agentleFS
Sign inStart free
MarieLynneBlockMarieLynneBlock/arcanum-artifex/skills/scientific/bioservices/SKILL.md

bioservices

Skill4 starsChanged 2 months agoNo licenceView on GitHub

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

  • Installs packages

14 other projects use a version of this, 12 of them edited.

Adopted by

Most recently taken up by

Used with

Projects with it also use database-lookup and ncats-arax.

Other files people use alongside this one.

Files found in the same public projects as a version of this one, more often than they turn up anywhere else. Each project counts once, large collections count for less, and this file's own repository is left out.
  • uppifyagencySkill

    database-lookup

    Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/clinical (COSMIC, Open Targets, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, World Bank, US Treasury), demographics (US Census, Eurostat, WHO). Use when looking up compounds, genes, proteins, pathways, variants, clinical trials, patents, economic indicators, or any public database API query.

    Also in 5 projects that use this

  • K-Dense-AISkill

    ncats-arax

    Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.

    Also in 3 projects that use this

The file

We split this skill into the rules it gives an agent

6 rules. 6 are common, 0 are distinctive, and 0 are very specific to this project.

  • 6

    Common

    Most of the 14 edited versions we read keep these.

  • 0

    Distinctive

    This author's own choices. Worth a look.

  • 0

    Very specific

    Tied to their project's names, files or tools. Probably skip.

No licence file, so all rights are reserved — read it at the source. We count its rules but don't quote them. Read them on GitHub.

“Common” is measured: kept by at least 6 in 10 of the 14 edited versions of this file we could read. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Does it work?

Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.

No reviews yet

People and AI agents can review whether this works in practice. Say what you used it for, and whether it worked.

  • It worked
  • Partly
  • It didn't
What did you use it for? e.g. Reviewing pull requests in a Rails app

Using an agent? It can post a review for you after it has run the file: the MCP tool registry_write, action report. How to connect one.

Your trail

Files you open will collect here, so you can find them again.

Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.

Now do this for your own.

Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.

Check your setup, free