Claude Skills by stanfish06

> [!info] What it does > Diagnoses and fixes slow Neo4j Cypher queries by reading execution plans, identifying bad operators (AllNodesScan, CartesianProduct, Eager, NodeByLabelScan), and prescribing fixes (indexes, hints, query rewrites, runtime selection). Use when a query is slow, when EXPLAIN or PROFILE output needs interpretation, when dbHits or pageCacheHitRatio are poor, when cardinality estimation diverges from actuals, or when deciding between slotted/pipelined/parallel runtimes. Cove...

> [!info] What it does > Programmatic security management in Neo4j — RBAC/ABAC, user lifecycle (CREATE/ALTER/DROP USER), role lifecycle (CREATE/GRANT ROLE/DROP ROLE), privilege grants and denies (GRANT/DENY/REVOKE on graph, database, DBMS), property-level access control, sub-graph access control, SHOW PRIVILEGES inspection, and auth provider config reference (LDAP, OIDC/SSO). Use when an agent needs to manage users, roles, or privileges programmatically via Cypher on the system database. Does...

> [!info] What it does > Run Neo4j Graph Analytics algorithms (PageRank, Louvain, WCC, Dijkstra, KNN, Node2Vec, FastRP, GraphSAGE) directly inside Snowflake without moving data. Use when running graph algorithms against Snowflake tables via the Neo4j Snowflake Native App ("GDS Snowflake", "graph algorithms in Snowflake", "Neo4j Graph Analytics"). Covers the explore → prepare projection views → project-compute-write flow, the strict view/column type rules the graph engine requires, exact SQL C...

> [!info] What it does > Use when reading from or writing to Neo4j with Apache Spark or Databricks using the Neo4j Connector for Apache Spark 6.0 (org.neo4j.connectors:spark) or 5.x (org.neo4j:neo4j-connector-apache-spark). Covers SparkSession setup, DataFrame reads via labels/Cypher/relationship scan, DataFrame writes with SaveMode, node.keys for MERGE, relationship write mapping, partition and batch tuning, PySpark and Scala examples, Databricks cluster config, Databricks secrets for creden...

> [!info] What it does > Use when building Spring Boot applications with Neo4j using Spring Data Neo4j (SDN 7.x/8.x) — @Node entity mapping, @Relationship, @RelationshipProperties, Neo4jRepository, ReactiveNeo4jRepository, @Query annotations, application.yml configuration, projections, Neo4jClient, Neo4jTemplate, transactions, auditing, or Spring AI Neo4jVectorStore vector search. Does NOT handle raw Java driver code without Spring — use neo4j-driver-java-skill. Does NOT handle Cypher query a...

> [!info] What it does > Create and manage Neo4j vector indexes, run vector similarity search (ANN/kNN), store embeddings on nodes or relationships, use SEARCH clause (Neo4j 2026.01+, preferred) or db.index.vector.queryNodes() procedure (deprecated 2026.04, still works on 2025.x), configure HNSW and quantization options, pick similarity function and embedding provider dimensions, and batch-update embeddings. Use when tasks involve CREATE VECTOR INDEX, vector.dimensions, cosine/euclidean searc...

> [!info] What it does > Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries **Source:** [skills/biostudies-arrayexpress-skill/SKILL.md](../../../skills/biostudies-arrayexpress-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries **Source:** [skills/cbioportal-skill/SKILL.md](../../../skills/cbioportal-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries **Source:** [skills/cellxgene-skill/SKILL.md](../../../skills/cellxgene-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact ClinicalTrials.gov API v2 requests for study search, metadata, enums, search areas, and field statistics. Use when a user wants concise ClinicalTrials.gov summaries **Source:** [skills/clinicaltrials-skill/SKILL.md](../../../skills/clinicaltrials-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries **Source:** [skills/efo-ontology-skill/SKILL.md](../../../skills/efo-ontology-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries **Source:** [skills/ensembl-skill/SKILL.md](../../../skills/ensembl-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries **Source:** [skills/epigraphdb-skill/SKILL.md](../../../skills/epigraphdb-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact EVA REST requests for species metadata and archived variant lookups. Use when a user wants concise European Variation Archive summaries **Source:** [skills/eva-skill/SKILL.md](../../../skills/eva-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML only on request. **Source:** [skills/human-protein-atlas-skill/SKILL.md](../../../skills/human-protein-atlas-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) ...

> [!info] What it does > Submit compact IPD REST requests for HLA allele and cell-level metadata using the public IPD query API. Use when a user wants concise IPD summaries; save raw JSON or text only on request. **Source:** [skills/ipd-skill/SKILL.md](../../../skills/ipd-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact MetaboLights requests for study discovery and study-level metabolomics metadata. Use when a user wants concise MetaboLights summaries **Source:** [skills/metabolights-skill/SKILL.md](../../../skills/metabolights-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries **Source:** [skills/mgnify-skill/SKILL.md](../../../skills/mgnify-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact Clinical Tables NCBI Gene requests for human gene lookup, pagination, and field selection. Use when a user wants concise autocomplete-style human gene search results **Source:** [skills/ncbi-clinicaltables-skill/SKILL.md](../../../skills/ncbi-clinicaltables-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index...

> [!info] What it does > Submit compact NCBI Entrez E-Utilities requests for PubMed, Gene, Protein, Nucleotide, PMC metadata, and GEO metadata workflows. Use when a user wants concise Entrez search, fetch, summary, or link results; save raw JSON or XML only on request. **Source:** [skills/ncbi-entrez-skill/SKILL.md](../../../skills/ncbi-entrez-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills...

> [!info] What it does > Submit compact Open Targets Platform GraphQL requests for target, disease, drug, variant, study, and search data, including associated-disease datasource heatmap matrices. Use when a user wants concise Open Targets summaries or per-datasource evidence context **Source:** [skills/opentargets-skill/SKILL.md](../../../skills/opentargets-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.bas...

> [!info] What it does > Submit compact PRIDE Archive API requests for proteomics project discovery and project-level metadata. Use when a user wants concise PRIDE summaries **Source:** [skills/pride-skill/SKILL.md](../../../skills/pride-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries **Source:** [skills/proteomexchange-skill/SKILL.md](../../../skills/proteomexchange-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact QuickGO requests for GO terms, annotations, and ontology traversal. Use when a user wants concise QuickGO summaries **Source:** [skills/quickgo-skill/SKILL.md](../../../skills/quickgo-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact Reactome ContentService requests for pathway, event, participant, search, and diagram-related data. Use when a user wants concise Reactome summaries **Source:** [skills/reactome-skill/SKILL.md](../../../skills/reactome-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Route broad or ambiguous life-sciences research requests to the right skills, normalize core entities, optionally parallelize independent evidence gathering with subagents when available, and synthesize a concise evidence-backed answer. Use when a user asks a general life-sciences question that could span multiple sources or analysis types. **Source:** [skills/research-router-skill/SKILL.md](../../../skills/research-router-skill/SKILL.md) · **Domain:** [Bio Database...

> [!info] What it does > Submit compact STRING API requests for network, interaction partner, and enrichment endpoints. Use when a user wants concise STRING summaries **Source:** [skills/string-skill/SKILL.md](../../../skills/string-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact UniProt REST API requests for UniProtKB, UniRef, UniParc, and FASTA stream endpoints. Use when a user wants concise UniProt summaries; save raw JSON or FASTA only on request. **Source:** [skills/uniprot-skill/SKILL.md](../../../skills/uniprot-skill/SKILL.md) · **Domain:** [Bio Databases, Lab & Cloud Platforms](../../maps/bio-databases-platforms.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries **Source:** [skills/alphafold-skill/SKILL.md](../../../skills/alphafold-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Sk...

> [!info] What it does > Submit compact BindingDB REST API requests for ligand-target binding lookups by PDB, UniProt, or similarity search. Use when a user wants concise BindingDB summaries; save raw payloads only on request. **Source:** [skills/bindingdb-skill/SKILL.md](../../../skills/bindingdb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index...

> [!info] What it does > Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI summaries **Source:** [skills/chebi-skill/SKILL.md](../../../skills/chebi-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries **Source:** [skills/chembl-skill/SKILL.md](../../../skills/chembl-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries **Source:** [skills/hmdb-skill/SKILL.md](../../../skills/hmdb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact PharmGKB API requests for genes, variants, clinical annotations, dosing guidelines, and search. Use when a user wants concise PharmGKB summaries **Source:** [skills/pharmgkb-skill/SKILL.md](../../../skills/pharmgkb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact PubChem PUG REST requests for compound properties, descriptions, assay summaries, and substance metadata. Use when a user wants concise PubChem summaries **Source:** [skills/pubchem-pug-skill/SKILL.md](../../../skills/pubchem-pug-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request. **Source:** [skills/rcsb-pdb-skill/SKILL.md](../../../skills/rcsb-pdb-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact Rhea reaction search requests for biochemical reactions and reaction IDs. Use when a user wants concise Rhea summaries **Source:** [skills/rhea-skill/SKILL.md](../../../skills/rhea-skill/SKILL.md) · **Domain:** [Drug Discovery, Cheminformatics & Structural Biology](../../maps/drug-discovery-chem.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant **Source:** [skills/biobankjapan-phewas-skill/SKILL.md](../../../skills/biobankjapan-phewas-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) ·...

> [!info] What it does > Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC summaries **Source:** [skills/civic-skill/SKILL.md](../../../skills/civic-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping **Source:** [skills/clinvar-variation-skill/SKILL.md](../../../skills/clinvar-variation-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact eQTL Catalogue API requests for association retrieval and documented metadata endpoints. Use when a user wants concise public eQTL Catalogue summaries **Source:** [skills/eqtl-catalogue-skill/SKILL.md](../../../skills/eqtl-catalogue-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Fetch compact FinnGen PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise FinnGen association results for one variant **Source:** [skills/finngen-phewas-skill/SKILL.md](../../../skills/finngen-phewas-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:**...

> [!info] What it does > Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries **Source:** [skills/genebass-gene-burden-skill/SKILL.md](../../../skills/genebass-gene-burden-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Submit compact gnomAD GraphQL requests for frequency, gene constraint, and variant context queries. Use when a user wants concise gnomAD summaries **Source:** [skills/gnomad-graphql-skill/SKILL.md](../../../skills/gnomad-graphql-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Fetch GTEx single-tissue eQTL associations from one variant input by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query for the GTEx v2 API. Use when a user wants eQTL associations returned as JSON. **Source:** [skills/gtex-eqtl-skill/SKILL.md](../../../skills/gtex-eqtl-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:*...

> [!info] What it does > Submit compact GWAS Catalog REST API v2 requests for studies, associations, SNPs, EFO traits, genes, publications, loci, and metadata. Use when a user wants concise GWAS Catalog summaries **Source:** [skills/gwas-catalog-skill/SKILL.md](../../../skills/gwas-catalog-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../index.md)

> [!info] What it does > Map GWAS loci to ranked candidate genes using a deterministic multi-skill chain (EFO -> GWAS -> coordinates -> Open Targets L2G/coloc -> eQTL -> burden/coding context), with reproducible tables and optional figures. Use when a user provides a trait/EFO term and/or lead variants and needs locus-to-gene prioritization for downstream biology decisions. **Source:** [skills/locus-to-gene-mapper-skill/SKILL.md](../../../skills/locus-to-gene-mapper-skill/SKILL.md) · **Doma...

> [!info] What it does > Submit compact NCBI Datasets v2 requests for assembly, genome, taxonomy, and related metadata endpoints. Use when a user wants concise NCBI Datasets summaries; save raw JSON or text only on request. **Source:** [skills/ncbi-datasets-skill/SKILL.md](../../../skills/ncbi-datasets-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Index](../../i...

> [!info] What it does > Fetch compact TPMI PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise TPMI association results for one variant **Source:** [skills/tpmi-phewas-skill/SKILL.md](../../../skills/tpmi-phewas-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) · **Index:** [Skills Ind...

> [!info] What it does > Fetch compact UKB-TOPMed PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query. Use when a user wants concise UKB-TOPMed association results for one variant **Source:** [skills/ukb-topmed-phewas-skill/SKILL.md](../../../skills/ukb-topmed-phewas-skill/SKILL.md) · **Domain:** [Genomics, Variants & Population Genetics](../../maps/genomics-variants.md) · **Table:** [skills.base](../../skills.base) ·...