Data & Analytics

Extract experimental models, experimental methods, and biomarker information from paper Markdown (typically produced by PDF-to-Markdown tools) when a user provides paper Markdown and needs a structured, evidence-backed summary (1 Markdown + 3 CSVs).

Produce a structured close-reading report from a paper's full PDF-to-Markdown text (with `## Page XX` pagination and image references) when you need to systematically extract background, research questions, methods, results, limitations, and reproducible experimental details.

Calculate literature growth velocity and acceleration to assess research.

Extracts and summarizes key takeaways from documents, meeting notes, articles, and other text content. Use when the user asks for summaries, bullet points, main points, highlights, or a TL;DR of any document or body of text. Produces structured outputs such as numbered lists, executive summaries, and action items. Supports configurable output formats including JSON export for downstream use.

Direct access to KEGG via the REST API for academic-only pathway/gene/compound/drug queries; use when you need precise HTTP-level control or targeted KEGG ID mapping.

Access the KEGG database API to retrieve biological data (genes, pathways, compounds, drugs). Invoke when the user asks to search, list, or get details from KEGG.

Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal recommendation/matching, submission strategy, PubMed search, or similar-literature statistics.

Analyzes academic paper abstracts to recommend optimal journals for submission, considering impact factors, scope alignment, and domain expertise.

Retrieve the latest journal issue's table of contents and abstracts from URL/DOI/PMID/RSS/TOC sources, then generate Chinese key points locally (no external translation APIs) when a new issue needs quick review and archiving.

Show journal impact factor and quartile trends over 5 years.

Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Use when user wants to search for transcription factors, retrieve matrix details (PFM/PWM), infer profiles from protein sequences, or explore JASPAR collections.

Summarize core safety information from Investigator's Brochures for clinical.

Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML mining.

Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

Use grant gantt chart gen for evidence insight workflows that need structured execution, explicit assumptions, and clear output boundaries.

NIH funding trend analysis to identify high-priority research areas.

Unified CLI/Python interface for querying genomic, proteomic, structure, and expression data across 20+ bioinformatics databases; use when you need fast, scriptable retrieval by gene/protein IDs or keywords.

Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.

Retrieves comprehensive gene information including PubMed publication counts, NCBI summaries, and Ensembl transcript data. Supports batch processing and file input. Invoke when the user asks for gene details, publication statistics, or needs to analyze a list of genes.

Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.

Analyze funding abstracts and project metadata to identify topic shifts and forecast near-term grant priorities.

Search FDA industry guidelines by therapeutic area or topic.

Query the openFDA API to retrieve FDA regulatory datasets (drugs, devices, adverse events, recalls, submissions, UNII) when you need programmatic safety/regulatory evidence for analysis or research.