BioPropaPhenKG on Multi-Relation Extraction Methods on Online Newspapers

The coronavirus disease (COVID-19) spread rampantly around the world at the beginning of 2020 before the governments of each country could prevent it by making decisions based on medical data analysis. With proper formalization, the terabytes of new textual data available online every day could have been used for the early description and detection of cases of this virus. Since then, the number of Event-Based Surveillance (EBS) applications has increased exponentially. These applications aim to mine channels of unstructured data to detect signs of possible public health events. However, one problem with such systems is the need for expert intervention to define which event will be captured, which relevant terms should be used in the search, and to analyze the events to modify the search procedure constantly. Another problem is that many of these applications do not consider both spatial and temporal characteristics. Addressing such limitations, this article presents a novel approach. We propose the biomedical domain specialization of the Core Propagation Phenomenon Ontology (PropaPhen) to capture spatiotemporal characteristics of the propagation of health-related phenomena. We also propose the Description-Detection-Framework (DDF), which leverages PropaPhen, UMLS, and OpenStreetMaps to detect new medical events automatically. Finally, we demonstrate a use case with experiments on extracts from online newspapers about COVID-19. The results show that DDF can be useful for detecting clusters of suspicious cases of possible emerging health-related phenomena.

BioPropaPhenKG, its ontology and other useful information can be found in https://zenodo.org/records/10911980. The code used for this use case can be found in https://github.com/Gabriel382/DDPF-Health-Risks . Finally, the datasets used where UMLS MetamorphoSys, OpenStreetMaps, Wikidata, Aylien (data only from November of 2019).

To read, you just need to load it with Neo4j:4.4.3. Alternatively, you can open it with docker using the following command: 

docker run --interactive --tty --rm \    --publish=7474:7474 --publish=7687:7687 \    --volume=/path-to-data-folder:/data --user="$(id -u):$(id -g)"\    neo4j:4.4.3 \neo4j-admin load --from=/data/BioPropaPhenKG-Journal-MultiRE.dump --database "neo4j" --force