We propose methods for extracting triples from Wikipedia’s HTML tables using a reference knowledge graph. Our methods use a distant-supervision approach to find existing triples in the knowledge graph for pairs of entities on the same row of a table, postulating the corresponding relation for pairs of entities from other rows in the corresponding columns, thus extracting novel candidate triples. Binary classifiers are applied on these candidates to detect correct triples and thus increase the precision of the output triples. We extend this approach with a preliminary step where we first group and merge similar tables, thereafter applying extraction on the larger merged tables. More specifically, we propose anobserved schemafor individual tables, which is used to group and merge tables. We compare the precision and number of triples extracted with and without table merging, where we show that with merging, we can extract a larger number of triples at a similar precision. Ultimately, from the tables of English Wikipedia, we extract 5.9 million novel and unique triples for Wikidata at an estimated precision of 0.718.

Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is time-consuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model. It uses statistical relational learning on top of phosphorylation networks interpreted as knowledge graphs, a simple yet robust model for representing networked knowledge. Compared to a representative selection of six existing systems, our model has the highest kinome coverage and produces biologically valid high-confidence predictions not possible with the other tools. Specifically, we have experimentally validated predictions of previously unknown phosphorylations by the LATS1, AKT1, PKA and MST2 kinases in human. Thus, our tool is useful for focusing phosphoproteomic experiments, and facilitates the discovery of new phosphorylation reactions. Our model can be accessed publicly via an easy-to-use web interface (LinkPhinder).

Timely identification of adverse drug reactions (ADRs) is highly important in the domains of public health and pharmacology. Early discovery of potential ADRs can limit their effect on patient lives and also make drug development pipelines more robust and efficient. Reliable in silico prediction of ADRs can be helpful in this context, and thus, it has been intensely studied. Recent works achieved promising results using machine learning. The presented work focuses on machine learning methods that use drug profiles for making predictions and use features from multiple data sources. We argue that despite promising results, existing works have limitations, especially regarding flexibility in experimenting with different data sets and/or predictive models. We suggest to address these limitations by generalization of the key principles used by the state of the art. Namely, we explore effects of: (1) using knowledge graphs-machine-readable interlinked representations of biomedical knowledge-as a convenient uniform representation of heterogeneous data; and (2) casting ADR prediction as a multi-label ranking problem. We present a specific way of using knowledge graphs to generate different feature sets and demonstrate favourable performance of selected off-the-shelf multi-label learning models in comparison with existing works. Our experiments suggest better suitability of certain multi-label learning methods for applications where ranking is preferred. The presented approach can be easily extended to other feature sources or machine learning methods, making it flexible for experiments tuned toward specific requirements of end users. Our work also provides a clearly defined and reproducible baseline for any future related experiments.

The tables embedded in Wikipedia articles contain rich, semi-structured encyclopaedic content. However, the cumulative content of these tables cannot be queried against. We thus propose methods to recover the semantics of Wikipedia tables and, in particular, to extract facts from them in the form of RDF triples. Our core method uses an existing Linked Data knowledge-base to find pre-existing relations between entities in Wikipedia tables, suggesting the same relations as holding for other entities in analogous columns on different rows. We find that such an approach extracts RDF triples from Wikipedia's tables at a raw precision of 40%. To improve the raw precision, we define a set of features for extracted triples that are tracked during the extraction phase. Using a manually labelled gold standard, we then test a variety of machine learning methods for classifying correct/incorrect triples. One such method extracts 7.9 million unique and novel RDF triples from over one million Wikipedia tables at an estimated precision of 81.5%.