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1. Rosetta Statements: Lowering the Barrier for Semantic Parsing and Increasing the Cognitive Interoperability of Knowledge Graphs

Author

Vogt, Lars, Konrad, Marcel, Farfar, Kheir Eddine, Prinz, Manuel, and Oelen, Allard

Subjects
Computer Science - Databases
Abstract

Machines need data and metadata to be machine-actionable and FAIR (findable, accessible, interoperable, reusable) to manage increasing data volumes. Knowledge graphs and ontologies are key to this, but their use is hampered by high access barriers due to required prior knowledge in semantics and data modelling. The Rosetta Statement approach proposes modeling English natural language statements instead of a mind-independent reality. We propose a metamodel for creating semantic schema patterns for simple statement types. The approach supports versioning of statements and provides a detailed editing history. Each Rosetta Statement pattern has a dynamic label for displaying statements as natural language sentences. Implemented in the Open Research Knowledge Graph (ORKG) as a use case, this approach allows domain experts to define data schema patterns without needing semantic knowledge. Future plans include combining Rosetta Statements with semantic units to organize ORKG into meaningful subgraphs, improving usability. A search interface for querying statements without needing SPARQL or Cypher knowledge is also planned, along with tools for data entry and display using Large Language Models and NLP. The Rosetta Statement metamodel supports a two-step knowledge graph construction procedure. Domain experts can model semantic content without support from ontology engineers, lowering entry barriers and increasing cognitive interoperability. The second level involves developing semantic graph patterns for reasoning, requiring collaboration with ontology engineers.

Published
2024

2. Semantic Units: Increasing Expressivity and Simplicity of Formal Representations of Data and Knowledge in Knowledge Graphs

Author

Vogt, Lars

Subjects
Computer Science - Databases
Abstract

Knowledge graphs and ontologies are becoming increasingly vital as they align with the FAIR Guiding Principles (Findable, Accessible, Interoperable, Reusable). We address eleven challenges that may impede the full realization of the potential of FAIR knowledge graphs, as conventional solutions are perceived to be overly complex and lacking in cognitive interoperability. We extend the concept of "semantic units" as a conceptual solution by adding further subcategories. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs, with each subgraph being represented by a resource that instantiates a semantic unit class. We introduce some-instance, most-instances, every-instance, and all-instances resources as new types of representational entities in addition to named-individual, class, and property resources. We combine these new resource types with the concept of semantic units and introduce new subcategories of statement units and semantically meaningful collections of statement units (i.e., compound units) that provide solutions to the eleven challenges. These include, for instance, schemes for modelling assertional, contingent, prototypical, and universal statements, including class axioms, as well as absence statements, negations, and cardinality restrictions. The schemes are alternatives to existing OWL-based modelling schemes, and we provide corresponding representations for them that do not involve blank nodes. With question units we also introduce a way of representing questions in a knowledge graph that can be made readily executable as graph queries. We also provide schemes for directive statements, directive conditional statements, and logical arguments. We argue that semantic units provide a framework that increases the overall expressivity and cognitive interoperability of knowledge graphs compared to conventional OWL-based solutions., Comment: arXiv admin note: text overlap with arXiv:2301.01227

Published
2024

3. FAIR 2.0: Extending the FAIR Guiding Principles to Address Semantic Interoperability

Author

Vogt, Lars, Strömert, Philip, Matentzoglu, Nicolas, Karam, Naouel, Konrad, Marcel, Prinz, Manuel, and Baum, Roman

Subjects
Computer Science - Databases
Abstract

FAIR data presupposes their successful communication between machines and humans while preserving their meaning and reference, requiring all parties involved to share the same background knowledge. Inspired by English as a natural language, we investigate the linguistic structure that ensures reliable communication of information and draw parallels with data structures, understanding both as models of systems of interest. We conceptualize semantic interoperability as comprising terminological and propositional interoperability. The former includes ontological (i.e., same meaning) and referential (i.e., same referent/extension) interoperability and the latter schema (i.e., same data schema) and logical (i.e., same logical framework) interoperability. Since no best ontology and no best data schema exists, establishing semantic interoperability and FAIRness of data and metadata requires the provision of a comprehensive set of relevant ontological and referential entity mappings and schema crosswalks. We therefore propose appropriate additions to the FAIR Guiding Principles, leading to FAIR 2.0. Furthermore, achieving FAIRness of data requires the provision of FAIR services in addition to organizing data into FAIR Digital Objects. FAIR services include a terminology, a schema, and an operations service.

Published
2024

4. FAIR Knowledge Graphs with Semantic Units: a Prototype

Author

Vogt, Lars

Subjects
Computer Science - Databases
Abstract

Knowledge graphs and ontologies are becoming increasingly important in the context of making data and metadata findable, accessible, interoperable, and reusable (FAIR). We introduce the concept of Semantic Units for organizing Knowledge Graphs into identifiable and semantically meaningful subgraphs. Each Semantic Unit is represented in the graph by its own resource that instantiates a Semantic Unit class. Different types of Semantic Units are distinguished, and together they can organize a Knowledge Graph into different levels of representational granularity with partially overlapping, partially enclosed subgraphs that users of Knowledge Graphs can refer to for making statements about statements. The use of Semantic Units in Knowledge Graphs supports making them FAIR and increases the human-reader-actionability of their data and metadata by increasing the graph's cognitive interoperability by increasing its explorability for a human reader. We introduce a minimal prototype web application for a user-driven FAIR Knowledge Graph that is based on Semantic Units.

Published
2023

5. Towards a Rosetta Stone for (meta)data: Learning from natural language to improve semantic and cognitive interoperability

Author

Vogt, Lars, Konrad, Marcel, and Prinz, Manuel

Subjects
Computer Science - Databases
Abstract

In order to effectively manage the overwhelming influx of data, it is crucial to ensure that data is findable, accessible, interoperable, and reusable (FAIR). While ontologies and knowledge graphs have been employed to enhance FAIRness, challenges remain regarding semantic and cognitive interoperability. We explore how English facilitates reliable communication of terms and statements, and transfer our findings to a framework of ontologies and knowledge graphs, while treating terms and statements as minimal information units. We categorize statement types based on their predicates, recognizing the limitations of modeling non-binary predicates with multiple triples, which negatively impacts interoperability. Terms are associated with different frames of reference, and different operations require different schemata. Term mappings and schema crosswalks are therefore vital for semantic interoperability. We propose a machine-actionable Rosetta Stone Framework for (meta)data, which uses reference terms and schemata as an interlingua to minimize mappings and crosswalks. Modeling statements rather than a human-independent reality ensures cognitive familiarity and thus better interoperability of data structures. We extend this Rosetta modeling paradigm to reference schemata, resulting in simple schemata with a consistent structure across statement types, empowering domain experts to create their own schemata using the Rosetta Editor, without requiring knowledge of semantics. The Editor also allows specifying textual and graphical display templates for each schema, delivering human-readable data representations alongside machine-actionable data structures. The Rosetta Query Builder derives queries based on completed input forms and the information from corresponding reference schemata. This work sets the conceptual ground for the Rosetta Stone Framework that we plan to develop in the future.

Published
2023

8. Knowledge Graph Building Blocks: An easy-to-use Framework for developing FAIREr Knowledge Graphs

Author

Vogt, Lars, Konrad, Marcel, and Prinz, Manuel

Subjects
Computer Science - Databases
Abstract

Knowledge graphs and ontologies provide promising technical solutions for implementing the FAIR Principles for Findable, Accessible, Interoperable, and Reusable data and metadata. However, they also come with their own challenges. Nine such challenges are discussed and associated with the criterion of cognitive interoperability and specific FAIREr principles (FAIR + Explorability raised) that they fail to meet. We introduce an easy-to-use, open source knowledge graph framework that is based on knowledge graph building blocks (KGBBs). KGBBs are small information modules for knowledge-processing, each based on a specific type of semantic unit. By interrelating several KGBBs, one can specify a KGBB-driven FAIREr knowledge graph. Besides implementing semantic units, the KGBB Framework clearly distinguishes and decouples an internal in-memory data model from data storage, data display, and data access/export models. We argue that this decoupling is essential for solving many problems of knowledge management systems. We discuss the architecture of the KGBB Framework as we envision it, comprising (i) an openly accessible KGBB-Repository for different types of KGBBs, (ii) a KGBB-Engine for managing and operating FAIREr knowledge graphs (including automatic provenance tracking, editing changelog, and versioning of semantic units); (iii) a repository for KGBB-Functions; (iv) a low-code KGBB-Editor with which domain experts can create new KGBBs and specify their own FAIREr knowledge graph without having to think about semantic modelling. We conclude with discussing the nine challenges and how the KGBB Framework provides solutions for the issues they raise. While most of what we discuss here is entirely conceptual, we can point to two prototypes that demonstrate the principle feasibility of using semantic units and KGBBs to manage and structure knowledge graphs.

Published
2023

9. The FAIREr Guiding Principles: Organizing data and metadata into semantically meaningful types of FAIR Digital Objects to increase their cognitive interoperability and human explorability

Author

Vogt, Lars

Subjects
Computer Science - Databases
Abstract

Ensuring the FAIRness (Findable, Accessible, Interoperable, Reusable) of data and metadata is an important goal in research and industry. Knowledge graphs and ontologies have been central in achieving this goal, with interoperability receiving much attention. The European Open Science Cloud Interoperability Framework (EOSC IF) distinguishes four layers of interoperability: technical, semantic, organizational, and legal. This paper argues that the emphasis on machine-actionability has overshadowed the essential need for human-actionability of data and describes two cases within knowledge graphs in which human-actionability is challenged. In response, it propagates incorporating cognitive interoperability as fifth layer within the EOSC IF and discusses the relation between human explorability and cognitive interoperability, resulting in the suggestion to add the Principle of human Explorability, extending FAIR to the FAIREr Guiding Principles. The subsequent sections present the concept of semantic units, elucidating their importance in enhancing the human explorability and cognitive interoperability of knowledge graphs. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs, each represented with its own resource constituting a FAIR Digital Object (FDO) that instantiates a corresponding FDO class. Various categories of FDOs are distinguished. The content of a FDO can be displayed in a user interface either as a mind-map-like graph or as natural language text. Organizing knowledge graphs into FDOs based on semantic units supports the cognitive interoperability of data and metadata and facilitates their human explorability. The development of innovative user interfaces enabled by such FDOs empowers users to access, navigate, and explore information in knowledge graphs with enhanced efficiency.

Published
2023

10. Semantic Units: Organizing knowledge graphs into semantically meaningful units of representation

Author

Vogt, Lars, Kuhn, Tobias, and Hoehndorf, Robert

Subjects
Computer Science - Databases
Abstract

Knowledge graphs and ontologies are becoming increasingly important as technical solutions for Findable, Accessible, Interoperable, and Reusable data and metadata (FAIR Guiding Principles). We discuss four challenges that impede the use of FAIR knowledge graphs and propose semantic units as their potential solution. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs. Each unit is represented by its own resource, instantiates a corresponding semantic unit class, and can be implemented as a FAIR Digital Object and a nanopublication in RDF/OWL and property graphs. We distinguish statement and compound units as basic categories of semantic units. Statement units represent smallest, independent propositions that are semantically meaningful for a human reader. They consist of one or more triples and mathematically partition a knowledge graph. We distinguish assertional, contingent (prototypical), and universal statement units as basic types of statement units and propose representational schemes and formal semantics for them (including for absence statements, negations, and cardinality restrictions) that do not involve blank nodes and that translate back to OWL. Compound units, on the other hand, represent semantically meaningful collections of semantic units and we distinguish various types of compound units, representing different levels of representational granularity, different types of granularity trees, and different frames of reference. Semantic units support making statements about statements, can be used for graph-alignment, subgraph-matching, knowledge graph profiling, and for managing access restrictions to sensitive data. Organizing the graph into semantic units supports the separation of ontological, diagnostic (i.e., referential), and discursive information, and it also supports the differentiation of multiple frames of reference.

Published
2023

11. Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary

Author

Müller Carsten HG, Møller Ole S, Kaul Sabrina, Heuer Carsten M, Grobe Peter, Fritsch Martin, Faller Simone, Döring Carmen, Brenneis Georg, Wanninger Andreas, Vogt Lars, Stach Thomas, Scholtz Gerhard, Schmidt-Rhaesa Andreas, Purschke Günter, Loesel Rudi, Richter Stefan, Rieger Verena, Rothe Birgen H, Stegner Martin EJ, and Harzsch Steffen

Subjects
Zoology, QL1-991
Abstract

Abstract Background Invertebrate nervous systems are highly disparate between different taxa. This is reflected in the terminology used to describe them, which is very rich and often confusing. Even very general terms such as 'brain', 'nerve', and 'eye' have been used in various ways in the different animal groups, but no consensus on the exact meaning exists. This impedes our understanding of the architecture of the invertebrate nervous system in general and of evolutionary transformations of nervous system characters between different taxa. Results We provide a glossary of invertebrate neuroanatomical terms with a precise and consistent terminology, taxon-independent and free of homology assumptions. This terminology is intended to form a basis for new morphological descriptions. A total of 47 terms are defined. Each entry consists of a definition, discouraged terms, and a background/comment section. Conclusions The use of our revised neuroanatomical terminology in any new descriptions of the anatomy of invertebrate nervous systems will improve the comparability of this organ system and its substructures between the various taxa, and finally even lead to better and more robust homology hypotheses.

Published
2010
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12. Spatio-structural granularity of biological material entities

Author

Vogt Lars

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities. Results The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the compositional object perspective as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities. Conclusions The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different views on its content (i.e. data, knowledge), each organized into different levels of detail.

Published
2010
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13. Transforming the study of organisms: Phenomic data models and knowledge bases.

Author

Thessen, Anne E, Walls, Ramona L, Vogt, Lars, Singer, Jessica, Warren, Robert, Buttigieg, Pier Luigi, Balhoff, James P, Mungall, Christopher J, McGuinness, Deborah L, Stucky, Brian J, Yoder, Matthew J, and Haendel, Melissa A

Subjects
Animals, Humans, Models, Statistical, Computational Biology, Ecosystem, Phenotype, Models, Biological, Models, Genetic, Classification, Semantics, Databases, Genetic, Knowledge Bases, Gene-Environment Interaction, Phenomics, Human Genome, Genetics, Bioinformatics, Mathematical Sciences, Biological Sciences, Information and Computing Sciences
Abstract

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

Published
2020

14. Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

Author

Stefen, Clara, Wagner, Franziska, Asztalos, Marika, Giere, Peter, Grobe, Peter, Hiller, Michael, Hofmann, Rebecca, Jähde, Maria, Lächele, Ulla, Lehmann, Thomas, Ortmann, Sylvia, Peters, Benjamin, Ruf, Irina, Schiffmann, Christian, Thier, Nadja, Unterhitzenberger, Gabriele, Vogt, Lars, Rudolf, Matthias, Wehner, Peggy, and Stuckas, Heiko

Published
2022
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16. Using Semantic Programming for Developing a Web Content Management System for Semantic Phenotype Data

Author

Vogt, Lars, Baum, Roman, Köhler, Christian, Meid, Sandra, Quast, Björn, Grobe, Peter, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Auer, Sören, editor, and Vidal, Maria-Esther, editor

Published
2019
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18. Figure 6 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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19. Figure 7 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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20. Figure 4 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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21. Figure 8 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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22. Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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23. Figure 2 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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24. Figure 5 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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25. Figure 1 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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26. Figure 3 from: Bernard-Verdier M, Heger T, Mietchen D, Musseau CL, Brinner M, Hillig A, Kraker P, Lokatis S, Nunes AL, Scheidweiler N, Stocker M, Vial R, Vogt L, Bacher S, Baklouti E, Gupta HB, Beisel J-N, Bertolino S, Briski E, Castellanos-Galindo GA, Courchamp F, Daly E, Dawson W, Dickey J, Evans T, Itescu Y, Koenig-Ries B, Kumar L, Kumschick S, Meyerson LA, Pattison Z, Pfadenhauer W, Renault D, Rickowski F, Ruland F, Schittko C, Straka T, Yannelli F, Jeschke JM (2023) Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9: e115395. https://doi.org/10.3897/rio.9.e115395

Author

Bernard-Verdier, Maud, primary, Heger, Tina, additional, Mietchen, Daniel, additional, Musseau, Camille, additional, Brinner, Marc, additional, Hillig, Alexander, additional, Kraker, Peter, additional, Lokatis, Sophie, additional, Nunes, Ana Luisa, additional, Scheidweiler, Nils, additional, Stocker, Markus, additional, Vial, Roxane, additional, Vogt, Lars, additional, Bacher, Sven, additional, Baklouti, Eya, additional, Gupta, Harsh Bardhan, additional, Beisel, Jean-Nicolas, additional, Bertolino, Sandro, additional, Briski, Elizabeta, additional, Castellanos-Galindo, Gustavo, additional, Courchamp, Franck, additional, Daly, Ella, additional, Dawson, Wayne, additional, Dickey, James, additional, Evans, Thomas, additional, Itescu, Yuval, additional, Koenig-Ries, Birgitta, additional, Kumar, Lohith, additional, Kumschick, Sabrina, additional, Meyerson, Laura, additional, Pattison, Zarah, additional, Pfadenhauer, William, additional, Renault, David, additional, Rickowski, Fiona, additional, Ruland, Florian, additional, Schittko, Conrad, additional, Straka, Tanja, additional, Yannelli, Florencia, additional, and Jeschke, Jonathan, additional

Published
2023
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28. Emerging semantics to link phenotype and environment

Author

Thessen, Anne E, Bunker, Daniel E, Buttigieg, Pier Luigi, Cooper, Laurel D, Dahdul, Wasila M, Domisch, Sami, Franz, Nico M, Jaiswal, Pankaj, Lawrence-Dill, Carolyn J, Midford, Peter E, Mungall, Christopher J, Ramírez, Martín J, Specht, Chelsea D, Vogt, Lars, Vos, Rutger Aldo, Walls, Ramona L, White, Jeffrey W, Zhang, Guanyang, Deans, Andrew R, Huala, Eva, Lewis, Suzanna E, and Mabee, Paula M

Subjects
Epidemiology, Biological Sciences, Health Sciences, Networking and Information Technology R&D (NITRD), Phenotype, Environment, Ontology, Semantic web, Biodiversity, Data integration, Medical and Health Sciences
Abstract

Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

Published
2015

31. Converging on a Semantic Interoperability Framework for the European Data Space for Science, Research and Innovation (EOSC)

Author

David, Romain, Baumann, Kurt, Le Franc, Yann, Magagna, Barbara, Vogt, Lars, Widmann, Heinrich, Jouneau, Thomas, Koivula, Hanna, Madon, Bénédicte, Åkerström, Wolmar Nyberg, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, Letizia, Vancauwenbergh, Sadia, European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), SWITCH, e-Science Data Factory [Paris] (e-SDF), GO FAIR Foundation, TIB Leibniz Information Centre For Science and Technology University Library, German Climate Computing Center (DKRZ), Université de Lorraine (UL), Life Science Center Keilaniemi, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Universidad de Sevilla / University of Sevilla, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University-Stockholm University-Department of Biochemistry and Biophysics, Stockholm University-Stockholm University, Faculty of Electrical Engineering and Computer Science, University of Maribor, Royal Netherlands Academy of Arts and Sciences (KNAW), Vienna University of Technology (TU Wien), Université Paris-Saclay, Politecnico di Milano [Milan] (POLIMI), Hasselt University (UHasselt), This research is a product of the Task Force 'Semantic Interoperability' of the EOSC Association,the legal entity established to govern the European Open Science Cloud (EOSC). Complementary support and information were provided through European projects projects 'EOSC-Life'(Nº824087), 'EOSC-Future' (Nº101017536) and 'FAIR Impact' (Nº101057344)., Cassia Trojahn, Luiz Olavo Bonino da Silva Santos, Giancarlo Guizzardi, Clement Jonquet, FAIR Impact, EOSC Association, EOSC Future, EOSC Life, European Project: 824087,EOSC-Life, European Project: EOSC Association, European Project: 101057344,FAIR-IMPACT, and European Project: 101017536,EOSC Future

Subjects
FAIR Principles, Roadmap, definitions, Semantic interoperability, Interoperable, Semantic interoperability, European Open Science Cloud, Crosswalk, Roadmap, Interoperable, FAIR Principles, definitions, linked data, machine actionability, Semantic interoperability European Open Science Cloud Crosswalk Roadmap Interoperable FAIR Principles definitions linked data machine actionability, [SCCO.COMP]Cognitive science/Computer science, machine actionability, linked data, [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL], European Open Science Cloud, Crosswalk
Abstract

Semantic interoperability (SI) is at the heart of the FAIR principles and the design of large-scale cross-disciplinary infrastructures. The European Open Science Cloud (EOSC) is a European-wide effort towards such an infrastructure, aiming to deepen regional research collaboration and realising a shared data space for science, research and innovation. In this context, the research community’s voice is represented by the EOSC Association (EOSC-A) and a number of advisory groups with a broad range of representatives from different stakeholder organisations. The advisory group on metadata and data quality has formed a task force focusing on developing and implementing recommendations for SI (EOSC SI Task Force) to converge on globally relevant and scalable SI solutions for EOSC. This paper provides context to SI in EOSC, the various components contributing to it, as well as some views on the socio-technical challenges to arriving at a consensus. In particular, the paper provides motivation for exploring the heterogeneity of SI solutions demonstrated across scientific communities and insight into the task force’s planned approach to conducting a survey to identify relevant components and structures. The paper is also an invitation to the global community to align and engage with the task force’s activities going forward., This research is a product of the Task Force "Semantic Interoperability" of the EOSC-Association European, the legal entity established to govern the European Open Science Cloud (EOSC). Complementary support and information were provided through European projects "EOSC-Life" (No824087) and "FAIR Impact" (No101057344). This paper is linked to the Supplementary Material - Magagna, Barbara, Baumann, Kurt, David, Romain, Jouneau, Thomas, Le Franc, Yann, Koivula, Hanna, Madon, Bénédicte, Nyberg Åkerström, Wolmar, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, Letizia, Vancauwenbergh, Sadia, Vogt, Lars, & Widmann, Heinrich. (2023). Proposal for the EOSC Semantic Interoperability Questionnaire (1.0.2). 2nd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR), Sherbrooke, Québec (Canada). Zenodo. https://doi.org/10.5281/zenodo.8028392 This Supplementary Material will be updated during the process of the survey-completion, {"references":["Magagna, Barbara, Baumann, Kurt, David, Romain, Jouneau, Thomas, Le Franc, Yann, Koivula, Hanna, Madon, Bénédicte, Nyberg Åkerström, Wolmar, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, Letizia, Vancauwenbergh, Sadia, Vogt, Lars, & Widmann, Heinrich. (2023). Proposal for the EOSC Semantic Interoperability Questionnaire (1.0.2). 2nd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR), Sherbrooke, Québec (Canada). Zenodo. https://doi.org/10.5281/zenodo.8028392"]}

Published
2023

32. PREreview of 'A maturity model for catalogues of semantic artefacts'

Author

Vogt, Lars

Abstract

This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/7936984. The authors provide a definition for 'semantic artefact catalogue (SAC)' and suggest a maturity model for evaluating SACs that is based on a set of criteria with multiple sub-criteria. Their approach is aligned with the FAIR Guiding Principles and the ongoing efforts of the EOSC Task Force of Semantic Interoperability to address interoperability challenges. The authors apply their maturity model to a set of 26 SACs and evaluate them. I enjoyed reading the paper and think that the maturity model represents an important contribution to the overall goal of increasing the semantic interoperability of (meta)data. I also think that the criteria (i.e., dimensions) and sub-criteria are well chosen and provide a good overview for a given SAC. However, I see also some points for potential improvement: 1) I think, the paper would benefit from a clear definition of 'semantic artefact'. In the introduction, the authors characterize 'semantic artefact as "a machine-actionable and machine-readable formalization of a conceptualization, enabling sharing and reuse by humans and machines, that may have a broad range of formalisations, from loose sets of terms, taxonomies, thesauri to higher-order logic constructs, vocabularies and ontologies". I agree that vocabularies/terminologies of the various sorts mentioned here represent very important semantic artefacts. However, I am missing (meta)data schemata and formats, term-mappings, and schema crosswalks in this list. Clarifying that semantic artefacts also include the latter is very important, because their importance in semantic interoperability is often overlooked, leaving the impression that semantic interoperability is 'only' providing controlled vocabularies that must be used by everyone. Semantic interoperability, however, is much more and includes terminological, schematic, logical, and ontological interoperability (https://arxiv.org/abs/2301.04202), each with its own set of requirements. 2) My second point somewhat relates to the first. Reading the paper, I had the impression that only vocabularies/terminologies were considered, and all the other types of semantic artefacts mentioned above were ignored. What is missing in the maturity model is a characterization of the different types of semantic artefacts that a catalogue is covering/documenting. This could be an additional dimension with the different types of artefacts as sub-criteria. 3) Vocabularies/terminologies (including ontologies etc.) only support terminological interoperability, and if different vocabularies/terminologies exist for the same types of entities, term mappings must be provided to guarantee terminological interoperability. Sometimes, those term mappings are provided within the vocabularies/terminologies themselves (e.g., via owl:sameAs), but this is not ideal. Better would be to provide term-mappings as stand-alone semantic artefacts. This should be mentioned in the paper and should be evaluated by the maturity model. 4) (Meta)data schemata provide schematic interoperability, and if different schemata for the same type of information exist, schema crosswalks must be provided for schematic interoperability. Schema crosswalks are another type of semantic artefact that should be mentioned in the paper and should also be evaluated by the maturity model. 5) Logical interoperability requires the use of the same logical framework such as OWL/description logic to guarantee the logical interoperability of (meta)data. Semantic artefacts should specify if and which logical framework they apply. Respective information should be covered by the maturity model. 6) Another candidate catalogue for evaluation: TIB Terminology Service (https://service.tib.eu/ts4tib/index). Following the maturity model, Felix Engel has evaluated the TIB Terminology Service (only the 'checks' mentioned): Me (custom vocabulary, primary metadata, human readable, machine readable) Op (customised oss, open model, open contribution) Qu (curation by owner only) Av (no restrictions) St (catalog statistics, resource statistics) Pi (-) Go (3rd party, description, rules) Co (read only) Su (organization, management board, (research) projects) Te (REST API, web search GUI) Tr (documented curation, automatic curation) As (-) List of additional comments: p. 2, last paragraph (see also p.4, 2.2, last paragraph): If a semantic artefact is machine-actionable it must also be machine-readable. The way it is written leaves the impression that machine-actionability and machine-readability would be independent criteria, which is not the case. p. 4, last paragraph (spelling): in the context of the H2020 p. 8, 4 Results: I would not characterize BioPortal or EBI OLS as 'metadata catalogues'. p. 10, Technology (d): "alignment – a service to align (part of) semantic artefacts that might be used within a catalog." It is not entirely clear what that means. p. 14, 2nd paragraph (spelling): In the future, we aim at p. 14, 2nd paragraph (spelling): Similarly, the work under development in Competing interests I am a member of the EOSC Task Force Semantic Interoperability but I was neither involved in writing the paper nor in discussing its topics.

Published
2023
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34. Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics

Author

Girón, Jennifer C, primary, Tarasov, Sergei, additional, González Montaña, Luis Antonio, additional, Matentzoglu, Nicolas, additional, Smith, Aaron D, additional, Koch, Markus, additional, Boudinot, Brendon E, additional, Bouchard, Patrice, additional, Burks, Roger, additional, Vogt, Lars, additional, Yoder, Matthew, additional, Osumi-Sutherland, David, additional, Friedrich, Frank, additional, Beutel, Rolf, additional, and Mikó, István, additional

Published
2023
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35. Consulting with Global Data Communities to Converge on Semantic Interoperability Solutions for the European Data Space for Science, Research and Innovation (EOSC)

Author

Baumann, Kurt, David, Romain, Le Franc, Yann, Vogt, Lars, Widmann, Heinrich, Juneau, Thomas, Koivula, Hanna, Madon, Bénédicte, Nyberg Åkerström, Wolmar, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, LETIZIA, Vancauwenbergh, Sadia, Baumann, Kurt, David, Romain, Le Franc, Yann, Vogt, Lars, Widmann, Heinrich, Juneau, Thomas, Koivula, Hanna, Madon, Bénédicte, Nyberg Åkerström, Wolmar, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, LETIZIA, and Vancauwenbergh, Sadia

Abstract

This poster was presented during the Poster Exhibition session at the Research Data Alliance (RDA) 21st Plenary during International Data Week 2023 in Salzburg, Austria on 23–26 October 2023. It was submitted by Kurt Baumann on behalf of the EOSC Semantic Interoperability Task Force. Description of the poster Interoperability is at the heart of the FAIR principles and the design of large-scale cross-disciplinary infrastructures. The European Open Science Cloud (EOSC) is a European-wide effort towards such an infrastructure, aiming to deepen regional research collaboration and realising a shared data space for science, research and innovation. The advisory group on metadata and data quality has formed a task force focusing on developing and implementing recommendations for SI (EOSC SI Task Force). This poster serves as an invitation to the global RDA community to join forces with the European research stakeholders to converge on globally relevant and scalable solutions for Semantic Interoperability (SI). Semantic Interoperability is in fact not easy to implement. Any strategy for achieving SI must take this complexity into account. The poster presents the work of a stakeholder organisation that represents the research community's voice in EOSC and focuses on the activities of a task force developing and implementing recommendations for SI. Realising solutions for semantic interoperability involves a broad spectrum of socio-technical challenges. The poster will give insights into the chosen approach and structure of an ongoing survey that will result in a landscape overview of the use of components required to enable SI across a wide range of disciplines and use cases. Individual members of the task force are already committed contributors across various RDA interest groups and working groups and by presenting this poster the ambition is to showcase existing synergies and to identify new venues for collaborations. EOSC Project m

Published
2023

36. Proposal for the EOSC Semantic Interoperability Questionnaire

Author

Magagna, Barbara, Baumann, Kurt, David, Romain, Jouneau, Thomas, Le Franc, Yann, Koivula, Hanna, Madon, Bénédicte, Nyberg Åkerström, Wolmar, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, Letizia, Vancauwenbergh, Sadia, Vogt, Lars, Widmann, Heinrich, Magagna, Barbara, Baumann, Kurt, David, Romain, Jouneau, Thomas, Le Franc, Yann, Koivula, Hanna, Madon, Bénédicte, Nyberg Åkerström, Wolmar, Ojsteršek, Milan, Scharnhorst, Andrea, Schubert, Chris, Shi, Zhengdong, Tanca, Letizia, Vancauwenbergh, Sadia, Vogt, Lars, and Widmann, Heinrich

Abstract

This document provides supplementary material for the paper "Converging towards a Semantic interoperability framework for EOSC: understanding the different community solutions to semantic interoperability" submitted as a contribution to the 2nd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR). Its purpose is to provide additional information and insights about the questionnaire approach proposed to survey the resources utilised by communities in addressing semantic interoperability issues. This document will be used as a guide in the implementation of the questionnaire, planned to be ready by the end of June. The survey itself will be ongoing over the summer and terminate at the end of September 2023.

Published
2023

37. Extending FAIR to FAIREr: Cognitive Interoperability and the Human Explorability of Data and Metadata

Author

Vogt, Lars and Vogt, Lars

Abstract

Making data and metadata FAIR (Findable, Accessible, Interoperable, Reusable) has become an important objective in research and industry, and knowledge graphs and ontologies have been cornerstones in many going-FAIR strategies. In this process, however, human-actionability of data and metadata has been lost sight of. Here, in the first part, I discuss two issues exemplifying the lack of human-actionability in knowledge graphs and I suggest adding the Principle of human Explorability to extend FAIR to the FAIREr Guiding Principles. Moreover, in its interoperability framework and as part of its GoingFAIR strategy, the European Open Science Cloud initiative distinguishes between technical, semantic, organizational, and legal interoperability and I argue to add cognitive interoperability. In the second part, I provide a short introduction to semantic units and discuss how they increase the human explorability and cognitive interoperability of knowledge graphs. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs, each represented with its own resource that instantiates a corresponding semantic unit class. Three categories of semantic units can be distinguished: Statement units model individual propositions, compound units are semantically meaningful collections of semantic units, and question units model questions that translate into queries. I conclude with discussing how semantic units provide a framework for the development of innovative user interfaces that support exploring and accessing information in the graph by reducing its complexity to what currently interests the user, thereby significantly increasing the cognitive interoperability and thus human-actionability of knowledge graphs.

Published
2023

39. FAIR scientific information with the Open Research Knowledge Graph

Author

Stocker, Markus, primary, Oelen, Allard, additional, Jaradeh, Mohamad Yaser, additional, Haris, Muhammad, additional, Oghli, Omar Arab, additional, Heidari, Golsa, additional, Hussein, Hassan, additional, Lorenz, Anna-Lena, additional, Kabenamualu, Salomon, additional, Farfar, Kheir Eddine, additional, Prinz, Manuel, additional, Karras, Oliver, additional, D’Souza, Jennifer, additional, Vogt, Lars, additional, and Auer, Sören, additional

Published
2023
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43. University Libraries and the Open Research Knowledge Graph

Author

Auer, Sorën, Sens, Irina, Stocker, Markus, Vogt, Lars, and Lorenz, Anna-Lena

Subjects
Library and Information Science
Abstract

The transfer of knowledge has not changed fundamentally for many hundreds of years: It is usually document-based - formerly printed on paper as a classic essay and nowadays as PDF. With around 2.5 million new research contributions every year, researchers drown in a flood of pseudo-digitized PDF publications. As a result research is seriously weakened. In this article, we argue for representing scholarly contributions in a structured and semantic way as a knowledge graph. The advantage is that information represented in a knowledge graph is readable by machines and humans. As an example, we give an overview on the Open Research Knowledge Graph (ORKG), a service implementing this approach. For creating the knowledge graph representation, we rely on a mixture of manual (crowd/expert sourcing) and (semi-)automated techniques. Only with such a combination of human and machine intelligence, we can achieve the required quality of the representation to allow for novel exploration and assistance services for researchers. As a result, a scholarly knowledge graph such as the ORKG can be used to give a condensed overview on the state-of-the-art addressing a particular research quest, for example as a tabular comparison of contributions according to various characteristics of the approaches. Further possible intuitive access interfaces to such scholarly knowledge graphs include domain-specific (chart) visualizations or answering of natural language questions.

Published
2022

44. Figure 2 from: Stocker M, Heger T, Schweidtmann AM, Ćwiek-Kupczyńska H, Penev L, Dojchinovski M, Willighagen E, Vidal M-E, Turki HA, Balliet D, Tiddi I, Kuhn T, Mietchen D, Karras O, Vogt L, Hellmann S, Jeschke JM, Krajewski P, Auer S (2022) SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. https://doi.org/10.3897/rio.8.e83789

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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45. Figure 1 from: Stocker M, Heger T, Schweidtmann AM, Ćwiek-Kupczyńska H, Penev L, Dojchinovski M, Willighagen E, Vidal M-E, Turki HA, Balliet D, Tiddi I, Kuhn T, Mietchen D, Karras O, Vogt L, Hellmann S, Jeschke JM, Krajewski P, Auer S (2022) SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. https://doi.org/10.3897/rio.8.e83789

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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46. Figure 5 from: Stocker M, Heger T, Schweidtmann AM, Ćwiek-Kupczyńska H, Penev L, Dojchinovski M, Willighagen E, Vidal M-E, Turki HA, Balliet D, Tiddi I, Kuhn T, Mietchen D, Karras O, Vogt L, Hellmann S, Jeschke JM, Krajewski P, Auer S (2022) SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. https://doi.org/10.3897/rio.8.e83789

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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47. Figure 7 from: Stocker M, Heger T, Schweidtmann AM, Ćwiek-Kupczyńska H, Penev L, Dojchinovski M, Willighagen E, Vidal M-E, Turki HA, Balliet D, Tiddi I, Kuhn T, Mietchen D, Karras O, Vogt L, Hellmann S, Jeschke JM, Krajewski P, Auer S (2022) SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. https://doi.org/10.3897/rio.8.e83789

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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48. Figure 4 from: Stocker M, Heger T, Schweidtmann AM, Ćwiek-Kupczyńska H, Penev L, Dojchinovski M, Willighagen E, Vidal M-E, Turki HA, Balliet D, Tiddi I, Kuhn T, Mietchen D, Karras O, Vogt L, Hellmann S, Jeschke JM, Krajewski P, Auer S (2022) SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. https://doi.org/10.3897/rio.8.e83789

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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49. SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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50. Figure 3 from: Stocker M, Heger T, Schweidtmann AM, Ćwiek-Kupczyńska H, Penev L, Dojchinovski M, Willighagen E, Vidal M-E, Turki HA, Balliet D, Tiddi I, Kuhn T, Mietchen D, Karras O, Vogt L, Hellmann S, Jeschke JM, Krajewski P, Auer S (2022) SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. https://doi.org/10.3897/rio.8.e83789

Author

Stocker, Markus, primary, Heger, Tina, additional, Schweidtmann, Artur, additional, Ćwiek-Kupczyńska, Hanna, additional, Penev, Lyubomir, additional, Dojchinovski, Milan, additional, Willighagen, Egon, additional, Vidal, Maria-Esther, additional, Turki, Houcemeddine, additional, Balliet, Daniel, additional, Tiddi, Ilaria, additional, Kuhn, Tobias, additional, Mietchen, Daniel, additional, Karras, Oliver, additional, Vogt, Lars, additional, Hellmann, Sebastian, additional, Jeschke, Jonathan, additional, Krajewski, Paweł, additional, and Auer, Sören, additional

Published
2022
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