sciminer-skills

Build evidence-graded compound–target–disease network-pharmacology hypotheses for natural products, herbal medicines, formulae, and small molecules using live SciMiner tools plus public life-science evidence. Use when an agent must curate compounds, predict or verify targets, prioritize disease-relevant targets, assess ADMET or off-target risk, run docking as supporting evidence, create interactive network visualizations, or produce reproducible network-pharmacology reports without R.

In-depth, multi-region pharmaceutical intelligence search and synthesis, plus drug repurposing, target discovery, clinical evidence review, and bioactivity analysis. Use this skill whenever the user asks about drug approvals, clinical trials, regulatory submissions, pipeline assets, patent landscapes, competitive intelligence, scientific evidence, disease targets, genetic associations, or compound bioactivity for any drug, target, indication, or company — especially when coverage of China, US, Europe, Japan, South Korea, or Australia is needed. Trigger even for casual queries like "what's the approval status of X in China", "find trials for Y in Japan", "compare pipeline coverage across regions", "find drugs for disease Z", or "what targets are associated with condition W". Always consult this skill before answering any pharma or biomedical research question that requires source-grounded data.

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.

Structure-activity relationship analysis workflows using SciMiner's MCS-based and scaffold-based SAR APIs for file or inline table inputs, plus an AlphaFold3-based binding-mode prediction workflow for target-aware SAR.

Virtual screening workflows for open and proprietary chemical libraries, including transformer-based screening and docking-based screening through SciMiner.

Antibody engineering workflow combining ANARCI, BioPhi, IgFold, FoldX, and Rosetta tools through SciMiner.

Binding-site and pocket prediction workflows using P2Rank, AF2BIND, and fpocket through SciMiner.

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.

Relative binding free-energy and activity-label prediction workflows using PBCNet 2.0 on SciMiner, with Gnina docking and PDB/database retrieval to complete missing inputs.

General life-sciences research copilot bundling 50 modular sub-skills across human genetics, variant interpretation, functional genomics, expression, pathway biology, protein structure, chemistry, clinical evidence, literature, and public study discovery. Use when a user asks any life-sciences question that may require one or more public databases. The research-router-skill is the default entry point for broad or ambiguous requests; individual sub-skills can be invoked directly for narrow, single-source lookups.

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

Submit compact Bgee SPARQL requests for healthy wild-type expression metadata and ontology-aware lookup patterns. Use when a user wants concise Bgee summaries; save raw results only on request.

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.

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

Submit compact bioRxiv and medRxiv API requests for details, publication-linkage, and DOI lookups. Use when a user wants concise preprint metadata summaries

Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries

Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples. Use when a user wants concise cBioPortal summaries

Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries

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

Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries

Submit compact CIViC GraphQL requests for cancer variant interpretation schema inspection and targeted evidence retrieval. Use when a user wants concise CIViC summaries

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

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

Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries

Submit compact ENCODE REST API requests for object lookups, portal-style search, and metadata retrieval. Use when a user wants concise ENCODE summaries

Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries

Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries

Submit compact eQTL Catalogue API requests for association retrieval and documented metadata endpoints. Use when a user wants concise public eQTL Catalogue summaries

Submit compact EVA REST requests for species metadata and archived variant lookups. Use when a user wants concise European Variation Archive summaries

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

Submit compact Genebass gene burden requests for one Ensembl gene ID and one burden set. Use when a user wants concise Genebass PheWAS summaries

Submit compact gnomAD GraphQL requests for frequency, gene constraint, and variant context queries. Use when a user wants concise gnomAD summaries

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.

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

Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries

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.

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.

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.

Submit compact MetaboLights requests for study discovery and study-level metabolomics metadata. Use when a user wants concise MetaboLights summaries

Submit compact MGnify API requests for microbiome studies, samples, and biome metadata. Use when a user wants concise MGnify summaries