SemClinBr - a multi-institutional and multi-specialty semantically annotated corpus for Portuguese clinical NLP tasks.

BACKGROUND: The high volume of research focusing on extracting patient information from electronic health records (EHRs) has led to an increase in the demand for annotated corpora, which are a precious resource for both the development and evaluation of natural language processing (NLP) algorithms. The absence of a multipurpose clinical corpus outside the scope of the English language, especially in Brazilian Portuguese, is glaring and severely impacts scientific progress in the biomedical NLP field. METHODS: In this study, a semantically annotated corpus was developed using clinical text from multiple medical specialties, document types, and institutions. In addition, we present, (1) a survey listing common aspects, differences, and lessons learned from previous research, (2) a fine-grained annotation schema that can be replicated to guide other annotation initiatives, (3) a web-based annotation tool focusing on an annotation suggestion feature, and (4) both intrinsic and extrinsic evaluation of the annotations. RESULTS: This study resulted in SemClinBr, a corpus that has 1000 clinical notes, labeled with 65,117 entities and 11,263 relations. In addition, both negation cues and medical abbreviation dictionaries were generated from the annotations. The average annotator agreement score varied from 0.71 (applying strict match) to 0.92 (considering a relaxed match) while accepting partial overlaps and hierarchically related semantic types. The extrinsic evaluation, when applying the corpus to two downstream NLP tasks, demonstrated the reliability and usefulness of annotations, with the systems achieving results that were consistent with the agreement scores. CONCLUSION: The SemClinBr corpus and other resources produced in this work can support clinical NLP studies, providing a common development and evaluation resource for the research community, boosting the utilization of EHRs in both clinical practice and biomedical research. To the best of our knowledge, SemClinBr is the first available Portuguese clinical corpus.

Identification of human papillomavirus in oral rinse specimens from women with and without cervical intraepithelial lesions.

OBJECTIVES: The objective of this study was to evaluate the frequency of human papillomavirus (HPV) in the oral cavity of women with and without abnormal cervical cytology and to determine whether there is an association of oral HPV infection with infection of the cervix or with cervical cancer precursor lesions. METHODS: The present study was conducted among 406 women, aged 18-82 years, who attended the Prevention Department of Barretos Cancer Hospital (HCB), Brazil due to a previous altered cervical cytology result. Oral rinse, cervical cytology and biopsy were collected at the same day. The participants also answered a questionnaire about socioeconomic characteristics and risk factors for cervical cancer. Molecular screening for HPV16, HPV18 and 12 other high-risk HPV types was performed on cervical and oral rinse specimens using Cobas 4800 (Roche Molecular Systems, USA). RESULTS: HPV was detected in the oral rinse of 3.9% of participants. Infection of the oral cavity with a non-HPV16 or 18 type was most frequent (81.2%), followed by HPV16 (18.7%). Infection with HPV in the cervix and oral cavity was present in 11 (2.7%) of participants. There were no differences observed in the smoking status (p value 0.62), mean age of first sexual intercourse (p value 0.25), mean age of the first oral sex (p value 0.90) or mean lifetime number of sexual partners (p value 0.08) between the participants with oral HPV infection or not. CONCLUSION: The presence of HPV infection in the oral cavity was low in the group of women with abnormal cervical cancer screening findings and a high rate of cervical HPV infection.