Agnieszka Ławrynowicz

Ania Wróblewska, Agnieszka Kaliska, Maciej Pawłowski et al.

Food Computing is currently a fast-growing field of research. Natural language processing (NLP) is also increasingly essential in this field, especially for recognising food entities. However, there are still only a few well-defined tasks that serve as benchmarks for solutions in this area. We introduce a new dataset -- called \textit{TASTEset} -- to bridge this gap. In this dataset, Named Entity Recognition (NER) models are expected to find or infer various types of entities helpful in processing recipes, e.g.~food products, quantities and their units, names of cooking processes, physical quality of ingredients, their purpose, taste. The dataset consists of 700 recipes with more than 13,000 entities to extract. We provide a few state-of-the-art baselines of named entity recognition models, which show that our dataset poses a solid challenge to existing models. The best model achieved, on average, 0.95 $F_1$ score, depending on the entity type -- from 0.781 to 0.982. We share the dataset and the task to encourage progress on more in-depth and complex information extraction from recipes.

Agnieszka Lawrynowicz, Luis Galarraga, Mehwish Alam et al.

In this chapter, we address the problem of rule mining, beginning with essential background information, including measures of rule quality. We then explore various rule mining methodologies, categorized into three groups: inductive logic programming, path sampling and generalization, and linear programming. Following this, we delve into neurosymbolic methods, covering topics such as the integration of deep learning with rules, the use of embeddings for rule learning, and the application of large language models in rule learning.

Zuzanna Gawrysiak, Agata Żywot, Agnieszka Ławrynowicz

We present WineGraph, an extended version of FlavorGraph, a heterogeneous graph incorporating wine data into its structure. This integration enables food-wine pairing based on taste and sommelier-defined rules. Leveraging a food dataset comprising 500,000 reviews and a wine reviews dataset with over 130,000 entries, we computed taste descriptors for both food and wine. This information was then utilised to pair food items with wine and augment FlavorGraph with additional data. The results demonstrate the potential of heterogeneous graphs to acquire supplementary information, proving beneficial for wine pairing.

Agnieszka Ławrynowicz

The aim of this primer is to introduce the subject of knowledge engineering in a concise but synthetic way to develop the reader's intuition about the area.

Dawid Wiśniewski, Jędrzej Potoniec, Agnieszka Ławrynowicz

Competency Questions (CQs) are used in many ontology engineering methodologies to collect requirements and track the completeness and correctness of an ontology being constructed. Although they are frequently suggested by ontology engineering methodologies, the publicly available datasets of CQs and their formalizations in ontology query languages are very scarce. Since first efforts to automate processes utilizing CQs are being made, it is of high importance to provide large and diverse datasets to fuel these solutions. In this paper, we present BigCQ, the biggest dataset of CQ templates with their formalizations into SPARQL-OWL query templates. BigCQ is created automatically from a dataset of frequently used axiom shapes. These pairs of CQ templates and query templates can be then materialized as actual CQs and SPARQL-OWL queries if filled with resource labels and IRIs from a given ontology. We describe the dataset in detail, provide a description of the process leading to the creation of the dataset and analyze how well the dataset covers real-world examples. We also publish the dataset as well as scripts transforming axiom shapes into pairs of CQ patterns and SPARQL-OWL templates, to make engineers able to adapt the process to their particular needs.

C. Maria Keet, Kieren Davies, Agnieszka Lawrynowicz

Ontology authoring is a complex process, where commonly the automated reasoner is invoked for verification of newly introduced changes, therewith amounting to a time-consuming test-last approach. Test-Driven Development (TDD) for ontology authoring is a recent {\em test-first} approach that aims to reduce authoring time and increase authoring efficiency. Current TDD testing falls short on coverage of OWL features and possible test outcomes, the rigorous foundation thereof, and evaluations to ascertain its effectiveness. We aim to address these issues in one instantiation of TDD for ontology authoring. We first propose a succinct, logic-based model of TDD testing and present novel TDD algorithms so as to cover also any OWL 2 class expression for the TBox and for the principal ABox assertions, and prove their correctness. The algorithms use methods from the OWL API directly such that reclassification is not necessary for test execution, therewith reducing ontology authoring time. The algorithms were implemented in TDDonto2, a Protégé plugin. TDDonto2 was evaluated on editing efficiency and by users. The editing efficiency study demonstrated that it is faster than a typical ontology authoring interface, especially for medium size and large ontologies. The user evaluation demonstrated that modellers make significantly less errors with TDDonto2 compared to the standard Protégé interface and complete their tasks better using less time. Thus, the results indicate that Test-Driven Development is a promising approach in an ontology development methodology.

Dawid Wisniewski, Jedrzej Potoniec, Agnieszka Lawrynowicz et al.

Competency Questions (CQs) are natural language questions outlining and constraining the scope of knowledge represented by an ontology. Despite that CQs are a part of several ontology engineering methodologies, we have observed that the actual publication of CQs for the available ontologies is very limited and even scarcer is the publication of their respective formalisations in terms of, e.g., SPARQL queries. This paper aims to contribute to addressing the engineering shortcomings of using CQs in ontology development, to facilitate wider use of CQs. In order to understand the relation between CQs and the queries over the ontology to test the CQs on an ontology, we gather, analyse, and publicly release a set of 234 CQs and their translations to SPARQL-OWL for several ontologies in different domains developed by different groups. We analysed the CQs in two principal ways. The first stage focused on a linguistic analysis of the natural language text itself, i.e., a lexico-syntactic analysis without any presuppositions of ontology elements, and a subsequent step of semantic analysis in order to find patterns. This increased diversity of CQ sources resulted in a 5-fold increase of hitherto published patterns, to 106 distinct CQ patterns, which have a limited subset of few patterns shared across the CQ sets from the different ontologies. Next, we analysed the relation between the found CQ patterns and the 46 SPARQL-OWL query signatures, which revealed that one CQ pattern may be realised by more than one SPARQL-OWL query signature, and vice versa. We hope that our work will contribute to establishing common practices, templates, automation, and user tools that will support CQ formulation, formalisation, execution, and general management.

Gustavo Correa Publio, Diego Esteves, Agnieszka Ławrynowicz et al.

The ML-Schema, proposed by the W3C Machine Learning Schema Community Group, is a top-level ontology that provides a set of classes, properties, and restrictions for representing and interchanging information on machine learning algorithms, datasets, and experiments. It can be easily extended and specialized and it is also mapped to other more domain-specific ontologies developed in the area of machine learning and data mining. In this paper we overview existing state-of-the-art machine learning interchange formats and present the first release of ML-Schema, a canonical format resulted of more than seven years of experience among different research institutions. We argue that exposing semantics of machine learning algorithms, models, and experiments through a canonical format may pave the way to better interpretability and to realistically achieve the full interoperability of experiments regardless of platform or adopted workflow solution.

Jedrzej Potoniec, Piotr Jakubowski, Agnieszka Ławrynowicz

In this study, we present Swift Linked Data Miner, an interruptible algorithm that can directly mine an online Linked Data source (e.g., a SPARQL endpoint) for OWL 2 EL class expressions to extend an ontology with new SubClassOf: axioms. The algorithm works by downloading only a small part of the Linked Data source at a time, building a smart index in the memory and swiftly iterating over the index to mine axioms. We propose a transformation function from mined axioms to RDF Data Shapes. We show, by means of a crowdsourcing experiment, that most of the axioms mined by Swift Linked Data Miner are correct and can be added to an ontology. We provide a ready to use Protégé plugin implementing the algorithm, to support ontology engineers in their daily modeling work.

C. Maria Keet, Agnieszka Lawrynowicz

Emerging ontology authoring methods to add knowledge to an ontology focus on ameliorating the validation bottleneck. The verification of the newly added axiom is still one of trying and seeing what the reasoner says, because a systematic testbed for ontology authoring is missing. We sought to address this by introducing the approach of test-driven development for ontology authoring. We specify 36 generic tests, as TBox queries and TBox axioms tested through individuals, and structure their inner workings in an `open box'-way, which cover the OWL 2 DL language features. This is implemented as a Protege plugin so that one can perform a TDD test as a black box test. We evaluated the two test approaches on their performance. The TBox queries were faster, and that effect is more pronounced the larger the ontology is. We provide a general sequence of a TDD process for ontology engineering as a foundation for a TDD methodology.