Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Due to growing population and technological advances, global electricity consumption, and consequently also CO2 emissions are increasing. The residential sector makes up 25% of global electricity consumption and has great potential to increase efficiency and reduce CO2 footprint without sacrificing comfort. However, a lack of uniform consumption data at the household level spanning multiple regions hinders large-scale studies and robust multi-region model development. This paper introduces a multi-region dataset compiled from publicly available sources and presented in a uniform format. This data enables machine learning tasks such as disaggregation, demand forecasting, appliance ON/OFF classification, etc. Furthermore, we develop an RDF knowledge graph that characterizes the electricity consumption of the households and contextualizes it with household related properties enabling semantic queries and interoperability with other open knowledge bases like Wikidata and DBpedia. This structured data can be utilized to inform various stakeholders towards data-driven policy and business development.

We present a knowledge integration framework (called KIF) that uses Wikidata as a lingua franca to integrate heterogeneous knowledge bases. These can be triplestores, relational databases, CSV files, etc., which may or may not use the Wikidata dialect of RDF. KIF leverages Wikidata's data model and vocabulary plus user-defined mappings to expose a unified view of the integrated bases while keeping track of the context and provenance of their statements. The result is a virtual knowledge base which behaves like an "extended Wikidata" and which can be queried either through an efficient filter interface or using SPARQL. We present the design and implementation of KIF, discuss how we have used it to solve a real integration problem in the domain of chemistry (involving Wikidata, PubChem, and IBM CIRCA), and present experimental results on the performance and overhead of KIF.

We present SemOpenAlex, an extensive RDF knowledge graph that contains over 26 billion triples about scientific publications and their associated entities, such as authors, institutions, journals, and concepts. SemOpenAlex is licensed under CC0, providing free and open access to the data. We offer the data through multiple channels, including RDF dump files, a SPARQL endpoint, and as a data source in the Linked Open Data cloud, complete with resolvable URIs and links to other data sources. Moreover, we provide embeddings for knowledge graph entities using high-performance computing. SemOpenAlex enables a broad range of use-case scenarios, such as exploratory semantic search via our website, large-scale scientific impact quantification, and other forms of scholarly big data analytics within and across scientific disciplines. Additionally, it enables academic recommender systems, such as recommending collaborators, publications, and venues, including explainability capabilities. Finally, SemOpenAlex can serve for RDF query optimization benchmarks, creating scholarly knowledge-guided language models, and as a hub for semantic scientific publishing.

Application developers today have three choices for exploiting the knowledge present in Wikidata: they can download the Wikidata dumps in JSON or RDF format, they can use the Wikidata API to get data about individual entities, or they can use the Wikidata SPARQL endpoint. None of these methods can support complex, yet common, query use cases, such as retrieval of large amounts of data or aggregations over large fractions of Wikidata. This paper introduces KGTK Kypher, a query language and processor that allows users to create personalized variants of Wikidata on a laptop. We present several use cases that illustrate the types of analyses that Kypher enables users to run on the full Wikidata KG on a laptop, combining data from external resources such as DBpedia. The Kypher queries for these use cases run much faster on a laptop than the equivalent SPARQL queries on a Wikidata clone running on a powerful server with 24h time-out limits.

Graphs are data structures that are useful to represent ubiquitous phenomena, such as social networks, chemical molecules and recommendation systems. One of their strengths lies in the fact that they explicitly model relations (i.e. We can illustrate the added value of this data enrichment using the Cora citation network. This dataset contains a bag-of-words representation for a few hundred papers and the citation relations between each of these papers. If we apply dimensionality reduction (t-SNE) to create a 2D plot of the bag-of-words representations (Figure 1, left), we can see clusters (they are colored according to their research topic) arise but they overlap.

In recent years, Semantic Web technologies have been increasingly adopted by researchers, industry and public institutions to describe and link data on the Web, create web annotations and consume large knowledge graphs like Wikidata and DBPedia. However, there is still a knowledge gap between ontology engineers, who design, populate and create knowledge graphs; and web developers, who need to understand, access and query these knowledge graphs but are not familiar with ontologies, RDF or SPARQL. In this paper we describe the Ontology-Based APIs framework (OBA), our approach to automatically create REST APIs from ontologies while following RESTful API best practices. Given an ontology (or ontology network) OBA uses standard technologies familiar to web developers (OpenAPI Specification, JSON) and combines them with W3C standards (OWL, JSON-LD frames and SPARQL) to create maintainable APIs with documentation, units tests, automated validation of resources and clients (in Python, Javascript, etc.) for non Semantic Web experts to access the contents of a target knowledge graph. We showcase OBA with three examples that illustrate the capabilities of the framework for different ontologies.

While the biomedical community has published several "open data" sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, query, and integrate heterogeneous data and knowledge from multiple sources. To tackle these challenges, the community has experimented with Semantic Web and linked data technologies to create the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we extract schemas from more than 80 publicly available biomedical linked data graphs into an LSLOD schema graph and conduct an empirical meta-analysis to evaluate the extent of semantic heterogeneity across the LSLOD cloud. We observe that several LSLOD sources exist as stand-alone data sources that are not inter-linked with other sources, use unpublished schemas with minimal reuse or mappings, and have elements that are not useful for data integration from a biomedical perspective. We envision that the LSLOD schema graph and the findings from this research will aid researchers who wish to query and integrate data and knowledge from multiple biomedical sources simultaneously on the Web.

Predicate constraints of general-purpose knowledge bases (KBs) like Wikidata, DBpedia and Freebase are often limited to subproperty, domain and range constraints. In this demo we showcase CounQER, a system that illustrates the alignment of counting predicates, like staffSize, and enumerating predicates, like workInstitution^{-1} . In the demonstration session, attendees can inspect these alignments, and will learn about the importance of these alignments for KB question answering and curation. CounQER is available at https://counqer.mpi-inf.mpg.de/spo.

ArCo is the Italian Cultural Heritage knowledge graph, consisting of a network of seven vocabularies and 169 million triples about 820 thousand cultural entities. It is distributed jointly with a SPARQL endpoint, a software for converting catalogue records to RDF, and a rich suite of documentation material (testing, evaluation, how-to, examples, etc.). ArCo is based on the official General Catalogue of the Italian Ministry of Cultural Heritage and Activities (MiBAC) - and its associated encoding regulations - which collects and validates the catalogue records of (ideally) all Italian Cultural Heritage properties (excluding libraries and archives), contributed by CH administrators from all over Italy.