Symbolic Methods Project

collaboration between Nenad Macesic and Kernyu Park

Tackling Antibiotic Resistance (aka AMR) Using Ontology Learning

Aiming at an ontology-based approach to tackle antibiotic resistance.

Method(s)

• Ontology Learning process (semi-automated)
  • Topic-modeling methods using tf-idf weighting of terms
  • annotation of biomedical texts using Metamap
  • network analysis (clustering and community detection)

Tasks

1. obtain MEDLINE corpus of abstracts and MeSH terms

2. process abstracts using tf-idf weighting of terms and constrain to an adjacency matrix of co-occurrences between all terms occurring in all abstract texts (obtain "tokens", or "terms")

3. map to UMLS using Metamap to identify concepts in the term cloud (obtain "concepts")

4. combine with matrix of MeSH terms to identify hierarchical as well as modifier relationships between terms (define relationships)

5. expert validation of the established concepts and their relationships

6. construct an ontology (ontology generation)

7. expert validation of the obtained ontology for further improvement