PubTator Central

SemEHR

Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research

CRAFT

The Colorado Richly Annotated Full-Text (CRAFT) Corpus is a collection of 97 biomedical articles from PubMed Central, each annotated across multiple dimensions including structural elements, coreferences, and biomedical concepts. It serves as a valuable resource for natural language processing research, biomedical text mining, and training machine learning models in the biomedical domain. ## Key Features - **Multi-dimensional annotations** — Articles are annotated for structure, coreference, and biomedical concepts - **MONDO ontology integration** — Version 5 includes annotations linking concepts to the MONDO disease ontology - **Format conversion** — Includes scripts to convert annotations between different file formats - **Stable releases** — Versioned releases available for consistent research use - **PubMed Central source** — All articles sourced from the PubMed Central Open Access subset ## Philosophy The CRAFT corpus is designed to provide comprehensive, high-quality annotations to support advanced biomedical text analysis and natural language processing research.

NCBI Disease Corpus

paper - A corpus of 793 biomedical abstracts annotated with names of diseases and related concepts from MeSH and OMIM

BioScope

paper - a corpus of sentences from medical and biological documents, annotated for negation, speculation, and linguistic scope