidence_tier so a statistical prediction is never mistaken for proof of efficacy.

Tools

• herb_search(keyword, category?) — resolve a name to an id. Accepts Chinese characters, pinyin, English/Latin names, gene names/aliases, disease names, or a HERB id itself. category is one of herb / ingredient / target / disease (default herb).
• herb_browse(category, page?, page_size?) — page through the full herb/ingredient/target/disease list (7,263 / 49,258 / 12,933 / 28,212 rows respectively).
• herb_detail(id, category) — the full record for one id: composition, traditional-use summary, and every predicted or literature-backed target/disease relationship, each carrying its evidence_tier.
• herb_papers(drug_type?, experiment_type?, sort_by?, limit?, offset?) — list PubMed-cited references, each tagged human_clinical or laboratory.
• herb_paper_detail(paper_id) — one reference’s bibliographic record plus the specific targets/diseases it reports.
• herb_experiments(drug_type?, species?, experiment_type?, limit?, offset?) — list GEO-deposited herb/ingredient-vs-control transcriptomic experiments.
• herb_experiment_detail(experiment_id) — differential-expression results for one experiment: top up/down genes, enriched GO/KEGG terms, connectivity-map hit counts. Always evidence_tier: computational_prediction.

Evidence tiers

Every relationship row carries one of:

herb_target / herb_disease (statistical enrichment, p-value + FDR_BH columns), ingredient_target / ingredient_disease / target_disease (curated cross-references with no clinical backing) and every herb_experiment_detail row are computational_prediction. drug_paper_target / drug_paper_disease (PubMed-cited) are split into human_clinical or laboratory by resolving each cited paper’s own “Experiment type” — see Data sources below for how.

Auth

Keyless. herb.ac.cn requires no account, token or payment — it is public data served to anyone.

Data sources

• http://herb.ac.cn/chedi/api/ — herb.ac.cn is a umi single-page app with no REST surface (every path returns the same ~900-byte shell). The real API is this one POST endpoint, dispatching on a func_name body field, found in the site’s own JS bundle (http://herb.ac.cn/static/umi.js). Seven verbs, confirmed live 2026-09-08: search_api, detail_api, browse_api, paper_api, paper_detail_api, experiment_api, experiment_detail_api.

Notes for the next person:

• http only, and Chinese-hosted — measured 200ms-1.5s per call from this session but expect latency and occasional unreachability; several .cn sources are known-flaky from our vantage. This is a known class, not a bug — report it rather than retrying hard.
• Every response is served as text/html, including successful ones — do not branch on Content-Type. The only reliable signal for “no such id” is the HTTP status: a bad key_id/label/paper_key_id/drug_GSE_id returns HTTP 500 with an HTML “Internal Server Error” page; an unknown func_name returns HTTP 200 with the literal body null. parseJson/httpError from @pipeworx/shared handle both shapes.
• Cells in every table are either a plain value or {link, title} / {style, title} — even header cells in the differential-expression tables come this way ({filterable, sortable, title}). tableToRows in src/index.ts unwraps every shape to a plain string/number.
• detail_api needs three params, not just the id: key_id, label (must match the id’s category — HERB… ids need label: "Herb", etc.) and v (the site’s own UI passes the id again under this name; omitting it was not tested and isn’t worth risking).
• drug_paper_target/drug_paper_disease rows (inside herb_detail) carry a Paper id but not that paper’s own experiment type, and a cited herb can reference 20-100+ papers. Rather than firing one paper_detail_api call per paper (impolite fan-out against a slow host), herb_detail makes ONE extra call to paper_api unfiltered — which returns HERB’s entire ~2,000-row reference index including “Experiment type” per id — and resolves the tier from that in-memory lookup. Nothing from it is cached across tool calls; it is refetched live every time herb_detail needs it.
• Ingredient_alias (inside an ingredient’s detail_api response) is not a table — it’s a one-element array holding one semicolon-joined string of synonyms. Treating it as a table throws (table[0].map is not a function); split on ; instead.
• experiment_detail_api’s Experiment_detail field nests everything one level deeper than expected: it’s an object with exactly one key, named “HBEXP000001 Data Detail” (the experiment id plus a fixed suffix), whose value is { data: {...} }. The differential-expression/GO/KEGG/CMAP tables live under that single value’s data field — src/index.ts grabs it with Object.values(...)[0]?.data rather than building the key string, since the exact suffix isn’t documented anywhere.
• paper_api and experiment_api have no server-side pagination — each call returns the FULL filtered list (~2,000 papers / ~1,000 experiments unfiltered) in one response. herb_papers/herb_experiments slice client-side with limit/offset; a tighter drug_type/experiment_type filter reduces what herb.ac.cn itself has to compute and send.
• Licensing: settled by Bruce, fleet #1389 (2026-09-08) — a live per-request proxy call is a client, not a publisher, so it needs no explicit reuse grant the way bulk-copying the dataset would. This pack must stay a proxy: no bulk download, no full local mirror, no cached complete copy of herb.ac.cn’s data.

Tools

• herb_search — Search HERB 2.0 for a herb, ingredient, gene target or disease by Chinese name, pinyin, English name,
• herb_browse — Page through HERB 2.0’s full herb, ingredient, target or disease list (7,263 herbs / 49,258 ingredients /
• herb_detail — Full record for one HERB id: herb (composition + traditional-use summary + predicted and literature
• herb_papers — List PubMed-cited papers in HERB’s reference index — the literature backing herb/ingredient-target and
• herb_paper_detail — One reference’s bibliographic record (journal, PubMed id, experiment type, phenotype) plus the specific
• herb_experiments — List HERB’s transcriptomic experiments (herb/ingredient treatment vs. control, GEO-deposited) — the raw
• herb_experiment_detail — Differential-expression results for one HERB transcriptomic experiment: top up/down-regulated genes and