Public Db Lookup

---
name: public-db-lookup
description: Fetch compact JSON records from UniProt, NCBI, MGnify, InterPro, AlphaFold DB, STRING, or ENA. Use when looking up an accession, taxon, entry, or structure in a public database.
---

# Public Database Lookup

One bounded GET against a public life-science REST API. The bundled script picks the base URL, adds a User-Agent, retries on 429 and 5xx, and prints a compact JSON envelope instead of the full payload.

## Instructions

1. Pick the service that owns the record: `uniprot`, `ncbi-entrez`, `ncbi-datasets`, `mgnify`, `interpro`, `alphafold`, `string`, or `ena`.
2. Read the card for that service in [references/services.md](references/services.md) for the path, parameters, and the right `--record-path`.
3. Run the wrapper, `scripts/lookup` in this skill's directory (installed at `~/.agents/skills/public-db-lookup/scripts/lookup`).
4. Keep `--max-items` small (default 5). Raise it only when the user needs more rows.
5. When the full payload matters, add `--save-raw PATH` and work from the file; the envelope still carries the compacted view.
6. For the two NCBI services, the script reads `NCBI_API_KEY`, `NCBI_EMAIL` and `NCBI_TOOL` from the environment, adds them as request parameters, and redacts the key from its output. Use only values the user exported; never set `NCBI_EMAIL` to an address from the conversation or system context.
7. Requests are paced across invocations, so calling the CLI in a loop stays inside each service's documented rate. The timestamps live under `$XDG_STATE_HOME/omics-skills/public-db-lookup`; override with `--state-dir`. Never pass a credential in `--path` or `--param`: the script refuses it, because it would be echoed back in the emitted URL and land in shell history.
8. Route PubMed and PMC literature searches to `/polars-dovmed`; this skill does not cover them.

### Execution behavior

- Summarize the JSON envelope in Markdown by default.
- Return raw JSON only when the user asks for machine-readable output.
- When the payload is large, use `--save-raw` and report the path instead of pasting the content.
- Re-run the lookup rather than trust tool output from earlier in a long conversation.

## Quick Reference

| Flag | Meaning |
|------|---------|
| `--service NAME` | One of the eight services (required) |
| `--path PATH` | Endpoint path relative to the service base URL, or a full URL under that base (required) |
| `--param KEY=VALUE` | Query parameter; repeat as needed |
| `--record-path a.b.c` | Dotted path to the record list; inferred from common keys when omitted |
| `--max-items N` | Records, list items, and dict keys kept per level (default 5) |
| `--max-depth N` | Nesting depth kept before containers collapse (default 3) |
| `--format auto\|json\|text` | Parse as JSON, or keep the first 800 characters of text (default auto) |
| `--save-raw PATH` | Write the full response body to PATH |
| `--timeout SEC` | Request timeout (default 30) |

## Input Requirements

- `uv` and network access; the PEP 723 script installs its pinned HTTP dependency
- A service name and an endpoint path from the service card
- Optional query parameters, one `--param` each
- Optional `NCBI_API_KEY`, `NCBI_EMAIL`, `NCBI_TOOL` in the environment for NCBI services

## Output

One JSON object on stdout.

- Success: `ok`, `source`, `url` (api_key value removed), `status_code`, `warnings`, `raw_output_path` (the path given to `--save-raw`, else null), plus one of:
  - list results: `record_path`, `record_count_returned`, `record_count_available`, `truncated`, `records`
  - other JSON: `summary`, `top_keys`
  - text: `text_head`, `text_head_truncated`
- Failure: `ok: false`, `source`, and `error` with `code` (`invalid_input`, `network_error`, `http_error`, `invalid_response`) and `message`
- Exit code 0 on success, 2 for `invalid_input`, 1 for the other errors
- Compaction: strings cut at 240 characters, lists at `--max-items` with a trailing count marker, dicts at `--max-items` keys with a `_truncated_keys` count, deeper containers replaced by an ellipsis

## Quality Gates

- [ ] `--max-items` is the smallest count that answers the question
- [ ] `--record-path` matches the service card, or the inferred path in the envelope is the intended list
- [ ] NCBI credentials come from the environment, never from the command line
- [ ] `warnings` and `truncated` from the envelope reach the user
- [ ] Every accession or identifier in the reply came from the response, not from memory

## Troubleshooting

**Issue**: `http_error` with HTTP 429 after retries.

**Solution**: The service is rate limiting you. Wait, lower the request rate, and for NCBI set `NCBI_API_KEY` to raise the allowed rate.

**Issue**: `records` is empty or the envelope falls back to `summary` with a warning.

**Solution**: The record list is not under an inferred key. Read `top_keys` and pass the right `--record-path` from the service card.

**Issue**: NCBI rejects or throttles requests that carry no contact details.

**Solution**: Ask the user to export `NCBI_EMAIL` and `NCBI_TOOL`; NCBI asks for both on every E-utilities request.

## Non-Goals

- No POST requests, ID-mapping jobs, or other asynchronous job APIs
- No bulk downloads of sequence or structure files
- No literature search; use `/polars-dovmed`
- No JGI-internal data access (GOLD, IMG, JAMO); this skill covers public endpoints only