@pipeworx/catnap

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

Tools: 3

HIV-1 broadly neutralizing antibody potency (LANL CATNAP: IC50/IC80/ID50 across antibody-virus panels) plus HIV T-cell epitope and antibody-binding-site records (LANL HIV Molecular Immunology Database).

Tools

• catnap_search_neutralization(antibody?, virus?, limit?) — antibody-virus neutralization measurements (IC50/IC80/ID50), the antibody’s potency compared across viral strains. Censored bounds (>150, <.05) are returned as censored: true with numeric_value: null — never coerced to a number.
• catnap_antibody_info(name, limit?) — antibody metadata: epitope/binding region, structure (PDB), isolation paper, panel summary stats.
• immunology_search(table, mab_name?, epitope?, protein_name?, limit?) — T-cell epitopes (CTL/CD8+ or T-helper/CD4+) or antibody binding sites, queried live from LANL’s own API.

Auth

Keyless. catnap_search_neutralization and catnap_antibody_info return neutralization/antibody data ingested monthly from LANL’s CATNAP bulk files (credentials injected by the gateway). immunology_search calls LANL’s public JSON API directly on every call — no ingest.

Data sources

• https://www.hiv.lanl.gov/components/sequence/HIV/neutralization/index.html (CATNAP) — antibody-virus neutralization panels (IC50/IC80/ID50), compiled by LANL from published papers. Monthly bulk tab-delimited files (assay_*.txt, abs_*.txt, viruses_*.txt), filename dated at each drop — the ingest scrapes the download page for the current links rather than hardcoding a date. Ingested by workers/data-pipeline/src/datasets/catnap.ts on a monthly cadence into catnap_neutralization, catnap_antibodies, catnap_viruses (see supabase/migrations/170_catnap_neutralization.sql).
• https://www.hiv.lanl.gov/mojo/immunology/api/v2 (HIV Molecular Immunology Database JSON API) — CTL/CD8+, T-helper/CD4+ and antibody epitope/binding-site records. Keyless, queried live, no ingest.

What to get right

• Censored values are never coerced. IC50/IC80/ID50 in the source are sometimes a bound (>150 = not neutralized up to the highest concentration tested; <.05 = fully neutralized at the lowest concentration tested), not a point estimate. Every measurement carries _raw (verbatim string), _value (numeric, null when censored) and _censor ('<'/'>', null otherwise). A >50 stored as 50 would invert a potency ranking.
• Assay context travels with every value. IC50/IC80 from different papers use different protocols and virus stocks — the tool always returns reference/pubmed_id and never implies cross-study comparability just because two values are both labelled “IC50”.
• Two different questions live in this one pack. catnap_search_neutralization/catnap_antibody_info answer “how potent is this antibody” (CATNAP); immunology_search answers “where on the virus does this immune response target, and which HLA restricts it” (Immunology DB) — a different upstream database with its own record IDs.

Refresh path

workers/data-pipeline/src/datasets/catnap.ts, registered in workers/data-pipeline/src/datasets/index.ts, schedule: 'monthly'. Re-fetches and re-parses all three CATNAP bulk files each run (the neutralization file is ~200k rows / ~16MB, chunk-upserted with a cursor across invocations); no stale-row delete — CATNAP accumulates measurements rather than retracting them.

Tools

• catnap_search_neutralization — HIV broadly neutralizing antibody POTENCY: IC50/IC80/ID50 measurements for an antibody across viral strains, or for a strain across antibodies, from LANL CATNAP. Answers “how potent is VRC01 against t
• catnap_antibody_info — Metadata for an HIV antibody in LANL CATNAP: which region of the virus it binds (CD4 binding site, V3 glycan, MPER, …), its aliases, the paper that isolated it with PubMed id, light chain type, ADCC a
• immunology_search — Search the LANL HIV Molecular Immunology Database for T-cell epitopes (CTL/CD8+ or T-helper/CD4+) or antibody binding sites — a different question from catnap_search_neutralization: this is about WHER