Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE).

ABSTRACT: The Transformer-based approaches to solving natural language processing (NLP) tasks such as BERT and GPT are gaining popularity due to their ability to achieve high performance. These approaches benefit from using enormous data sizes to create pre-trained models and the ability to understand the context of words in a sentence. Their use in the information retrieval domain is thought to increase effectiveness and efficiency. This paper demonstrates a BERT-based method (CASBERT) implementation to build a search tool over data annotated compositely using ontologies. The data was a collection of biosimulation models written using the CellML standard in the Physiome Model Repository (PMR). A biosimulation model structurally consists of basic entities of constants and variables that construct hi

SUBMITTER: Munarko Y 

PROVIDER: S-EPMC10570691 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature