Tables in scientific papers contain a wealth of valuable knowledge for the scientific enterprise. To help the many of us who frequently consult this type of knowledge, we present Tab2Know, a new end-to-end system to build a Knowledge Base (KB) from tables in scientific papers. Tab2Know addresses the challenge of automatically interpreting the tables in papers and of disambiguating the entities that they contain. To solve these problems, we propose a pipeline that employs both statistical-based classifiers and logic-based reasoning. First, our pipeline applies weakly supervised classifiers to recognize the type of tables and columns, with the help of a data labeling system and an ontology specifically designed for our purpose. Then, logic-based reasoning is used to link equivalent entities (via sameAs links) in different tables. An empirical evaluation of our approach using a corpus of papers in the Computer Science domain has returned satisfactory performance. This suggests that ours is a promising step to create a large-scale KB of scientific knowledge.

The inexpressive Description Logic (DL) $\mathcal{FL}_0$, which has conjunction and value restriction as its only concept constructors, had fallen into disrepute when it turned out that reasoning in $\mathcal{FL}_0$ w.r.t. general TBoxes is ExpTime-complete, i.e., as hard as in the considerably more expressive logic $\mathcal{ALC}$. In this paper, we rehabilitate $\mathcal{FL}_0$ by presenting a dedicated subsumption algorithm for $\mathcal{FL}_0$, which is much simpler than the tableau-based algorithms employed by highly optimized DL reasoners. Our experiments show that the performance of our novel algorithm, as prototypically implemented in our $\mathcal{FL}_o$wer reasoner, compares very well with that of the highly optimized reasoners. $\mathcal{FL}_o$wer can also deal with ontologies written in the extension $\mathcal{FL}_{\bot}$ of $\mathcal{FL}_0$ with the top and the bottom concept by employing a polynomial-time reduction, shown in this paper, which eliminates top and bottom. We also investigate the complexity of reasoning in DLs related to the Horn-fragments of $\mathcal{FL}_0$ and $\mathcal{FL}_{\bot}$.

Wikidata has been increasingly adopted by many communities for a wide variety of applications, which demand high-quality knowledge to deliver successful results. In this paper, we develop a framework to detect and analyze low-quality statements in Wikidata by shedding light on the current practices exercised by the community. We explore three indicators of data quality in Wikidata, based on: 1) community consensus on the currently recorded knowledge, assuming that statements that have been removed and not added back are implicitly agreed to be of low quality; 2) statements that have been deprecated; and 3) constraint violations in the data. We combine these indicators to detect low-quality statements, revealing challenges with duplicate entities, missing triples, violated type rules, and taxonomic distinctions. Our findings complement ongoing efforts by the Wikidata community to improve data quality, aiming to make it easier for users and editors to find and correct mistakes.

Healthcare representation learning on the Electronic Health Record (EHR) is seen as crucial for predictive analytics in the medical field. Many natural language processing techniques, such as word2vec, RNN and self-attention, have been adapted for use in hierarchical and time stamped EHR data, but fail when they lack either general or task-specific data. Hence, some recent works train healthcare representations by incorporating medical ontology (a.k.a. knowledge graph), by self-supervised tasks like diagnosis prediction, but (1) the small-scale, monotonous ontology is insufficient for robust learning, and (2) critical contexts or dependencies underlying patient journeys are never exploited to enhance ontology learning. To address this, we propose an end-to-end robust Transformer-based solution, Mutual Integration of patient journey and Medical Ontology (MIMO) for healthcare representation learning and predictive analytics. Specifically, it consists of task-specific representation learning and graph-embedding modules to learn both patient journey and medical ontology interactively. Consequently, this creates a mutual integration to benefit both healthcare representation learning and medical ontology embedding. Moreover, such integration is achieved by a joint training of both task-specific predictive and ontology-based disease typing tasks based on fused embeddings of the two modules. Experiments conducted on two real-world diagnosis prediction datasets show that, our healthcare representation model MIMO not only achieves better predictive results than previous state-of-the-art approaches regardless of sufficient or insufficient training data, but also derives more interpretable embeddings of diagnoses.

The current preprint is an update to SituationCO v1.1 (Situation Core Ontology), which represents its new version 1.2. It specifies and defines all the terms, properties, relationships and axioms of SituationCO v1.2, being an ontology for particular and generic Situations placed at the core level in the context of a four-layered ontological architecture called FCD-OntoArch (Foundational, Core, and Domain Ontological Architecture for Sciences). This is a four-layered ontological architecture, which considers Foundational, Core, Domain and Instance levels. In turn, the domain level is split down in two sub-levels, namely: Top-domain and Low-domain ontological levels. So in fact, we can consider it to be a five-tier architecture. Ontologies at the same level can be related to each other, except for the foundational level where only ThingFO (Thing Foundational Ontology) is found. In addition, ontologies' terms and relationships at lower levels can be semantically enriched by ontologies' terms and relationships from the higher levels. Note that both ThingFO and ontologies at the core level such as SituationCO, ProcessCO, among others, are domain independent. SituationCO's terms and relationships are specialized primarily from ThingFO. It also completely reuses terms primarily from ProcessCO, ProjectCO and GoalCO ontologies. Stereotypes are the used mechanism for enriching SituationCO terms. Note that in the end of this document, we address the SituationCO vs. ThingFO non-taxonomic relationship verification matrix.

The present preprint specifies and defines all Terms, Properties, Relationships and Axioms of ThingFO (Thing Foundational Ontology) v1.2, which is a slightly updated version of its predecessor, ThingFO v1.1. It is an ontology for particular and universal Things placed at the foundational level in the context of a four-layered ontological architecture named FCD-OntoArch (Foundational, Core, and Domain Ontological Architecture for Sciences). This is a five-layered ontological architecture, which considers Foundational, Core, Domain and Instance levels. In turn, the domain level is split down in two sub-levels, namely: Top-domain and Low-domain. Ontologies at the same level can be related to each other, except for the foundational level where only the ThingFO ontology is. In addition, ontologies' terms and relationships at lower levels can be semantically enriched by ontologies' terms and relationships from the higher levels. ThingFO and ontologies at the core level such as SituationCO, ProcessCO, ProjectCO, among others, are domain independent. ThingFO is made up of three main concepts, namely: Thing with the semantics of Particular, Thing Category with the semantics of Universal, and Assertion that represents human statements about different aspects of Particulars and Universals. Note that annotations of updates from the previous version (v1.1) to the current one (v1.2) can be found in Appendix A.

Biodiversity, the variation within and between species and ecosystems, is essential for human well-being and the equilibrium of the planet. It is critical for the sustainable development of human society and is an important global challenge. Biodiversity research has become increasingly data-intensive and it deals with heterogeneous and distributed data made available by global and regional initiatives, such as GBIF, ILTER, LifeWatch, BODC, PANGAEA, and TERN, that apply different data management practices. In particular, a variety of metadata and semantic resources have been produced by these initiatives to describe biodiversity observations, introducing interoperability issues across data management systems. To address these challenges, the InteroperAble Descriptions of Observable Property Terminology WG (I-ADOPT WG) was formed by a group of international terminology providers and data center managers in 2019 with the aim to build a common approach to describe what is observed, measured, calculated, or derived. Based on an extensive analysis of existing semantic representations of variables, the WG has recently published the I-ADOPT framework ontology to facilitate interoperability between existing semantic resources and support the provision of machine-readable variable descriptions whose components are mapped to FAIR vocabulary terms. The I-ADOPT framework ontology defines a set of high level semantic components that can be used to describe a variety of patterns commonly found in scientific observations. This contribution will focus on how the I-ADOPT framework can be applied to represent variables commonly used in the biodiversity domain.

In this paper, we consider existential rules, an expressive formalism well suited to the representation of ontological knowledge and data-to-ontology mappings in the context of ontology-based data integration. The chase is a fundamental tool to do reasoning with existential rules as it computes all the facts entailed by the rules from a database instance. We introduce parallelisable sets of existential rules, for which the chase can be computed in a single breadth-first step from any instance. The question we investigate is the characterization of such rule sets. We show that parallelisable rule sets are exactly those rule sets both bounded for the chase and belonging to a novel class of rules, called pieceful. The pieceful class includes in particular frontier-guarded existential rules and (plain) datalog. We also give another characterization of parallelisable rule sets in terms of rule composition based on rewriting.

The construction of an ontology of scientific knowledge objects, presented here, is part of the development of an approach oriented towards the visualization of scientific knowledge. It is motivated by the fact that the concepts that are used to organize scientific knowledge (theorem, law, experience, proof, etc.) appear in existing ontologies but that none of these ontologies is centered on this topic and presents them in a simple and easily understandable organization. This ontology has been constructed by 1) selecting concepts that appear in high level ontologies or in ontologies of knowledge objects of specific fields and 2) interviewing scientists in different fields. We have aligned this ontology with some of the sources used, which has allowed us to verify its consistency with respect to them. The validation of the ontology consists in using it to formalize knowledge from various sources, which we have begun to do in the field of physics. The access to scientific knowledge, whether general or factual, must necessarily involve a visual, auditory or other presentation that appeals to one or more senses of the human being.

Entity-Relationship (E-R) Modeling is one approach to visualize what story your data is trying to tell. This goal of this predecessor to object modeling (e.g. UML or CRC cards) is to give you a high-level, graphical view of the core components of an enterprise--the E-R diagram. An E-R diagram (sometimes called a Chen diagram, after its creator, Peter Chen) is a conceptual graph that captures meaning rather than implementation [1]. Once you have the diagram, you can convert it to a set of tables.