CHIFIR: Cytology and Histopathology Invasive Fungal Infection Reports

Surveillance of invasive fungal infection (IFI) in clinical settings is a
laborious process requiring a detailed review of patient medical history. One
of the key sources of clinical information is cytology and histopathology
reports: pathologist-produced free-text reports outlining the macroscopic and
microscopic structure of a specimen. The data was generated to facilitate the
development of an automated tool for the detection of IFI. The Cytology and
Histopathology Invasive Fungal Infection Reports (CHIFIR) corpus contains 283
de-identified reports annotated by infectious diseases physicians for
terminology relevant to the IFI diagnosis. These include IFI-specific concepts
and certainty cues, as well as relations between them. We release the
annotation schema and the original reports along with the corresponding
annotation files. We anticipate the CHIFIR corpus to be useful in the
development and validation of named entity recognition and relation extraction
methods with a focus on clinical data. Such methods can be instrumental in
processing other types of clinical documentation (radiology reports, clinical
notes, nursing notes) with various downstream tasks in mind.