157 skills found · Page 5 of 6
jaechang-hits / pdb-databaseQuery RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org.
jaechang-hits / unichem-databaseCross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity.
jaechang-hits / zinc-databaseQuery the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking.
jaechang-hits / reactome-databaseQuery Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
jaechang-hits / string-database-ppiQuery STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrichment, find partners, test PPI significance, visualize networks, analyze homology. For chemical interactions use chembl-database-bioactivity; pathways use kegg-database.
jaechang-hits / archs4-databaseQuery ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices.
jaechang-hits / cbioportal-databaseCancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis.
jaechang-hits / clinpgx-databaseQuery the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways.
jaechang-hits / cosmic-databaseQuery COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
jaechang-hits / dbsnp-databaseQuery NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key).
jaechang-hits / ena-databaseENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
jaechang-hits / encode-databaseENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene.
jaechang-hits / ensembl-databaseEnsembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
jaechang-hits / gnomad-databasegnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants.
jaechang-hits / gwas-databaseNHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.
jaechang-hits / jaspar-databaseJASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis.
jaechang-hits / kegg-databaseKEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
jaechang-hits / monarch-databaseMonarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking.
jaechang-hits / mouse-phenome-databaseRetrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nome…
jaechang-hits / quickgo-databaseQuery EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment.
jaechang-hits / regulomedb-databaseQuery RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none).
jaechang-hits / remap-databaseQuery ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair.
giuseppe-trisciuoglio / nestjsProvides comprehensive NestJS framework patterns with Drizzle ORM integration for building scalable server-side applications. Generates REST/GraphQL APIs, implements authentication guards, creates database schemas, and sets up microservices
giuseppe-trisciuoglio / unit-test-service-layerProvides patterns for unit testing service layer with Mockito. Creates isolated tests that mock repository calls, verify method invocations, test exception scenarios, and stub external API responses
datadrivenconstruction / oce-load-cost-basesLoad national and market cost bases into OpenConstructionERP: the 8 national bases (Turkey Birim Fiyat, China Dinge, Brazil SINAPI, Spain BCCA, Italy Prezzario Toscana, Greece GGDE, Vietnam Dinh Muc, Indonesia AHSP), the 30 global markets, and 48 PPP market catalogs per base
Avijit07x / claude-dbFree, open-source memory for Claude Code. Your own database, no cloud, no subscription.
Yurich-ru / yandex-ads-mcpMCP server for Yandex Direct, Metrika, Audience & Wordstat APIs — 152 tools for campaign management, audience segments, analytics, and keyword research
IA-Programming / Youtube-MCPYouTube MCP Server is an AI-powered solution designed to revolutionize your YouTube experience. It empowers users to search for YouTube videos, retrieve detailed transcripts, and perform semantic searches over video content—all without relying on the official API.
onlymoein / google-search-console-mcpLocal MCP server for the Google Search Console API: search analytics, hourly data, URL inspection and sitemaps, with guards for the API's quirks.
totalcms / cmsCommercial flat-file PHP CMS for web professionals: structured content modeling, no database, content stored as JSON on disk, Twig templating, a REST API, a CLI, and a built-in MCP server so AI agents can work with a live site.
