Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is the process of determining correspondences between entities across these resources, such as gene identifiers, disease concepts, or chemical entity identifiers. Many tools have been developed to compute such mappings based on common structural features and lexical information such as labels and synonyms. Lexical approaches in particular often provide very high recall, but low precision, due to lexical ambiguity. As a consequence of this, mapping efforts often resort to a labor intensive manual mapping refinement through a human curator. Large Language Models (LLMs), such as the ones employed by ChatGPT, have generalizable abilities to perform a wide range of tasks, including question-answering and information extraction. Here we present MapperGPT, an approach that uses LLMs to review and refine mapping relationships as a post-processing step, in concert with existing high-recall methods that are based on lexical and structural heuristics. We evaluated MapperGPT on a series of alignment tasks from different domains, including anatomy, developmental biology, and renal diseases. We devised a collection of tasks that are designed to be particularly challenging for lexical methods. We show that when used in combination with high-recall methods, MapperGPT can provide a substantial improvement in accuracy, beating state-of-the-art (SOTA) methods such as LogMap.

Entity linking (EL) is the process of linking entity mentions appearing in web text with their corresponding entities in a knowledge base. EL plays an important role in the fields of knowledge engineering and data mining, underlying a variety of downstream applications such as knowledge base population, content analysis, relation extraction, and question answering. In recent years, deep learning (DL), which has achieved tremendous success in various domains, has also been leveraged in EL methods to surpass traditional machine learning based methods and yield the state-of-the-art performance. In this survey, we present a comprehensive review and analysis of existing DL based EL methods. First of all, we propose a new taxonomy, which organizes existing DL based EL methods using three axes: embedding, feature, and algorithm. Then we systematically survey the representative EL methods along the three axes of the taxonomy. Later, we introduce ten commonly used EL data sets and give a quantitative performance analysis of DL based EL methods over these data sets. Finally, we discuss the remaining limitations of existing methods and highlight some promising future directions.

Named entity linking is to map an ambiguous mention in documents to an entity in a knowledge base. The named entity linking is challenging, given the fact that there are multiple candidate entities for a mention in a document. It is difficult to link a mention when it appears multiple times in a document, since there are conflicts by the contexts around the appearances of the mention. In addition, it is difficult since the given training dataset is small due to the reason that it is done manually to link a mention to its mapping entity. In the literature, there are many reported studies among which the recent embedding methods learn vectors of entities from the training dataset at document level. To address these issues, we focus on how to link entity for mentions at a sentence level, which reduces the noises introduced by different appearances of the same mention in a document at the expense of insufficient information to be used. We propose a new unified embedding method by maximizing the relationships learned from knowledge graphs. We confirm the effectiveness of our method in our experimental studies.