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Exa 網路工具套件

由 Exa 驅動的網路工具套件,專為科學與技術內容最佳化。當使用者需要搜尋網路或擷取/提取 URL 內容時,請使用此技能。涵蓋:網路搜尋(語意查詢、研究、即時資訊 — 可選研究論文類別與學術網域過濾)和 URL 提取(批次提取網頁、文章、學術 PDF)。當使用者想要高品質搜尋或透過 category=research paper 進行學術過濾時,請使用此技能。觸發條件為搜尋、查詢、擷取頁面或提取文章等請求。

Exa 網路工具套件 是什麼?

Exa 網路工具套件 (exa-search) 是一個專為 AI 代理設計的技能,透過 Exa 的 API 提供高品質的網路搜尋與 URL 內容提取功能。其核心優勢在於 Exa 索引結合了關鍵字與語意檢索,特別適合科學、技術及概念性查詢。此技能支援 Claude Code、Coder、Cursor、Codex 等平台,使用者可透過路由指南選擇「網路搜尋」或「網頁提取」功能。學術研究方面,它提供雙重過濾機制:使用 --category "research paper" 偏向學術來源,並搭配 --include-domains 允許清單(如 arxiv.org、nature.com)以嚴格限制網域。技能透過 Python 指令稿 (exa_search.py 與 exa_extract.py) 運作,依賴 exa-py SDK,並要求設定 EXA_API_KEY 環境變數進行驗證。所有請求會加入自訂標頭 x-exa-integration 以追蹤使用來源。

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

在你喜歡的 AI 中提問

開啟一個已預先載入此 Agent Skill 的新對話。

說明文件

Exa 網路工具套件 是做什麼的?

由 Exa 驅動的網路研究任務技能:網路搜尋與 URL 提取。Exa 的索引結合了高品質的關鍵字與語意檢索,使其非常適合科學、技術及概念性查詢。

路由 — 選擇正確的能力

閱讀使用者的請求,並將其對應到下列其中一種能力。在執行指令前,請先閱讀對應的參考檔案以取得詳細指示。

使用者想要...能力參考位置
查詢某項資訊、研究主題、尋找即時資訊網路搜尋references/web-search.md
從特定 URL 提取內容(網頁、文章、PDF)網頁提取references/web-extract.md
安裝或驗證設定下方

決策指南

  • 預設使用網路搜尋:適用於主題查詢、研究問題或「什麼是 X?」這類查詢。當主題是科學或技術性時,傳遞 --category "research paper" 以偏向學術來源,並/或使用學術 --include-domains 允許清單。詳見 references/web-search.md 中的二次學術策略。
  • 使用網頁提取:當使用者提供 URL 或要求你讀取/擷取特定頁面時。對於批次提取(一次呼叫多個 URL)和學術 PDF,應優先使用此功能而非內建的網頁提取。

學術來源優先級

對於技術或科學查詢,優先選擇學術與科學來源:

  • 同儕審查期刊文章與會議論文優先於部落格文章或新聞
  • 預印本(arXiv、bioRxiv、medRxiv)在無同儕審查版本時使用
  • 機構與政府來源(NIH、WHO、NASA、NIST)優先於商業網站
  • 原始研究優先於二次摘要

引導 Exa 偏向學術內容的兩個槓桿:

  1. --category "research paper" 將檢索偏向學術來源。
  2. --include-domains 搭配學術允許清單(arxiv.org、nature.com、pubmed.ncbi.nlm.nih.gov 等)限制網域範圍。

兩者結合可獲得嚴格的學術結果。完整模式請參閱 references/web-search.md。

引用學術來源時,請在標準引用格式之外,盡可能包含作者姓名與出版年份(例如 Smith et al., 2025)。若有 DOI,請優先使用 DOI 連結。


設定

此技能使用 exa-py Python SDK。scripts/ 中的指令稿透過 PEP 723 內嵌中繼資料宣告其相依性,因此你可以直接使用 uv run 執行,無需額外安裝步驟:

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

若你偏好持久安裝:

uv pip install "exa-py>=1.14.0"

驗證

所有指令會從 EXA_API_KEY 環境變數讀取 API 金鑰。前往 dashboard.exa.ai/api-keys 取得你的 Exa API 金鑰。

首先,檢查專案根目錄是否存在 .env 檔案且包含 EXA_API_KEY。若有,請載入它:

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

若 dotenv 不可用,請安裝它:uv pip install python-dotenv[cli]。

若無 .env,請匯出金鑰至工作階段:

export EXA_API_KEY="your-key"

透過執行任何指令稿加上 --help 來驗證 — 若金鑰已設定,指令稿將正常退出;只有在執行實際查詢時才會執行驗證檢查。

追蹤標頭

此技能中的所有指令稿都會將 x-exa-integration 請求標頭設為 k-dense-ai--scientific-agent-skills,以便 Exa 將來自 K-Dense AI scientific-agent-skills 儲存庫的使用量歸因至此整合。調整指令稿時,請勿移除或重新命名此標頭。


此技能包含的檔案

  • SKILL.md — 此檔案(路由與設定)
  • references/web-search.md — 詳細的網路搜尋參考(含學術策略)
  • references/web-extract.md — URL 內容提取參考
  • scripts/exa_search.py — 圍繞 client.search_and_contents 的 CLI 包裝器
  • scripts/exa_extract.py — 圍繞 client.get_contents 的 CLI 包裝器

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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