An annotated dataset for extracting gene-melanoma relations from scientific literature

Abstract

Abstract Background Melanoma is one of the least common but the deadliest of skin cancers. This cancer begins when the genes of a cell suffer damage or fail, and identifying the genes involved in melanoma is crucial for understanding the melanoma tumorigenesis. Thousands of publications about human melanoma appear every year. However, while biological curation of data is costly and time-consuming, to date the application of machine learning for gene-melanoma relation extraction from text has been severely limited by the lack of annotated resources. Results To overcome this lack of resources for melanoma, we have exploited the information of the Melanoma Gene Database (MGDB, a manually curated database of genes involved in human melanoma) to automatically build an annotated dataset of binary relations between gene and melanoma entities occurring in PubMed abstracts. The entities were automatically annotated by state-of-the-art text-mining tools. Their annotation includes both the mention text spans and normalized concept identifiers. The relations among the entities were annotated at concept- and mention-level. The concept-level annotation was produced using the information of the genes in MGDB to decide if a relation holds between a gene and melanoma concept in the whole abstract. The exploitability of this dataset was tested with both traditional machine learning, and neural network-based models like BERT. The models were then used to automatically extract gene-melanoma relations from the biomedical literature. Most of the current models use context-aware representations of the target entities to establish relations between them. To facilitate researchers in their experiments we generated a mention-level annotation in support to the concept-level annotation. The mention-level annotation was generated by automatically linking gene and melanoma mentions co-occurring within the sentences that in MGDB establish the association of the gene with melanoma. Conclusions This paper presents a corpus containing gene-melanoma annotated relations. Additionally, it discusses experiments which show the usefulness of such a corpus for training a system capable of mining gene-melanoma relationships from the literature. Researchers can use the corpus to develop and compare their own models, and produce results which might be integrated with existing structured knowledge databases, which in turn might facilitate medical research.