R Interface to Europe PMC RESTful Web Service
Information extraction from unstructured text to build a knowledge graph using techniques from traditional NLP to pre-trained transformers and LLMs for NER and Linking, and Relation Extraction.
Open-source AI research assistant for VS Code + GitHub Copilot. Connects to PubMed, OpenAlex, Semantic Scholar, Europe PMC, CrossRef, and Zotero via MCP servers. Custom agents guide systematic reviews, academic writing, data analysis, and project management — all ICMJE-compliant with full audit trails.
🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more
A Java command-line tool and library to download and store publications with metadata by combining content from various online resources
QTLTableMiner++ tool for mining tables in scientific articles
Tool for visualization of research papers that have common accession numbers
NLP-powered tool to discover and classify biodiversity genomics publications using Europe PMC API
Code associated with our 2018 review in Current Opinion in Systems Biology
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