| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Hong, Judy Davoudi, Anahita Yu, Shun Mowery, Danielle L. |
| Abstract | Background Age and time information stored within the histories of clinical notes can provide valuable insights for assessing a patient’s disease risk, understanding disease progression, and studying therapeutic outcomes. However, details of age and temporally-specified clinical events are not well captured, consistently codified, and readily available to research databases for study. Methods We expanded upon existing annotation schemes to capture additional age and temporal information, conducted an annotation study to validate our expanded schema, and developed a prototypical, rule-based Named Entity Recognizer to extract our novel clinical named entities (NE). The annotation study was conducted on 138 discharge summaries from the pre-annotated 2014 ShARe/CLEF eHealth Challenge corpus. In addition to existing NE classes (TIMEX3, SUBJECT_CLASS, DISEASE_DISORDER), our schema proposes 3 additional NEs (AGE, PROCEDURE, OTHER_EVENTS). We also propose new attributes, e.g., “degree_relation” which captures the degree of biological relation for subjects annotated under SUBJECT_CLASS. As a proof of concept, we applied the schema to 49 H&P notes to encode pertinent history information for a lung cancer cohort study. Results An abundance of information was captured under the new OTHER_EVENTS, PROCEDURE and AGE classes, with 23%, 10% and 8% of all annotated NEs belonging to the above classes, respectively. We observed high inter-annotator agreement of >80% for AGE and TIMEX3; the automated NLP system achieved F1 scores of 86% (AGE) and 86% (TIMEX3). Age and temporally-specified mentions within past medical, family, surgical, and social histories were common in our lung cancer data set; annotation is ongoing to support this translational research study. Conclusions Our annotation schema and NLP system can encode historical events from clinical notes to support clinical and translational research studies. |
| Related Links | https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-020-01333-5.pdf |
| Ending Page | 15 |
| Page Count | 15 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 14726947 |
| DOI | 10.1186/s12911-020-01333-5 |
| Journal | BMC Medical Informatics and Decision Making |
| Issue Number | 11 |
| Volume Number | 20 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2020-12-30 |
| Access Restriction | Open |
| Subject Keyword | Health Informatics Information Systems and Communication Service Management of Computing and Information Systems Natural language processing Medical informatics Temporality |
| Content Type | Text |
| Resource Type | Article |
| Subject | Health Informatics Computer Science Applications Health Policy |
| Journal Impact Factor | 3.3/2023 |
| 5-Year Journal Impact Factor | 3.9/2023 |
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