Database Lookup
Look up scientific records—plasmids, protein structures, and related repositories—via documented HTTP APIs from an agent session.
Overview
Database-lookup is an agent skill most often used in Idea (also Build integrations, Grow content) that teaches agents how to query Addgene and AlphaFold DB HTTP APIs.
Install
npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill database-lookupWhat is this skill?
- Addgene REST patterns: plasmid by ID, keyword search, depositors, and articles with Token auth
- AlphaFold DB metadata via UniProt accession plus direct PDB/mmCIF/PAE file URL templates
- Documents .env loading for ADDGENE_API_KEY and no-auth public structure endpoints where applicable
- JSON response shapes called out for plasmid metadata and prediction metadata
- Agent-oriented integration skill for lab-adjacent and computational biology solo projects
- Documents Addgene endpoints for plasmids, search, depositors, and articles
- AlphaFold structure files use AF-{UNIPROT}-F1-model_v4 naming for PDB and mmCIF
Adoption & trust: 601 installs on skills.sh; 27.6k GitHub stars; 2/3 security scanners passed (skills.sh audits).
What problem does it solve?
You need plasmid or AlphaFold structure facts in your agent chat but keep looking up endpoints and auth formats from scratch.
Who is it for?
Solo builders on bioinformatics, lab informatics, or science-education agents who routinely hit Addgene or AlphaFold.
Skip if: Generic CRUD app developers with no scientific data sources, or teams that already centralize all lookups in a governed internal API.
When should I use this skill?
You need agent-guided HTTP lookups against Addgene or AlphaFold DB during research or integration work.
What do I get? / Deliverables
Your agent can fetch structured JSON metadata and construct correct AlphaFold download URLs using the documented API patterns.
- Fetched JSON metadata summaries
- Constructed structure file URLs or download instructions
Recommended Skills
Journey fit
Spans multiple journey phases - primary shelf plus alternate fits below.
Early journey research is where builders validate biology or bioinformatics ideas before writing custom ETL or UI. Research subphase fits API-backed lookups (Addgene, AlphaFold DB) that inform specs rather than production deploy artifacts.
Where it fits
Pull Addgene plasmid 12260 metadata while evaluating a CRISPR tooling idea.
Implement a small fetcher service that wraps the documented AlphaFold prediction endpoint.
Draft a blog post that links correct AF-UniProt structure files for cited proteins.
How it compares
Thin integration skill over public science APIs—not a database ORM skill or a local SQLite helper.
Common Questions / FAQ
Who is database-lookup for?
Indie builders and researchers automating scientific literature or entity lookups with Claude Code-style agents.
When should I use database-lookup?
Use it in Idea → research when scoping a biotech tool, in Build → integrations when wiring fetchers, and in Grow → content when citing structures or plasmids in public writeups.
Is database-lookup safe to install?
Review the Security Audits panel on this page; store Addgene API keys in .env, never commit tokens, and respect each database’s terms and rate-limit guidance.
SKILL.md
READMESKILL.md - Database Lookup
# Addgene (Plasmid Repository) ## Base URL ``` https://www.addgene.org/api/ ``` ## Auth API key required. Register at addgene.org and request API access. Pass as: `Authorization: Token <your_api_key>` Load from `.env` as `ADDGENE_API_KEY`. ## Key Endpoints | Endpoint | Description | |----------|-------------| | `/plasmids/{addgene_id}/` | Get plasmid details by ID | | `/plasmids/search/?q={query}` | Search plasmids by keyword | | `/depositors/{id}/` | Depositor information | | `/articles/{id}/` | Associated publications | ## Example Calls ``` # Get plasmid details (e.g., pSpCas9) GET https://www.addgene.org/api/plasmids/12260/ Authorization: Token YOUR_KEY # Search plasmids GET https://www.addgene.org/api/plasmids/search/?q=GFP Authorization: Token YOUR_KEY ``` ## Response Format JSON with plasmid name, backbone, inserts, resistance markers, depositor, sequences, publications. ## Rate Limits No published limits. Reasonable use expected. # AlphaFold DB (Predicted Protein Structures) ## Base URL ``` https://alphafold.ebi.ac.uk/api/ ``` ## Auth No auth required. ## Key Endpoints | Endpoint | Description | |----------|-------------| | `/prediction/{uniprot_accession}` | Prediction metadata by UniProt ID | ## Structure File URLs (direct download) ``` https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v4.pdb https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v4.cif https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-predicted_aligned_error_v4.json ``` ## Example Calls ``` # Get prediction metadata for EGFR https://alphafold.ebi.ac.uk/api/prediction/P00533 # Download PDB structure https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v4.pdb # Download PAE (predicted aligned error) https://alphafold.ebi.ac.uk/files/AF-P00533-F1-predicted_aligned_error_v4.json ``` ## Response Format JSON for metadata. PDB/mmCIF for structures. PAE as JSON matrix. ## Rate Limits No strict limits. Use FTP/Cloud for bulk downloads (~200M+ structures). # Alpha Vantage API Reference ## Overview Alpha Vantage provides free APIs for real-time and historical stock prices, forex rates, cryptocurrency data, technical indicators, and fundamental data (earnings, balance sheets, income statements). Covers global equities, ETFs, mutual funds, and commodities. ## Base URL ``` https://www.alphavantage.co/query ``` All requests use a single endpoint with `function` parameter to select the data type. ## Authentication - **API Key: REQUIRED.** Get a free key at https://www.alphavantage.co/support/#api-key - Pass as query parameter: `&apikey=YOUR_KEY` ## Rate Limits - **Free tier:** 25 requests per day. 5 calls per minute (as of late 2024; previously was 5/min + 500/day). - **Premium tiers** available for higher limits (30, 75, 150+ calls/min). - Exceeding limits returns a polite JSON message, not an error code. --- ## Key Endpoints (by `function` parameter) ### 1. Stock Time Series #### Intraday ``` GET /query?function=TIME_SERIES_INTRADAY&symbol={symbol}&interval={interval}&apikey={key} ``` | Parameter | Required | Values | |-----------|----------|--------| | `symbol` | Yes | Ticker symbol (e.g., `AAPL`, `MSFT`) | | `interval` | Yes | `1min`, `5min`, `15min`, `30min`, `60min` | | `outputsize` | No | `compact` (last 100 points, default) or `full` (full history) | | `adjusted` | No | `true` (default) or `false` | | `datatype` | No | `json` (default) or `csv` | **Example:** ``` https://www.alphavantage.co/query?function=TIME_SERIES_INTRADAY&symbol=AAPL&interval=5min&apikey=YOUR_KEY ``` #### Daily ``` GET /query?function=TIME_SERIES_DAILY&symbol=AAPL&apikey=YOUR_KEY ``` #### Daily (Adjusted for splits/dividends) ``` GET /query?function=TIME_SERIES_DAILY_ADJUSTED&symbol=AAPL&outputsize=full&apikey=YOUR_KEY ``` #### Weekly / Monthly ``` GET /query?function=TIME_SERIES_WEEKLY_ADJUSTED&symbol=AAPL&apikey=YOUR_KEY GET /query?function=TIME_SERIES_MONTHLY_ADJUSTED&symbol=AAPL&apikey=YOUR_KEY ``` **Response (Daily):** ```json { "Meta Da