Build and Query Indexes of Clinical Documents with Easy-to-Reuse Pipelines

Electronic Health Records are a central source of healthcare data, containing structured data alongside unstructured clinical texts. The latter capture detailed reasoning, observations, treatment plans and clinical evolutions, which are crucial for phenotyping, and real-world evidence generation. Natural language processing enables the extraction, thus the subsequent use, of these crucial elements; however, these extractions remain one-off, study-specific efforts. This is detrimental as the extracted elements could be valuable for future research. We present medkit Seshat, an open-source Python pipeline that: (1) ingests free text, (2) recognizes relevant entities, (3) normalizes them with OMOP vocabularies, (4) builds an index that can either be searched by concept or by document. In addition, we share a flexible web UI to illustrate the interest of built indexes in terms of search, text analysis and export. Seshat aims at facilitating the reuse and adaptation of this prototypical pipeline to various purposes, with the main objective of enabling the secondary use of results of phenotyping campaigns.