The impact of learning Unified Medical Language System knowledge embeddings in relation extraction from biomedical texts

Considering non-hospital data in clinical informatics use cases, a review of the National Emergency Medical Services Information System (NEMSIS)

Background

The National Emergency Medical Services (EMS) Information System (NEMSIS) Technical Assistance Center (TAC) collects and curates EMS activation level records for the United States. Originated as an outcomes assessment and service comparison tool, NEMSIS may have other high value clinical and public health uses.

Methods

This study acquired a 100% activation level public dataset for 2019 from NEMSIS TAC and assessed item response quantities. Subsumption of NEMSIS terms within other controlled clinical vocabularies was also considered.

Results

None of the assessed terminologies (LOINC, ICD10-CM, SNOMED-CT) could describe meaningful volumes of NEMSIS item response codes. The 2019 activation year dataset included 36,525 non-date/time or calculated distinct item responses for 43 activation descriptive items. Said item responses yielded 2,101,844,053 activation distinct non-blank responses. Several NEMSIS item responses had high clinical and public health value.

Conclusions

NEMSIS can support multiple public health use cases in addition to EMS outcomes assessment. A comprehensive custom value set is appropriate to integrate NEMSIS item response codes into controlled terminologies, FHIR or hospital Electronic Health Record applications.

Synthetic Biology Knowledge System

The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub repository that includes text and data information that has been mined from papers published in ACS Synthetic Biology. This paper describes the SBKS curation framework that is being developed to construct the knowledge stored in this repository. The text mining pipeline performs automatic annotation of the articles using natural language processing techniques to identify salient content such as key terms, relationships between terms, and main topics. The data mining pipeline performs automatic annotation of the sequences extracted from the supplemental documents with the genetic parts used in them. Together these two pipelines link genetic parts to papers describing the context in which they are used. Ultimately, SBKS will reduce the time necessary for synthetic biologists to find the information necessary to complete their designs.

Discovering microbe-disease associations from the literature using a hierarchical long short-term memory network and an ensemble parser model

With recent advances in biotechnology and sequencing technology, the microbial community has been intensively studied and discovered to be associated with many chronic as well as acute diseases. Even though a tremendous number of studies describing the association between microbes and diseases have been published, text mining methods that focus on such associations have been rarely studied. We propose a framework that combines machine learning and natural language processing methods to analyze the association between microbes and diseases. A hierarchical long short-term memory network was used to detect sentences that describe the association. For the sentences determined, two different parse tree-based search methods were combined to find the relation-describing word. The ensemble model of constituency parsing for structural pattern matching and dependency-based relation extraction improved the prediction accuracy. By combining deep learning and parse tree-based extractions, our proposed framework could extract the microbe-disease association with higher accuracy. The evaluation results showed that our system achieved an F-score of 0.8764 and 0.8524 in binary decisions and extracting relation words, respectively. As a case study, we performed a large-scale analysis of the association between microbes and diseases. Additionally, a set of common microbes shared by multiple diseases were also identified in this study. This study could provide valuable information for the major microbes that were studied for a specific disease. The code and data are available at https://github.com/DMnBI/mdi_predictor .