DEDUPED Hot AI repos, turned into use cases Get 5 a day

How to pull compound and protein records with source provenance with Scientific Agent Skills

Query public biology and chemistry databases and get each record with its source endpoint.

  • Top pick
  • Research
  • Intermediate
  • 45 minutes
  • From the README
  • Claude Code
  • Codex
  • Cursor

Credentials. Some databases need registered or licensed access, so store API keys outside shared notes and project files.

Who it is forA pharmacologist or research analyst who needs compound and protein records for a target list and must show where each value came from.

The problemGathering identifiers and properties from several databases by hand is slow, and records often lack a clear source trail.

The outcomeA table of records from the named databases, where every row lists the endpoint and access date used.

What you need first

  • An agent host that supports Agent Skills, such as Claude Code, Cursor, or Codex
  • Git, to clone the repository (inferred)
  • Python, since the repository language is Python
  • API keys or accounts for any registered or licensed database you plan to query

Steps

  1. git clone https://github.com/K-Dense-AI/scientific-agent-skills (inferred, check the README)
  2. Follow the install steps in the Getting Started section of the README for your agent host.
  3. Open skills/database-lookup/SKILL.md, which documents 80 databases with endpoint selection, pagination, and provenance.
  4. Give your agent the target list and the databases to query, such as PubChem, ChEMBL, or UniProt.
  5. Check that each row in the returned table lists its source endpoint before you use the data.

Prompt for your agent

Using the scientific-agent-skills repo, read skills/database-lookup/SKILL.md and query PubChem, ChEMBL, and UniProt for <target gene or compound list>. Return a table of identifiers and key properties, with the endpoint and access date for each row. Verify that every row names its source endpoint and flag any database that needs a key you do not have.

Caveat. The lookup skill covers 80 databases with different access rules, so check each database's terms before you use its data.

Share: X LinkedIn Hacker News Email Copy link

Disclaimer

Deduped lists open-source repositories that belong to other people. We do not own, maintain, audit, or vouch for any of them, and a repo appearing here is not an endorsement or a safety check. The use cases, steps, and prompts are written by AI and may be incomplete, outdated, or just wrong. Where a use case is marked "Seen in the wild", we link to public posts where someone described something similar, but we have not verified those posts and the use case itself is still our AI's own write-up. Use all of this at your own risk. Only run code, commands, or agents on systems and accounts you are authorized to use, and read the code and every command before you run it, especially anything that touches credentials, files, or the network. Nothing here is professional, security, legal, or financial advice. All trademarks and project names belong to their respective owners, and their use here does not imply affiliation. Content is provided as is, without warranties of any kind. Found a mistake, a safety problem, or something you want removed? Email [email protected] and we will look at it promptly. Full disclaimer page