Querying knowledge graphs in natural language

Informatic challenges and advances in illuminating the druggable proteome

The understudied members of the druggable proteomes offer promising prospects for drug discovery efforts. While large-scale initiatives have generated valuable functional information on understudied members of the druggable gene families, translating this information into actionable knowledge for drug discovery requires specialized informatics tools and resources. Here, we review the unique informatics challenges and advances in annotating understudied members of the druggable proteome. We demonstrate the application of statistical evolutionary inference tools, knowledge graph mining approaches, and protein language models in illuminating understudied protein kinases, pseudokinases, and ion channels.

A survey on semantic question answering systems

Recently, many question answering systems that derive answers from linked data repositories have been developed. The purpose of this survey is to identify the common features and approaches of the semantic question answering (SQA) systems, although many different and prototype systems have been designed. The SQA systems use a formal query language like SPARQL and knowledge of a specific vocabulary. This paper analyses different frameworks, architectures, or systems that perform SQA and classifies SQA systems based on different criteria.

CIDOC2VEC: Extracting Information from Atomized CIDOC-CRM Humanities Knowledge Graphs

The development of the field of digital humanities in recent years has led to the increased use of knowledge graphs within the community. Many digital humanities projects tend to model their data based on CIDOC-CRM ontology, which offers a wide array of classes appropriate for storing humanities and cultural heritage data. The CIDOC-CRM ontology model leads to a knowledge graph structure in which many entities are often linked to each other through chains of relations, which means that relevant information often lies many hops away from their entities. In this paper, we present a method based on graph walks and text processing to extract entity information and provide semantically relevant embeddings. In the process, we were able to generate similarity recommendations as well as explore their underlying data structure. This approach was then demonstrated on the Sphaera Dataset which was modeled according to the CIDOC-CRM data structure.