rag-implementation
wshobsonBuild Retrieval-Augmented Generation (RAG) systems for LLM applications with vector databases and semantic search. Use when implementing knowledge-grounded AI, building document Q&A systems, or integrating LLMs with external knowledge bases.
biomni
davila7Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
alphafold-database
davila7Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
chroma
davila7Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.
pinecone
davila7Managed vector database for production AI applications. Fully managed, auto-scaling, with hybrid search (dense + sparse), metadata filtering, and namespaces. Low latency (<100ms p95). Use for production RAG, recommendation systems, or semantic search at scale. Best for serverless, managed infrastructure.
n8n-workflow-patterns
davila7Proven workflow architectural patterns from real n8n workflows. Use when building new workflows, designing workflow structure, choosing workflow patterns, planning workflow architecture, or asking about webhook processing, HTTP API integration, database operations, AI agent workflows, or scheduled tasks.
cocoindex
davila7Comprehensive toolkit for developing with the CocoIndex library. Use when users need to create data transformation pipelines (flows), write custom functions, or operate flows via CLI or API. Covers building ETL workflows for AI data processing, including embedding documents into vector databases, building knowledge graphs, creating search indexes, or processing data streams with incremental updates.
DB migrations and schema changes
letta-aiWorkflows and commands for managing Alembic database migrations and schema changes in the letta-cloud core app, including using uv, just, LETTA_PG_URI, and switching between SQLite and Postgres.
rag-implementation
sickn33Build Retrieval-Augmented Generation (RAG) systems for LLM applications with vector databases and semantic search. Use when implementing knowledge-grounded AI, building document Q&A systems, or integrating LLMs with external knowledge bases.
context-manager
sickn33Elite AI context engineering specialist mastering dynamic context management, vector databases, knowledge graphs, and intelligent memory systems.
AgentDB Advanced Features
ruvnetMaster advanced AgentDB features including QUIC synchronization, multi-database management, custom distance metrics, hybrid search, and distributed systems integration. Use when building distributed AI systems, multi-agent coordination, or advanced vector search applications.
kegg-database
K-Dense-AIDirect REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
metabolomics-workbench-database
K-Dense-AIAccess NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
reactome-database
K-Dense-AIQuery Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
clinvar-database
K-Dense-AIQuery NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
clinpgx-database
K-Dense-AIAccess ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
ensembl-database
K-Dense-AIQuery Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
gene-database
K-Dense-AIQuery NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
literature-review
K-Dense-AIConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
fda-database
K-Dense-AIQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
zinc-database
K-Dense-AIAccess ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
brenda-database
K-Dense-AIAccess BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
chembl-database
K-Dense-AIQuery ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
openalex-database
K-Dense-AIQuery and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries.
gwas-database
K-Dense-AIQuery NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
geo-database
K-Dense-AIAccess NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
uniprot-database
K-Dense-AIDirect REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
pubchem-database
K-Dense-AIQuery PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
cosmic-database
K-Dense-AIAccess COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
gget
K-Dense-AIFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
bioservices
K-Dense-AIUnified 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.
pubmed-database
K-Dense-AIDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
pdb-database
K-Dense-AIAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
clinicaltrials-database
K-Dense-AIQuery ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
string-database
K-Dense-AIQuery STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
alphafold-database
K-Dense-AIAccess AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
uspto-database
K-Dense-AIAccess USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
ena-database
K-Dense-AIAccess European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
geopandas
K-Dense-AIPython library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
biorxiv-database
K-Dense-AIEfficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
opentargets-database
K-Dense-AIQuery Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
drugbank-database
K-Dense-AIAccess and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
schema-exploration
langchain-aiFor discovering and understanding database structure, tables, columns, and relationships
rag-architect
JeffallanUse when building RAG systems, vector databases, or knowledge-grounded AI applications requiring semantic search, document retrieval, or context augmentation.
n8n-workflow-patterns
czlonkowskiProven workflow architectural patterns from real n8n workflows. Use when building new workflows, designing workflow structure, choosing workflow patterns, planning workflow architecture, or asking about webhook processing, HTTP API integration, database operations, AI agent workflows, or scheduled tasks.
schema-exploration
apconwUsed to discover and understand database structures, tables, columns, and relationships
duckdb-en
openclawDuckDB CLI specialist for SQL analysis, data processing and file conversion. Use for SQL queries, CSV/Parquet/JSON analysis, database queries, or data conversion. Triggers on "duckdb", "sql", "query", "data analysis", "parquet", "convert data".
backup-script-gen
openclawGenerate database backup scripts with AI. Use when you need automated backups to S3, GCS, or local storage.