RadGraph is a dataset of entities and relations in radiology reports based on our novel information extraction schema, consisting of 600 reports with 30K radiologist annotations and 221K reports with 10.5M automatically generated annotations. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. We also release an inference dataset, which contains automatically generated annotations for 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs.
JNLPBA is a biomedical dataset that comes from the GENIA version 3.02 corpus (Kim et al., 2003). It was created with a controlled search on MEDLINE. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. 36 terminal classes were used to annotate the GENIA corpus.
Created by Smith et al. at 2008, the BioCreative II Gene Mention Recognition (BC2GM) Dataset contains data where participants are asked to identify a gene mention in a sentence by giving its start and end characters. The training set consists of a set of sentences, and for each sentence a set of gene mentions (GENE annotations). [registration required for access], in English language. Containing 20 in n/a file format.
Species-800 is a corpus for species entities, which is based on manually annotated abstracts. It comprises 800 PubMed abstracts that contain identified organism mentions. To increase the corpus taxonomic mention diversity the 800 abstracts were collected by selecting 100 abstracts from the following 8 categories: bacteriology, botany, entomology, medicine, mycology, protistology, virology and zoology. 800 has been annotated with a focus at the species level; however, higher taxa mentions (such as genera, families and orders) have also been considered.
A vast amount of information in the biomedical domain is available as natural language free text. An increasing number of documents in the field are written in languages other than English. Therefore, it is essential to develop resources, methods and tools that address Natural Language Processing in the variety of languages used by the biomedical community. In this paper, we report on the development of an extensive corpus of biomedical documents in French annotated at the entity and concept level. Three text genres are covered, comprising a total of 103,056 words. Ten entity categories corresponding to UMLS Semantic Groups were annotated, using automatic pre-annotations validated by trained human annotators. The pre-annotation method was found helful for entities and achieved above 0.83 precision for all text genres. Overall, a total of 26,409 entity annotations were mapped to 5,797 unique UMLS concepts.