Profiling Medical Journal Articles Using a Gene Ontology Semantic Tagger

Nathan Rutherford - 08 Jan 2019


In many areas of academic publishing, there is an explosion of literature, and sub-division of fields into subfields, leading to stove-piping where sub-communities of expertise become disconnected from each other. This is especially true in the genetics literature over the last 10 years where researchers are no longer able to maintain knowledge of previously related areas. # This paper extends several approaches based on natural language processing and corpus linguistics which allow us to examine corpora derived from bodies of genetics literature and will help to make comparisons and improve retrieval methods using domain knowledge via an existing gene ontology. # We derived two open access medical journal corpora from PubMed related to psychiatric genetics and immune disorder genetics. We created a novel Gene Ontology Semantic Tagger (GOST) and lexicon to annotate the corpora and are then able to compare subsets of literature to understand the relative distributions of genetic terminology, thereby enabling researchers to make improved connections between them. # Using this previous work, we developeda novel NLP pipeline that integrated this new semantic tagger and a corpus database management system - LexiDB. This allows biomedical researchers to query this dataset using corpus linguistic methods to generate and test new hyptheses