SchemaLink: An Intelligent Web Editor for LinkML Schema Curation

Motivation: LinkML is a suitable language for the representation of the structural and content constraints of different kinds of biomedical data. Even if it is a quite recent proposal, it has been applied in several biomedical contexts. Developing and maintaining LinkML schemas presents several challenges, particularly for novice curators. Non-expert bio-curators may struggle with LinkML syntax and best practices, requiring significant time and effort to develop well-structured schemas. Results: In this paper we propose SchemaLink, a web-based environment for the graphical construction and enhancement of LinkML schemas that address the following requirements: $(i)$ introduce a graphical language for the specification of LinkML schemas, $(ii)$ make uniform the specification of schemas in similar contexts, $(iii)$ simplify the design and curation processes by exploiting a RAG-based approach to assist curators in creating new schemas from scratch and editing already developed ones. Several experimental analyses show the quality of the produced LinkML schemas through the AI-based editing facilities. Availability and Implementation: SchemaLink is available online at: https://SchemaLink.biodata.di.unimi.it. SchemaLink code and testing data are available as open-source on GitHub at: https://github.com/AnacletoLAB/{schemalink-webapp,schemalink-api}.

RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are continuously produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph encompassing biological knowledge about RNAs gathered from more than 50 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.