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ClinPGx Database Access

clinpgx-database

K-Dense-AI/claude-scientific-skills

Provide REST API access to ClinPGx, the successor to PharmGKB, for querying gene-drug interactions, CPIC/DPWG/FDA guidelines, allele functions, and evidence that supports precision dosing and pharmacogenomics-driven clinical decisions.

ClinVar Variant Explorer

clinvar-database

K-Dense-AI/claude-scientific-skills

Query NCBI ClinVar for variant clinical significance, mixing gene/condition searches, API/FTP downloads, and VCF annotations to support genomic medicine interpretation workflows.

Data Commons Client

datacommons-client

K-Dense-AI/claude-scientific-skills

Provides a Python client for querying the Data Commons knowledge graph so teams can resolve entities, fetch statistical observations, and explore public demographic, economic, and health datasets with optional Pandas support.

Ensembl Genome API

ensembl-database

K-Dense-AI/claude-scientific-skills

Query Ensembl’s RESTful API to access gene annotations, sequences, variants, orthologs, and assembly mappings across 250+ species, enabling integration into genomic research pipelines.

Unified Bioinformatics Query

K-Dense-AI/claude-scientific-skills

gget is a CLI/Python client that unifies querying over 20+ bioinformatics databases, letting researchers fetch gene info, sequences, BLAST results, structures, and enrichment data interactively or within scripts.

GWAS Catalog Access

K-Dense-AI/claude-scientific-skills

Query the NHGRI-EBI GWAS Catalog for SNP-trait associations, fetch study metadata, variant and trait details, and download summary statistics via the web or REST APIs to support genetic epidemiology and polygenic risk modeling.

Cancer Imaging Data Access

imaging-data-commons

K-Dense-AI/claude-scientific-skills

Query and download the NCI Imaging Data Commons public cancer imaging datasets via idc-index, filter by metadata, fetch DICOM files, visualize series, and respect licensing details for AI training or research.

LaminDB Biological Data Platform

K-Dense-AI/claude-scientific-skills

LaminDB is a Python-driven open-source framework for managing biological datasets, ensuring traceable, reproducible, FAIR data through lineage tracking, schema validation, ontology annotation, workflow integration, and lakehouse-style querying.

Metabolomics Workbench API

metabolomics-workbench-database

K-Dense-AI/claude-scientific-skills

Query the NIH Metabolomics Workbench via REST API to fetch metabolites, RefMet nomenclature, mass-spec searches, and detailed study datasets for biomarker discovery and metabolomics research.

OpenAlex Research Explorer

openalex-database

K-Dense-AI/claude-scientific-skills

Use the OpenAlex client to query 240M+ scholarly works for literature searches, citation tracking, open access discovery, and bibliometric studies across papers, authors, and institutions.

PubChem Database Query

pubchem-database

K-Dense-AI/claude-scientific-skills

Leverages PubChem’s PUG-REST API or PubChemPy to search 110M+ compounds by name, CID, or structure, fetch properties, perform similarity/substructure lookups, and access bioactivity or format conversions for cheminformatics workflows.

Reactome Pathway Explorer

reactome-database

K-Dense-AI/claude-scientific-skills

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

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