database-lookup

Query 78 public database APIs with documented endpoints, pagination, and auditable provenance.

Updated Aug 12, 2026
One-click install
npx skills add https://github.com/Mzane0803/latent-minds-skills-marketplace --skill database-lookup-mzane0803
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: database-lookup
Source: https://github.com/Mzane0803/latent-minds-skills-marketplace/tree/main/plugins/research-writing/skills/database-lookup
Command: npx skills add https://github.com/Mzane0803/latent-minds-skills-marketplace --skill database-lookup-mzane0803

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve? Scientific, regulatory, and financial facts often need to be retrieved reproducibly from authoritative databases rather than inferred from general knowledge, but each database has different endpoints, identifier formats, pagination rules, and rate limits. This Skill turns a user's intent into a bounded, rate-limited, fully documented API retrieval that another agent or human can repeat. ## Core Features & Use Cases - 78 documented databases: Covers physics, chemistry, genomics, clinical, patents, economics, and demographics, each with a reference file detailing endpoints, parameters, and worked queries. - Identifier resolution workflows: Converts between UniProt, Ensembl, NCBI Gene, PubChem CID, ChEMBL, rsID, MONDO, and other identifier systems when a query fails. - Reproducible retrieval contract: Counts first, paginates exhaustively, reconciles retrieved vs expected totals, and returns provenance including endpoints, parameters, access date, and warnings. - Use Case: Ask for all clinical trials for a given drug target; the Skill selects ClinicalTrials.gov, resolves the target identifier, paginates through results, and returns a structured table with count reconciliation and query provenance. ## Quick Start Use the database-lookup skill to retrieve all known binding affinities for UniProt target P35355 from BindingDB with full provenance.

Frequently Asked Questions about database-lookup

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query public scientific databases via API reproducibly?▼

Define a retrieval contract specifying the target entity, identifiers, filters, and scope, then call the database's documented REST endpoint with bounded, rate-limited requests. Record endpoints, parameters, access date, and count reconciliation so the lookup can be repeated.

What databases can I query for gene, protein, and compound data?▼

This Skill documents 78 databases including UniProt, Ensembl, NCBI Gene, PubChem, ChEMBL, Reactome, STRING, and AlphaFold DB. Each has a reference file with endpoints, query formats, rate limits, and worked example calls.

How do I convert between gene and compound identifier formats?▼

Resolve gene symbols through NCBI Gene to get NCBI Gene IDs, then convert to Ensembl or UniProt accessions via their xref endpoints. For compounds, look up names in PubChem to get CIDs, then map to ChEMBL IDs via UniChem.

Does this work with APIs that require POST requests like Open Targets?▼

Yes, POST-only APIs such as Open Targets, gnomAD, and GDC/TCGA are supported via curl through the shell tool, since GET-only fetch tools cannot call GraphQL or complex filter endpoints. Example curl commands are documented for each.

What happens when an API query returns no results or fails?▼

The Skill checks identifier format first, tries alternative identifiers, then falls back to a different database listed in the selection guide. Failures are reported explicitly with the database name, error, and alternatives attempted.

Are there limits on large data retrievals from these APIs?▼

Retrievals are bounded at 10,000 records or 100 API calls unless the user confirms a larger plan. For bulk needs, official database dumps are recommended over looping through individual API requests.