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.

Network-based methods for outcome prediction in the "sample space"

In this thesis we present the novel semi-supervised network-based algorithm P-Net, which is able to rank and classify patients with respect to a specific phenotype or clinical outcome under study. The peculiar and innovative characteristic of this method is that it builds a network of samples/patients, where the nodes represent the samples and the edges are functional or genetic relationships between individuals (e.g. similarity of expression profiles), to predict the phenotype under study. In other words, it constructs the network in the "sample space" and not in the "biomarker space" (where nodes represent biomolecules (e.g. genes, proteins) and edges represent functional or genetic relationships between nodes), as usual in state-of-the-art methods. To assess the performances of P-Net, we apply it on three different publicly available datasets from patients afflicted with a specific type of tumor: pancreatic cancer, melanoma and ovarian cancer dataset, by using the data and following the experimental set-up proposed in two recently published papers [Barter et al., 2014, Winter et al., 2012]. We show that network-based methods in the "sample space" can achieve results competitive with classical supervised inductive systems. Moreover, the graph representation of the samples can be easily visualized through networks and can be used to gain visual clues about the relationships between samples, taking into account the phenotype associated or predicted for each sample. To our knowledge this is one of the first works that proposes graph-based algorithms working in the "sample space" of the biomolecular profiles of the patients to predict their phenotype or outcome, thus contributing to a novel research line in the framework of the Network Medicine.