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exa-search

Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and academic domain filtering) and URL extraction (fetching pages, articles, academic PDFs in batch). Use this skill for web-related tasks when the user wants high-quality search or scholarly filtering via category=research paper. Triggers on requests to search, look up, fetch a page, or extract an article.

Was ist exa-search?

exa-search is a Claude Code agent skill that web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and academic domain filtering) and URL extraction (fetching pages, articles, academic PDFs in batch). Use this skill for web-related tasks when the user wants high-quality search or scholarly filtering via category=research paper. Triggers on requests to search, look up, fetch a page, or extract an article.

Funktioniert mit✓Claude Code~Codex CLI~Cursor
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/exa-search
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Dokumentation

Exa Web Toolkit

A skill for web-powered research tasks backed by Exa: web search and URL extraction. Exa's index combines high-quality keyword and semantic retrieval, which makes it well-suited to scientific, technical, and conceptual queries.

Routing — pick the right capability

Read the user's request and match it to one of the capabilities below. Read the corresponding reference file for detailed instructions before running commands.

User wants to...CapabilityWhere
Look something up, research a topic, find current infoWeb Searchreferences/web-search.md
Fetch content from a specific URL (webpage, article, PDF)Web Extractreferences/web-extract.md
Install or authenticateSetupBelow

Decision guide

  • Default to Web Search for topic lookups, research questions, or "what is X?" queries. When the topic is scientific or technical, pass --category "research paper" to bias toward scholarly sources, and/or an academic --include-domains allowlist. See references/web-search.md for the two-pass academic strategy.
  • Use Web Extract when the user provides a URL or asks you to read/fetch a specific page. Prefer this over the built-in WebFetch for batch extraction (multiple URLs in one call) and for academic PDFs.

Academic source priority

For technical or scientific queries, prefer academic and scientific sources:

  • Peer-reviewed journal articles and conference proceedings over blog posts or news
  • Preprints (arXiv, bioRxiv, medRxiv) when peer-reviewed versions aren't available
  • Institutional and government sources (NIH, WHO, NASA, NIST) over commercial sites
  • Primary research over secondary summaries

Two levers to steer Exa toward scholarly content:

  1. --category "research paper" biases retrieval toward scholarly sources.
  2. --include-domains with a scholarly allowlist (arxiv.org, nature.com, pubmed.ncbi.nlm.nih.gov, etc.) restricts the domain pool.

Combine both for strictly academic results. See references/web-search.md for the full pattern.

When citing academic sources, include author names and publication year where available (e.g., Smith et al., 2025) in addition to the standard citation format. If a DOI is present, prefer the DOI link.

Setup

This skill uses the exa-py Python SDK. The scripts in scripts/ declare their dependencies via PEP 723 inline metadata, so you can run them directly with uv run without a separate install step:

uv run --with exa-py python "$SKILL_PATH/scripts/exa_search.py" --help

If you prefer a persistent install:

uv pip install "exa-py>=1.14.0"

Authentication

All commands read the API key from the EXA_API_KEY environment variable. Get your Exa API key at dashboard.exa.ai/api-keys.

First, check if a .env file exists in the project root and contains EXA_API_KEY. If so, load it:

dotenv -f .env run -- uv run --with exa-py python "$SKILL_PATH/scripts/exa_search.py" "your query"

If dotenv isn't available, install it: uv pip install python-dotenv[cli].

If there's no .env, export the key for the session:

export EXA_API_KEY="your-key"

Verify by running any script with --help — it will exit cleanly if the key is set and auth-check runs only when a real query is made.

Tracking header

Every script in this skill sets the x-exa-integration request header to k-dense-ai--scientific-agent-skills so Exa can attribute usage from the K-Dense AI scientific-agent-skills repo to this integration. Do not remove or rename this header when adapting the scripts.

Files in this skill

  • SKILL.md — this file (routing and setup)
  • references/web-search.md — detailed web search reference with academic strategy
  • references/web-extract.md — URL content extraction reference
  • scripts/exa_search.py — CLI wrapper around client.search_and_contents
  • scripts/exa_extract.py — CLI wrapper around client.get_contents

Individual skills in this repo

This repo contains 20 individual skills — each has its own dedicated page.

adaptyv

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

aeon

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

alphagenome

Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), score variants or scan windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and build Atlas website deep links. Use when the user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.

analytical-method-validation

Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

arbor

Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g.

arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

astropy

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.

autoskill

Observe the user

benchling-integration

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

bgpt-paper-search

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

bids

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biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

bioservices

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.

bulk-rnaseq

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g.

cellxgene-census

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

citation-management

Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

clinical-decision-support

Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.

clinical-reports

Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.

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