288 skills found · Page 7 of 10
aiskillstore / postgresqlPostgreSQL database documentation - SQL queries, database design, administration, performance tuning, and advanced features
aiskillstore / sqlite-opsPatterns for SQLite databases in Python projects - state management, caching, and async operations. Triggers on: sqlite, sqlite3, aiosqlite, local database, database schema, migration, wal mode.
Microck / AgentDB Performance OptimizationOptimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations
Microck / biorxiv-databaseEfficient 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.
Microck / clinvar-databaseQuery 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.
Microck / AgentDB Vector SearchImplement semantic vector search with AgentDB for intelligent document retrieval, similarity matching, and context-aware querying
Microck / Backend Models StandardsDefine database models with clear naming, appropriate data types, constraints, relationships, and validation at multiple layers. Use this skill when creating or modifying database model files, ORM classes, schema definitions, or data model relationships.
Microck / chembl-databaseQuery ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
Microck / cosmic-databaseAccess COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Microck / cloudbase-document-database-web-sdkUse CloudBase document database Web SDK to query, create, update, and delete data. Supports complex queries, pagination, aggregation, and geolocation queries.
spencermarx / sparc-supabase-admin🔐 Supabase Admin - You are the Supabase database, authentication, and storage specialist. You design and implement d...
spencermarx / ReasoningBank with AgentDBImplement ReasoningBank adaptive learning with AgentDB's 150x faster vector database. Includes trajectory tracking, verdict judgment, memory distillation, and pattern recognition
jaechang-hits / omics-plottingomics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested:…
jaechang-hits / hmdb-databaseParse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
jaechang-hits / interpro-databaseQuery InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam.
jaechang-hits / metabolomics-workbench-databaseQuery Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.
jaechang-hits / pride-databaseSearch the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download RAW/PEAK/RESULT/FASTA files (with FTP/Aspera URLs), look up which projects mention a UniProt accession, an…
jaechang-hits / uniprot-protein-databaseQuery UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures.
jaechang-hits / biorxiv-databaseQuery bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search use openalex-database.
jaechang-hits / openalex-databaseQuery OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth.
jaechang-hits / scientific-literature-searchSystematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools. Covers PICO framework for clinical questions, three-tiered search (database-specific, AI-assisted, content extraction), PubMed field tags and MeSH, boolean query construction, and f…
jaechang-hits / alphafold-database-accessAccess AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
jaechang-hits / chembl-database-bioactivityQuery ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug mechanism/indication data.
jaechang-hits / clinicaltrials-database-searchQuery ClinicalTrials.gov API v2 for trial data. Search by condition, drug/intervention, location, sponsor, or phase; fetch details by NCT ID; filter by status; paginate; export CSV. For clinical research, patient matching, and trial portfolio analysis.
jaechang-hits / dailymed-databaseQuery FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI; get indications, dosage, warnings, adverse reactions, packaging. No auth. For adverse events use fda-database; for DDIs use ddinter-database.
jaechang-hits / ddinter-databaseQuery DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for severity (major/moderate/minor), mechanisms, and clinical recommendations. No auth. For FDA labeling use dailymed-database; for pharmacogenomics use clinpgx-database.
jaechang-hits / drugbank-database-accessParse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs with severity, map targets/enzymes/transporters, compute SMILES similarity. Primary via local XML; REST API rate-limited (3k/month dev).
jaechang-hits / emdb-databaseLook up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth.
jaechang-hits / fda-databaseQuery openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name, ingredient, MedDRA, or NDC. 1k req/day no key; 120k with free key.
jaechang-hits / gtopdb-databaseQuery IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs. Affinities (pKi/pIC50/pKd), action (Agonist/Antagonist/etc.), species, structures (SMILES/InChI). No auth.
