Data & Analytics

Find validated alternative reagents based on literature citation data.

Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.

Automates Risk of Bias 2 (ROB2) assessment for RCT papers by analyzing text against specific domains and synthesizing a report. Use when you need to assess the quality of a clinical trial paper or evaluate risk of bias.

Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis.

Therapeutics Data Commons (PyTDC) for AI-ready therapeutic ML datasets and benchmarks; use it when you need standardized dataset loading, meaningful splits (e.g., scaffold/cold-start), and consistent evaluation for ADME/Toxicity/DTI/DDI or molecular optimization.

Generate ~5 actionable research topic recommendations by querying PubMed E-utilities; use when a user provides a research direction/constraints and needs evidence-backed topic ideas quickly.

Build complex Boolean query strings for precise PubMed/MEDLINE literature retrieval. Trigger when user needs MeSH term mapping, Boolean query construction, advanced PubMed filters, citation searching, systematic review search strategy, or clinical query optimization.

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.

Download PubMed/PMC literature using officially permitted PMC methods. Whenever the user wants to download PMC full text, batch-retrieve PMC Open Access Subset articles, save full text corresponding to PMID/PMCID locally, or needs to determine whether a PubMed article can be l...

Expert system for generating comprehensive biomedical phenotype introductions with structured academic content. Use when users request detailed explanations of cellular phenotypes including concept, mechanism, regulation, and detection methods in Chinese academic writing.

Extract experimental materials and instrument information from PDFs (or PDF-derived text/Markdown) into three CSV tables; use when a paper/report contains sections like Materials and Methods, Key Resources Table, Reagents, Antibodies, Consumables, Software, Equipment, Instruments, or Reagent Preparation.

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.

Generates comprehensive academic introductions for biological pathways, including signaling processes, markers, and inhibitors. Use when the user asks to introduce a pathway, molecule, or gene.

Use when analyzing biotech patent landscapes, identifying white spaces in pharmaceutical IP, tracking competitor patents, or assessing freedom to operate for drug development. Provides comprehensive patent analysis and strategic insights for life sciences innovation.

Use when mapping patent claims to products, analyzing patent infringement, or preparing freedom-to-operate analyses. Compares patent claims against product features for biotech and pharmaceutical IP assessment.

Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID lookups, abstracts, full text, open access, preprints, citation graphs, author search, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X" or "look up this DOI".

Access the OpenAlex database (240M+ scholarly works) for bibliometric analysis, literature search, and citation tracking; use when you need to query works/authors/institutions/concepts without an API key.

Query the Open Targets Platform to retrieve targets, diseases, or evidence records when you need target-disease association data and evidence-based scores for therapeutic discovery.

Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).

Use when finding open access journals, checking journal policies, or identifying predatory publishers. Helps researchers locate legitimate open access venues and avoid publication scams.

Extract experimental methods from one or more papers into a structured protocol-oriented summary; use when comparing methods across studies or drafting reproducible procedures.

Vector database retrieval and evidence-based answering for medical research topics. Use when users need knowledge-base-backed answers about methodology, disease mechanisms, drug effects, clinical research, or research tools. Input is a medical research question; output is a st...

Medicinal chemistry screening filters for compound prioritization; use when you need to apply drug-likeness rules, PAINS/structural alerts, and complexity metrics to triage or optimize libraries.