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概要と使いどころ
Enrich any entity — companies, domains, emails, or people — with verified data from multiple sources. Combines Apollo, Strale, LinkedIn, and Akta data to fill gaps in your CRM, lead databases, or research datasets with production-quality enrichment.
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Map any industry's competitive landscape using company databases, academic research, news coverage, LinkedIn activity, and job market signals. Produces industry overviews with key players, market segments, growth indicators, and emerging disruptors.
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Research emerging academic trends by combining scholarly databases, web sources, and news to identify rising research areas, breakthrough papers, and shifting scientific consensus. Ideal for R&D teams tracking frontier science.
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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.
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Processes environmental DNA metabarcoding data from raw amplicon reads to species occurrence tables using OBITools3, DADA2, and taxonomic assignment against BOLD, MIDORI2, or MitoFish databases. Handles COI, 12S, rbcL, and ITS barcode regions with primer removal, denoising, chimera detection, and contamination filtering via decontam. Includes occupancy modeling (occumb) for detection probability correction. Use when analyzing eDNA from water, soil, or bulk samples for biodiversity monitoring. Not for 16S human microbiome (see microbiome/amplicon-processing).
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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.
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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.
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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.
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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).
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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.
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Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".
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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.
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Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.
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Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.
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Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.
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Find academic papers across up to 8 sources (OpenAlex / Semantic Scholar / CrossRef / PubMed / arXiv for English, OpenReview for AI venues, plus native-Chinese retrieval via NSSD 国家哲社文献中心 + yiigle 中华医学期刊) with adjustable depth — Quick scan (5 min) to Audit prep (3 hr). Use when the user wants to find papers, run a literature search, gather references, scope a research topic, search Chinese-language / 中文原生 literature (中文文献/中文核心/CSSCI/C刊/国内研究/国内文献/中华××期刊/心理学报/经济研究), or filter results by journal tier (中科院分区/一区/几区, Q1, JCR/SJR quartile, 影响因子/impact factor, 期刊分区, 顶刊/top journal, '按分区筛'), or export paste-ready professional search strategies / 检索式 for external databases (PubMed / WOS / Scopus / Embase / 知网 CNKI / 万方 / SinoMed — '写检索式', '导出检索式', 'WOS 检索式', '知网专业检索', 'search strategy', 'boolean search strategy'). Triggers on search verbs ('find papers', 'literature search', 'papers about X'), review types ('scoping review', 'systematic review', 'SR prep', 'literature review', 'lit review', 'help me write a lit review'), Chinese ('找文献', '找论文', '论文搜索', '学术检索', '文献检索', '文献综述', '综述前期', '求文献', '中文文献', '中文核心', 'CSSCI', 'C刊', '国内研究', '找中文的'). Outputs Shadcn HTML report + BibTeX/RIS/CSV + PRISMA-S log. Do NOT use for: concept explanations ('what is X' / 'X 是什么', e.g. '影响因子怎么算'), writing ('帮我写' / 'help me write a paragraph'), single-paper interpretation or PDF download with metadata (use paper-downloader-portable), or when the user already has a literature set (use literature-set-review).
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Internal — for Boundless team members only. Query Boundless broker telemetry tables on Redshift for prod/staging operational data. Use when the user asks about broker health, request evaluations, request completions, proving times, skip rates, telemetry data, or wants to run SQL against the telemetry database on live networks. Also covers historical telemetry through 2026-04-24 stored as Parquet archives in S3 (queried via DuckDB). Do NOT use for debugging local code changes, reviewing PRs, or investigating issues in the codebase itself.
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Extract structured company lists from directories with Firecrawl. Use for scraping YC, Crunchbase, Product Hunt, G2, startup directories, category directories, or custom company databases into JSON, CSV, CRM-ready lists, or research tables.
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Generate structured lead lists from prospect databases and web directories with Firecrawl browser. Use for finding prospects by role, company type, industry, stage, location, technologies, or other criteria and exporting CRM-ready JSON or CSV.
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Analyze indexed codebases via graph database (neug) and vector index (zvec). Covers call graphs, dependencies, dead code, hotspots, module coupling, architecture reports, semantic search, impact analysis, bug root cause from GitHub issues, class diagrams (UML), and PR review (risk scoring, conflict detection, auto-merge candidates, labeling). Also covers creating, inspecting, and repairing a CodeScope index. Use for: code structure, who calls what, why something changed, similar functions, module boundaries, bug tracing, class relationships, PR risk/conflicts, or any question benefiting from a code knowledge graph. Applies when a `.codegraph` index exists in the workspace, or when the user wants to create one.
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Vulnerability audit and dataflow analysis built on the neug CPG engine. file_audit (default, recommended): first builds a function-level summary graph (tier1) over the entire project, then incrementally builds detailed CPGs (tier2) on demand for chosen functions; both tiers coexist in a single neug database (unified schema, cross-layer refines edges; C/Java/Python/Rust). All capabilities are exposed as CLI tool subcommands (audit/overview/build/query/methods/paths), so an agent can drive the audit step by step via shell; the audit subcommand can also run the built-in LLM loop. The same tooling also supports a dataflow analysis mode (Workflow C): no vulnerability hunting, only variable-level dataflow tracing for functions of interest, producing dataflow_analysis.json. repo_audit: multi-round LLM/Cypher audit over a full-repo CPG. Use when the user asks to audit a codebase/project for vulnerabilities, scan a project with CPG/neug, run repo_audit/file_audit, find source-to-sink taint paths, or analyze dataflow inside a function. Supports C, Java, Python, and Rust.
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Build local-first applications with ElectricSQL — sync Postgres data to client devices in real-time. Use when someone asks to "sync database to client", "local-first app", "ElectricSQL", "offline-first sync", "real-time Postgres sync", "sync Postgres to SQLite", or "build an app that works offline". Covers shape-based sync, real-time subscriptions, offline support, and conflict resolution.
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dlt (data load tool) is an open-source Python library that loads data from APIs, files and databases into warehouses and lakes, inferring the schema and tracking incremental state for you. Use when a user asks to build a data pipeline in Python, load a REST API into DuckDB, BigQuery, Snowflake or Postgres, set up incremental or merge loading, enforce a schema contract, or replace a hand-written ETL script or a hosted ELT connector.
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