Development skills

Manage AI coding agent sessions via Agent of Empires (aoe)

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Structured code review through the shared OpenClaw agent-skills installation.

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Explore and understand codebases using SocratiCode semantic search, dependency graphs, and context artifacts. Use when exploring code, understanding architecture, finding functions/types, analysing dependencies, searching database schemas or API specs, or when socraticode/codebase_search tools are available. Activates when the user asks about code structure, wants to find where a feature lives, or needs to understand how code is organised.

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Set up, index, and manage SocratiCode codebase indexing. Use when the user wants to index a project, check infrastructure health, start/stop file watching, configure context artifacts, troubleshoot indexing issues, manage the code graph, or any SocratiCode administrative task. Activates when the user mentions indexing, setting up search, SocratiCode infrastructure, or managing the codebase index.

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Push to GitHub and optionally bump version to trigger PyPI release

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Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).

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Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.

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Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

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Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.

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Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

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Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.

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Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, recalls, labeling, approvals, shortages, 510(k) clearances, NDC lookups, and any FDA safety or regulatory data query across all 28 API endpoints.

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Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.

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Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolutionarily conserved, functionally important, or bounded by TF regulators across major projects (ENCODE, JASPAR, ReMap).

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Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publications. Don't use for sequence alignment, protein folding, or sequence similarity search (use specialized skills for those tasks).

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Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

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Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.

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Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) search.

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Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.

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Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.

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Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.

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Score, annotate, and analyze the functional impact of genetic variants using AlphaGenome Variant Impact (AVI) scores. Query variants in chr:pos:ref>alt format, annotate VCF/tabular callsets, perform saturation mutagenesis window scans (1-based closed chr:start-end), and extract GENCODE v46 GTF gene/exon/junction coordinates all via the AlphaGenome Atlas API.

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Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.

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Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.

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