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Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the \"super-pattern\". We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door on the longer run for allowing researchers to express their high-level scientific findings in a manner they can be automatically interpreted. This in turn will allow for automated consistency checking, question answering, aggregation, and much more." } ], "http://purl.org/dc/terms/date": [ { "@value": "2021-12-02" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/np/RAXTZgKi-aszn_8uUgAlPr6D1FRzMDKnv5R_zpzox0hGs/kcap-2021" } ], "http://purl.org/dc/terms/title": [ { "@value": "Expressing High-Level Scientific Claims with Formal Semantics" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAXTZgKi-aszn_8uUgAlPr6D1FRzMDKnv5R_zpzox0hGs/author-list" } ], "http://purl.org/ontology/bibo/pageEnd": [ { "@value": "240" } ], "http://purl.org/ontology/bibo/pageStart": [ { "@value": "233" } ] }, { "@id": "https://w3id.org/np/RAXTZgKi-aszn_8uUgAlPr6D1FRzMDKnv5R_zpzox0hGs/kcap-2021", "http://purl.org/dc/terms/title": [ { "@value": "Proceedings of the 11th Knowledge Capture Conference (K-CAP 2021)" } ] }, { "@id": "https://w3id.org/np/RAXTZgKi-aszn_8uUgAlPr6D1FRzMDKnv5R_zpzox0hGs/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0002-7114-6459" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0002-3357-9130" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_4": [ { "@id": "https://orcid.org/0000-0002-7748-4715" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-3357-9130", "http://schema.org/affiliation": [ { "@id": "https://ror.org/00x7ekv49" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Davide Ceolin" } ] }, { "@id": "https://ror.org/00x7ekv49", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Centrum Wiskunde & Informatica, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-7114-6459", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Cristina-Iulia Bucur" } ] }, { "@id": "https://orcid.org/0000-0002-7748-4715", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Jacco van Ossenbruggen" } ] } ] }, { "@id": "https://w3id.org/sciencelive/np/RA8TJINeh2I8SAvvE8idDqOVLjF7_44JabLwsIyZ4uu0E/assertion", "@graph": [ { "@id": "https://doi.org/10.1233/abcssd", "@type": [ "http://purl.org/spar/fabio/ScholarlyWork" ], "http://purl.org/spar/cito/cites": [ { "@id": "https://doi.org/10.1136/oemed-2022-108371" }, { "@id": "https://doi.org/10.9876/another_2025" } ], "http://purl.org/spar/cito/citesAsAuthority": [ { "@id": "https://doi.org/10.9999/example.2026" } ] } ] }, { "@id": "https://w3id.org/sciencelive/np/RAOwNy8iktvBavMkQvUJm8zp73er6Bjw2mXQ54SDlJhHw/assertion", "@graph": [ { "@id": "https://w3id.org/sciencelive/np/RAcHVf4mO1B4E-S4qx3obilKj5vBXqajmgscykqUCcsg8", "@type": [ "http://purl.org/spar/fabio/ScholarlyWork" ], "http://purl.org/spar/cito/citesAsEvidence": [ { "@id": "https://doi.org/10.5281/zenodo.19709327" } ] } ] }, { "@id": "https://w3id.org/sciencelive/np/RAytjY2ptSUX7cA97EmKR5pff3Gvw-E3gqkXW9_WrjumA/assertion", "@graph": [ { "@id": "https://doi.org/10.1233/abcssd", "@type": [ "http://purl.org/spar/fabio/ScholarlyWork" ], "http://purl.org/spar/cito/agreesWith": [ { "@id": "https://doi.org/10.9876/another_2025" } ], "http://purl.org/spar/cito/cites": [ { "@id": "https://doi.org/10.1136/oemed-2022-108371" } ], "http://purl.org/spar/cito/citesAsDataSource": [ { "@id": "https://doi.org/10.9999/example.2026" } ] } ] }, { "@id": "https://w3id.org/np/RA3mHktF3PvegDW3gJOHpd2ql_NoCSpNyUYr2eUqF-uTI/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/0302-9743", "http://purl.org/dc/terms/title": [ { "@value": "Lecture Notes in Computer Science" } ] }, { "@id": "https://doi.org/10.1007/978-3-319-67256-4_23", "@type": [ "http://purl.org/spar/fabio/BookChapter" ], "http://purl.org/dc/terms/abstract": [ { "@value": "Climate change, vaccination, abortion, Trump: Many topics are surrounded by fierce controversies. 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"http://xmlns.com/foaf/0.1/name": [ { "@value": "Egon Willighagen" } ] }, { "@id": "https://ror.org/02jz4aj89", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Maastricht University, Maastricht, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0001-8499-824X", "http://schema.org/affiliation": [ { "@id": "https://ror.org/03qt6ba18" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Juan M. 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Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future." } ], "http://purl.org/dc/terms/date": [ { "@value": "2021-09-07" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/2046-1402" } ], "http://purl.org/dc/terms/title": [ { "@value": "Perspectives on automated composition of workflows in the life sciences" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/author-list" } ], "http://purl.org/ontology/bibo/pageStart": [ { "@value": "897" } ] }, { "@id": "https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0003-1953-5606" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_10": [ { "@id": "https://orcid.org/0000-0002-6899-4262" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_11": [ { "@id": "https://orcid.org/0000-0002-2961-9670" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_12": [ { "@id": "https://orcid.org/0000-0001-8465-8341" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_13": [ { "@id": "https://orcid.org/0000-0003-1219-2137" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_14": [ { "@id": "https://orcid.org/0000-0001-6801-2559" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_15": [ { "@id": "https://orcid.org/0000-0003-0183-6910" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_16": [ { "@id": "https://orcid.org/0000-0001-9727-2544" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_17": [ { "@id": "https://orcid.org/0000-0003-0984-0973" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_18": [ { "@id": "https://orcid.org/0000-0002-1509-4981" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_19": [ { "@id": "https://orcid.org/0000-0002-0097-1056" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-5865-8994" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_20": [ { "@id": "https://orcid.org/0000-0001-6811-9196" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_21": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_22": [ { "@id": "https://orcid.org/0000-0003-1781-5508" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_23": [ { "@id": "https://orcid.org/0000-0002-7552-1009" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_24": [ { "@id": "https://orcid.org/0000-0002-7187-4683" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_25": [ { "@id": "https://orcid.org/0000-0002-9984-2720" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_26": [ { "@id": "https://orcid.org/0000-0002-9370-4677" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_27": [ { "@id": "https://orcid.org/0000-0001-9842-9718" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_28": [ { "@id": "https://orcid.org/0000-0002-6038-9025" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_29": [ { "@id": "https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/szoke-szaniszlo" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0001-6666-1520" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_30": [ { "@id": "https://orcid.org/0000-0002-9609-9505" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_31": [ { "@id": "https://orcid.org/0000-0003-0373-9372" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_32": [ { "@id": "https://orcid.org/0000-0002-1279-5133" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_4": [ { "@id": "https://orcid.org/0000-0002-9708-6722" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_5": [ { "@id": "https://orcid.org/0000-0003-4647-3877" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_6": [ { "@id": "https://orcid.org/0000-0002-2196-0305" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_7": [ { "@id": "https://orcid.org/0000-0003-4004-6479" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_8": [ { "@id": "https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/ammar-ben-hadj-amor" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_9": [ { "@id": "https://orcid.org/0000-0002-0309-604X" } ] }, { "@id": "https://orcid.org/0000-0001-6666-1520", "http://schema.org/affiliation": [ { "@id": "https://ror.org/045f7pv37" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Jon Ison" } ] }, { "@id": "https://ror.org/045f7pv37", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Institut Français de Bioinformatique, Évry, France" } ] }, { "@id": "https://orcid.org/0000-0001-6801-2559", "http://schema.org/affiliation": [ { "@id": "https://ror.org/017zqws13" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Timothy J. 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A big inspiration to many, even though many things unfolded differently than envisaged in this paper." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Lassila et al. 2001. The Semantic Web. Scientific American." } ] } ] }, { "@id": "https://w3id.org/np/RAdz-aHYBhV1c2WpieJnDhP3_LptK4YHc_vRaZa9Q2Mac/assertion", "@graph": [ { "@id": "https://doi.org/10.1145/3587259.3627559", "@type": [ "http://purl.org/spar/fabio/ConferencePaper" ], "http://purl.org/dc/terms/abstract": [ { "@value": "In response to the increasing volume of research data being generated, more and more data portals have been designed to facilitate data findability and accessibility. However, a significant portion of this data remains confidential or restricted due to its sensitive nature, such as patient data or census microdata. While maintaining confidentiality prohibits its public release, the emergence of portals supporting rich metadata can help enable researchers to at least discover the existence of restricted access data, empowering them to assess the suitability of the data before requesting access. Existing standards, such as CSV on the Web and RDF Data Cube, have been adopted to facilitate data management, integration, and re-use of data on the Web. However, the current landscape still lacks adequate standards not only to effectively describe restricted access data while preserving confidentiality but also to facilitate its discovery. In this work, we investigate the relationship between the structural, statistical, and semantic elements of restricted access tabular data, and we explore how such relationship can be formally modeled in a way that is Findable, Accessible, Interoperable, and Reusable. We introduce the DataSet-Variable Ontology (DSV), that by combining CSV on the Web and RDF Data Cube standards, leveraging semantic technologies and Linked Data principles, and introducing variable-level metadata, aims to capture high-quality metadata to support the management and re-use of restricted access data on the Web. As evaluation, we conducted a case study where we applied DSV to four different datasets from different statistical governmental agencies. We employed a set of competency questions to assess the ontology's ability to support knowledge discovery and data exploration. By describing high-quality metadata, both at the dataset- and variable levels, while maintaining data privacy, this novel ontology facilitates data interoperability, discovery, and re-use and it empowers researchers to manage, integrate, and analyze complex restricted access data sources." } ], "http://purl.org/dc/terms/date": [ { "@value": "2023-12-05" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "https://w3id.org/np/RAdz-aHYBhV1c2WpieJnDhP3_LptK4YHc_vRaZa9Q2Mac/kcap-2023" } ], "http://purl.org/dc/terms/title": [ { "@value": "Advancing data sharing and reusability for restricted access data on the Web: introducing the DataSet-Variable Ontology" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAdz-aHYBhV1c2WpieJnDhP3_LptK4YHc_vRaZa9Q2Mac/author-list" } ], "http://purl.org/ontology/bibo/pageEnd": [ { "@value": "91" } ], "http://purl.org/ontology/bibo/pageStart": [ { "@value": "83" } ] }, { "@id": 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Pyle" } ] }, { "@id": "https://ror.org/04m60en37", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Bishop Museum, Honolulu, United States" } ] }, { "@id": "https://orcid.org/0000-0003-4766-1247", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Seyhan Demirov" } ] }, { "@id": "https://orcid.org/0009-0001-3489-2751", "http://schema.org/affiliation": [ { "@id": "https://ror.org/01znaqx63" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Iva Boyadzhieva" } ] } ] }, { "@id": "https://w3id.org/np/RA4c57BIY99eHu-WTrS7v3WFBoWkP9f-j2jAuV_dp0uoE/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/2367-7163", "http://purl.org/dc/terms/title": [ { "@value": "Research Ideas and Outcomes" } ] }, { "@id": "https://doi.org/10.3897/rio.8.e94150", "@type": [ "http://purl.org/spar/fabio/Article" ], "http://purl.org/dc/terms/abstract": [ { "@value": "Beginning in 1995, early Internet pioneers proposed Digital Objects as encapsulations of data and metadata made accessible through persistent identifier resolution services. In recent years, this Digital Object Architecture has been extended to include the FAIR Guiding Principles, resulting in the concept of a FAIR Digital Object (FDO), a minimal, uniform container making any digital resource machine-actionable. Beginning in 2009, nanopublications were independently conceived as a minimal, uniform container making individual semantic assertions and their associated provenance metadata, machine-actionable. These two technologies share the same vision of a data infrastructure, and act as instances of Machine-Actionable Containers (MACs) that make use of minimal uniform standards to enable FAIR operations. Here, we compare the structure and computational behaviors of the existing nanopublication infrastructure, to those in the proposed FAIR Digital Object Framework. Although developed independently there are clear parallels between the vision and the approach of nanopublication and FDOF. We find a remarkable congruence between the currently proposed FDO requirements and the existing nanopublication infrastructure, including several FDO-like qualities already embodied in the nanopublication ecosystem." } ], "http://purl.org/dc/terms/date": [ { "@value": "2022-10-12" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/2367-7163" } ], "http://purl.org/dc/terms/title": [ { "@value": "The Comparative Anatomy of Nanopublications and FAIR Digital Objects" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RA4c57BIY99eHu-WTrS7v3WFBoWkP9f-j2jAuV_dp0uoE/author-list" } ], "http://purl.org/ontology/bibo/volume": [ { "@value": "8" } ] }, { "@id": "https://w3id.org/np/RA4c57BIY99eHu-WTrS7v3WFBoWkP9f-j2jAuV_dp0uoE/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0001-8888-635X" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0003-2195-3997" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_4": [ { "@id": "https://orcid.org/0000-0001-7525-9218" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_5": [ { "@id": "https://orcid.org/0000-0002-1164-1351" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_6": [ { "@id": "https://orcid.org/0000-0003-3934-0072" } ] }, { "@id": "https://orcid.org/0000-0001-7525-9218", "http://schema.org/affiliation": [ { "@id": "https://ror.org/03kqpb082" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Marek Suchánek" } ] }, { "@id": "https://ror.org/03kqpb082", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Czech Technical University in Prague, Prague, Czech Republic" } ] }, { "@id": "https://orcid.org/0000-0001-8888-635X", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Erik Schultes" } ] }, { "@id": "https://orcid.org/0000-0002-1164-1351", "http://schema.org/affiliation": [ { "@id": "https://ror.org/006hf6230" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Luiz Bonino da Silva Santos" } ] }, { "@id": "https://ror.org/006hf6230", "http://xmlns.com/foaf/0.1/name": [ { "@value": "University of Twente, Enschede, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0003-2195-3997", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Barbara Magagna" } ] }, { "@id": "https://orcid.org/0000-0003-3934-0072", "http://schema.org/affiliation": [ { "@id": "https://ror.org/05xvt9f17" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Barend Mons" } ] }, { "@id": "https://ror.org/05xvt9f17", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Leiden University Medical Center, Leiden, Netherlands" } ] } ] }, { "@id": "https://w3id.org/np/RAQmbVb4PieBiVgPW-98_HiNSS-37Vq7oLTIOG4Jb1Mq0/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/0302-9743", "http://purl.org/dc/terms/title": [ { "@value": "Lecture Notes in Computer Science" } ] }, { "@id": "https://doi.org/10.1007/978-3-030-30760-8_6", "@type": [ "http://purl.org/spar/fabio/BookChapter" ], "http://purl.org/dc/terms/date": [ { "@value": "2019" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/0302-9743" } ], "http://purl.org/dc/terms/title": [ { "@value": "A Framework for Citing Nanopublications" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAQmbVb4PieBiVgPW-98_HiNSS-37Vq7oLTIOG4Jb1Mq0/author-list" } ], "http://purl.org/ontology/bibo/pageEnd": [ { "@value": "83" } ], "http://purl.org/ontology/bibo/pageStart": [ { "@value": "70" } ] }, { "@id": "https://w3id.org/np/RAQmbVb4PieBiVgPW-98_HiNSS-37Vq7oLTIOG4Jb1Mq0/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0003-1991-3267" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0003-4970-4554" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Vrije Universiteit Amsterdam" } ] }, { "@id": "https://orcid.org/0000-0003-1991-3267", "http://schema.org/affiliation": [ { "@id": "https://ror.org/00240q980" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Erika Fabris" } ] }, { "@id": "https://ror.org/00240q980", "http://xmlns.com/foaf/0.1/name": [ { "@value": "University of Padua, Padua, Italy" } ] }, { "@id": "https://orcid.org/0000-0003-4970-4554", "http://schema.org/affiliation": [ { "@id": "https://ror.org/00240q980" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Gianmaria Silvello" } ] } ] }, { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/0302-9743", "http://purl.org/dc/terms/title": [ { "@value": "Data Integration in the Life Sciences" } ] }, { "@id": "https://doi.org/10.1007/11799511_7", "@type": [ "http://purl.org/spar/fabio/BookChapter" ], "http://purl.org/dc/terms/abstract": [ { "@value": "Linking the biomedical literature to other data resources is notoriously difficult and requires text mining. Text mining aims to automatically extract facts from literature. Since authors write in natural language, text mining is a great natural language processing challenge, which is far from being solved. We propose an alternative: If authors and editors summarize the main facts in a controlled natural language, text mining will become easier and more powerful. To demonstrate this approach, we use the language Attempto Controlled English (ACE). We define a simple model to capture the main aspects of protein interactions. To evaluate our approach, we collected a dataset of 459 paragraph headings about protein interaction from literature. 56% of these headings can be represented exactly in ACE and another 23% partially. These results indicate that our approach is feasible." } ], "http://purl.org/dc/terms/date": [ { "@value": "2006" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/0302-9743" } ], "http://purl.org/dc/terms/title": [ { "@value": "Improving Text Mining with Controlled Natural Language: A Case Study for Protein Interactions" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/author-list" } ] }, { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/loic-royer" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/norbert-e-fuchs" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_4": [ { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/michael-schroeder" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/02crff812" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/02crff812", "http://xmlns.com/foaf/0.1/name": [ { "@value": "University of Zurich, Switzerland" } ] }, { "@id": "https://ror.org/042aqky30", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Technische Universität Dresden, Dresden, Germany" } ] }, { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/loic-royer", "http://schema.org/affiliation": [ { "@id": "https://ror.org/042aqky30" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Loic Royer" } ] }, { "@id": "https://w3id.org/np/RA3ynam1bWWwGynJTWVdYtxneUu6dr2O3ePoofL1YMnT4/norbert-e-fuchs", "http://schema.org/affiliation": [ { "@id": "https://ror.org/02crff812" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Norbert E. 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We discuss three challenges that may hinder the effective exploitation of the full potential of FAIR knowledge graphs. Results: We introduce \"semantic units\" as a conceptual solution, although currently exemplified only in a limited prototype. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs by adding another layer of triples on top of the conventional data layer. Semantic units and their subgraphs are represented by their own resource that instantiates a corresponding semantic unit class. We distinguish statement and compound units as basic categories of semantic units. A statement unit is the smallest, independent proposition that is semantically meaningful for a human reader. Depending on the relation of its underlying proposition, it consists of one or more triples. Organizing a knowledge graph into statement units results in a partition of the graph, with each triple belonging to exactly one statement unit. A compound unit, on the other hand, is a semantically meaningful collection of statement and compound units that form larger subgraphs. Some semantic units organize the graph into different levels of representational granularity, others orthogonally into different types of granularity trees or different frames of reference, structuring and organizing the knowledge graph into partially overlapping, partially enclosed subgraphs, each of which can be referenced by its own resource. Conclusions: Semantic units, applicable in RDF/OWL and labeled property graphs, offer support for making statements about statements and facilitate graph-alignment, subgraph-matching, knowledge graph profiling, and for management of access restrictions to sensitive data. Additionally, we argue that organizing the graph into semantic units promotes the differentiation of ontological and discursive information, and that it also supports the differentiation of multiple frames of reference within the graph." } ], "http://purl.org/dc/terms/date": [ { "@value": "2024-05-27" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/2041-1480" } ], "http://purl.org/dc/terms/title": [ { "@value": "Semantic units: organizing knowledge graphs into semantically meaningful units of representation" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAA1vf_GK8NLXPv36aXQIWMda4KwSayKMDcI3XP-T090A/author-list" } ] }, { "@id": "https://w3id.org/np/RAA1vf_GK8NLXPv36aXQIWMda4KwSayKMDcI3XP-T090A/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0002-8280-0487" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0001-8149-5890" } ] }, { "@id": "https://orcid.org/0000-0001-8149-5890", "http://schema.org/affiliation": [ { "@id": "https://ror.org/01q3tbs38" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Robert Hoehndorf" } ] }, { "@id": "https://ror.org/01q3tbs38", "http://xmlns.com/foaf/0.1/name": [ { "@value": "King Abdullah University of Science and Technology (KAUST)" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-8280-0487", "http://schema.org/affiliation": [ { "@id": "https://ror.org/04aj4c181" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Lars Vogt" } ] }, { "@id": "https://ror.org/04aj4c181", "http://xmlns.com/foaf/0.1/name": [ { "@value": "TIB – Leibniz Information Centre for Science and Technology and University Library" } ] } ] }, { "@id": "https://w3id.org/np/RAxZ0qev1P7TROw0baRlrMOXuB7jtESos3IErGOOFmbQs/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/0302-9743", "http://purl.org/dc/terms/title": [ { "@value": "Lecture Notes in Computer Science" } ] }, { "@id": "https://doi.org/10.1007/978-3-030-61244-3_7", "@type": [ "http://purl.org/spar/fabio/BookChapter" ], "http://purl.org/dc/terms/abstract": [ { "@value": "Scientific publishing is the means by which we communicate and share scientific knowledge, but this process currently often lacks transparency and machine-interpretable representations. Scientific articles are published in long coarse-grained text with complicated structures, and they are optimized for human readers and not for automated means of organization and access. Peer reviewing is the main method of quality assessment, but these peer reviews are nowadays rarely published and their own complicated structure and linking to the respective articles is not accessible. In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent in a semantic way the elements of publications, their assessments, as well as the involved processes, actors, and provenance in general. To evaluate our approach, we present a dataset of 627 nanopublications representing an interlinked network of the elements of articles (such as individual paragraphs) and their reviews (such as individual review comments). Focusing on the specific scenario of editors performing a meta-review, we introduce seven competency questions and show how they can be executed as SPARQL queries. We then present a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful to answer their competency questions. In summary, we demonstrate that a unified and semantic publication model based on nanopublications can make scientific communication more effective and user-friendly." } ], "http://purl.org/dc/terms/date": [ { "@value": "2020" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/0302-9743" } ], "http://purl.org/dc/terms/title": [ { "@value": "A Unified Nanopublication Model for Effective and User-Friendly Access to the Elements of Scientific Publishing" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAxZ0qev1P7TROw0baRlrMOXuB7jtESos3IErGOOFmbQs/author-list" } ], "http://purl.org/ontology/bibo/pageEnd": [ { "@value": "119" } ], "http://purl.org/ontology/bibo/pageStart": [ { "@value": "104" } ] }, { "@id": "https://w3id.org/np/RAxZ0qev1P7TROw0baRlrMOXuB7jtESos3IErGOOFmbQs/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0002-7114-6459" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0002-3357-9130" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-3357-9130", "http://schema.org/affiliation": [ { "@id": "https://ror.org/00x7ekv49" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Davide Ceolin" } ] }, { "@id": "https://ror.org/00x7ekv49", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Centrum Wiskunde & Informatica, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-7114-6459", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Cristina-Iulia Bucur" } ] } ] }, { "@id": "https://w3id.org/np/RAf2arM57QSYuW7fV-Po8Ql97cJlGFdoPpczWgvFpdYZg/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/2052-4463", "http://purl.org/dc/terms/title": [ { "@value": "Scientific Data" } ] }, { "@id": "https://doi.org/10.1038/s41597-019-0184-5", "@type": [ "http://purl.org/spar/fabio/Article" ], "http://purl.org/dc/terms/date": [ { "@value": "2019-09-20" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/2052-4463" } ], "http://purl.org/dc/terms/title": [ { "@value": "Evaluating FAIR maturity through a scalable, automated, community-governed framework" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAf2arM57QSYuW7fV-Po8Ql97cJlGFdoPpczWgvFpdYZg/author-list" } ], "http://purl.org/ontology/bibo/volume": [ { "@value": "6" } ] }, { "@id": "https://w3id.org/np/RAf2arM57QSYuW7fV-Po8Ql97cJlGFdoPpczWgvFpdYZg/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0001-6960-357X" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_10": [ { "@id": "https://orcid.org/0000-0003-1304-1939" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_11": [ { "@id": "https://orcid.org/0000-0001-8888-635X" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0003-4727-9435" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0001-5306-5690" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_4": [ { "@id": "https://orcid.org/0000-0002-1164-1351" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_5": [ { "@id": "https://orcid.org/0000-0001-9833-8031" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_6": [ { "@id": "https://orcid.org/0000-0002-2109-489X" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_7": [ { "@id": "https://orcid.org/0000-0003-2687-1982" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_8": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_9": [ { "@id": "https://orcid.org/0000-0001-9853-5668" } ] }, { "@id": "https://orcid.org/0000-0001-5306-5690", "http://schema.org/affiliation": [ { "@id": "https://ror.org/052gg0110" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Susanna-Assunta Sansone" } ] }, { "@id": "https://ror.org/052gg0110", "http://xmlns.com/foaf/0.1/name": [ { "@value": "University of Oxford, Oxford, United Kingdom" } ] }, { "@id": "https://orcid.org/0000-0001-6960-357X", "http://schema.org/affiliation": [ { "@id": "https://ror.org/03n6nwv02" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Mark D. Wilkinson" } ] }, { "@id": "https://ror.org/03n6nwv02", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Universidad Politécnica de Madrid, Madrid, Spain" } ] }, { "@id": "https://orcid.org/0000-0001-8888-635X", "http://schema.org/affiliation": [ { "@id": "https://ror.org/05xvt9f17" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Erik Schultes" } ] }, { "@id": "https://ror.org/05xvt9f17", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Leiden University Medical Center, Leiden, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0001-9833-8031", "http://schema.org/affiliation": [ { "@id": "https://ror.org/03n6nwv02" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Mario Prieto" } ] }, { "@id": "https://orcid.org/0000-0001-9853-5668", "http://schema.org/affiliation": [ { "@id": "https://ror.org/052gg0110" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Philippe Rocca-Serra" } ] }, { "@id": "https://orcid.org/0000-0002-1164-1351", "http://schema.org/affiliation": [ { 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States" } ] }, { "@id": "https://orcid.org/0000-0003-2687-1982", "http://schema.org/affiliation": [ { "@id": "https://ror.org/052gg0110" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Peter McQuilton" } ] }, { "@id": "https://orcid.org/0000-0003-4727-9435", "http://schema.org/affiliation": [ { "@id": "https://ror.org/02jz4aj89" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Michel Dumontier" } ] }, { "@id": "https://ror.org/02jz4aj89", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Maastricht University, Maastricht, Netherlands" } ] } ] }, { "@id": "https://w3id.org/np/RAQWWWHWHKUyA760ogJxfva0t-FOD1Tvoy4a8HZ_p0sVI/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/2451-8484", "http://purl.org/dc/terms/title": [ { "@value": "Data Science" } ] }, { "@id": "https://doi.org/10.3233/DS-220055", "@type": [ "http://purl.org/spar/fabio/Article" ], "http://purl.org/dc/terms/date": [ { "@value": "2022-03-15" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": 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"http://xmlns.com/foaf/0.1/name": [ { "@value": "Vrije Universiteit Amsterdam" } ] }, { "@id": "https://orcid.org/0000-0002-7114-6459", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Cristina-Iulia Bucur" } ] } ] }, { "@id": "https://w3id.org/sciencelive/np/RAreS6gFgC2w2IOPuWgHZ7FazhZtj9zYRTuh_Q0Z8kY5M/assertion", "@graph": [ { "@id": "https://abc.def", "@type": [ "http://purl.org/spar/fabio/ScholarlyWork" ], "http://purl.org/spar/cito/cites": [ { "@id": "https://abc123.def" } ] } ] }, { "@id": "https://w3id.org/np/RATiBhg9mOyCdsFNxB5rbpJa9BlGsx5BJrMOPQdG-VmVA/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/0302-9743", "http://purl.org/dc/terms/title": [ { "@value": "Lecture Notes in Computer Science" } ] }, { "@id": "https://doi.org/10.1007/978-3-319-25007-6_38", "@type": [ "http://purl.org/spar/fabio/BookChapter" ], "http://purl.org/dc/terms/date": [ { "@value": "2015" } ], 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"@value": "Yale University, New Haven, United States" } ] }, { "@id": "https://orcid.org/0000-0003-4727-9435", "http://schema.org/affiliation": [ { "@id": "https://ror.org/00f54p054" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Michel Dumontier" } ] }, { "@id": "https://ror.org/00f54p054", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Stanford University, Stanford, United States" } ] } ] }, { "@id": "https://w3id.org/np/RATBxHvSZMdfCeNL6dft5xVztnbLwIZ2Dkak0s-a56c34/assertion", "@graph": [ { "@id": "https://w3id.org/sciencelive/citex2026-abstract", "@type": [ "http://purl.org/spar/fabio/ScholarlyWork" ], "http://purl.org/spar/cito/citesAsDataSource": [ { "@id": "https://doi.org/10.5281/zenodo.18070378" } ] } ] }, { "@id": "https://w3id.org/np/RAjWXV2CVxtuCIxXxL4fRIdmk32d4h1MAvdOldr6Qf4FY/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/0922-6389", "http://purl.org/dc/terms/title": [ { "@value": "Frontiers in Artificial Intelligence and Applications" } ] }, { "@id": "https://doi.org/10.3233/978-1-61499-904-1-52", "@type": [ "http://purl.org/spar/fabio/BookChapter" ], "http://purl.org/dc/terms/abstract": [ { "@value": "Scientific communication still mainly relies on natural language written in scientific papers, which makes the described knowledge very difficult to access with automatic means. We can therefore only make limited use of formal knowledge organization methods to support researchers and other interested parties with features such as automatic aggregations, fact checking, consistency checking, question answering, and powerful semantic search. Existing approaches to solve this problem by improving the scientific communication methods have either very restricted coverage, require formal logic skills on the side of the researchers, or depend on unreliable machine learning for the formalization of knowledge. Here, I propose an approach to this problem that is general, intuitive, and flexible. It is based on a unique kind of controlled natural language, called AIDA, consisting of English sentences that are atomic, independent, declarative, and absolute. Such sentences can then serve as nodes in a network of scientific claims linked to publications, researchers, and domain elements. I present here some small studies on preliminary applications of this language. 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While the FAIR Guiding Principles have been introduced to help researchers to make data Findable, Accessible, Interoperable and Reusable, it is still unclear how the notions of FAIR and Openness can be applied in the context of restricted data. Many methods have been proposed in support of the implementation of the principles, but there is yet no consensus among the scientific community as to the suitable mechanisms of making restricted data FAIR. We present here a systematic literature review to identify the methods applied by scientists when researching restricted data in a FAIR-compliant manner in the context of the FAIR principles. Through the employment of a descriptive and iterative study design, we aim to answer the following three questions: (1) What methods have been proposed to apply the FAIR principles to restricted data?, (2) How can the relevant aspects of the methods proposed be categorized?, (3) What is the maturity of the methods proposed in applying the FAIR principles to restricted data?. After analysis of the 40 included publications, we noticed that the methods found, reflect the stages of the Data Life Cycle, and can be divided into the following Classes: Data Collection, Metadata Representation, Data Processing, Anonymization, Data Publication, Data Usage and Post Data Usage. We observed that a large number of publications used 'Access Control' and 'Usage and License Terms' methods, while others such as 'Embargo on Data Release' and the use of 'Synthetic Data' were used in fewer instances. In conclusion, we are presenting the first extensive literature review on the methods applied to confidential data in the context of FAIR, providing a comprehensive conceptual framework for future research on restricted access data." } ], "http://purl.org/dc/terms/date": [ { "@value": "2022-07-20" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/2376-5992" } ], "http://purl.org/dc/terms/title": [ { "@value": "Aligning restricted access data with FAIR: a systematic review" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAFTcnP9fBOBEtsBSmI4zGtMertVyuomkJ_NXfNB3hS18/author-list" } ] }, { "@id": "https://w3id.org/np/RAFTcnP9fBOBEtsBSmI4zGtMertVyuomkJ_NXfNB3hS18/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0001-8004-0464" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0001-8772-7904" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_4": [ { "@id": "https://orcid.org/0000-0002-7748-4715" } ] }, { "@id": "https://orcid.org/0000-0001-8004-0464", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Margherita Martorana" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0001-8772-7904", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Ronald Siebes" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://orcid.org/0000-0002-7748-4715", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Jacco van Ossenbruggen" } ] } ] }, { "@id": "https://w3id.org/np/RAQ-Y_IhBVzKWrntPuM9IOow4b84QNbQblxjEJffA4DNs/assertion", "@graph": [ { "@id": "https://doi.org/10.1145/2740908.2742014", "@type": [ "http://purl.org/spar/fabio/ConferencePaper" ], "http://purl.org/dc/terms/date": [ { "@value": "2015-05-18" } ], "http://purl.org/dc/terms/title": [ { "@value": "Science Bots: A Model for the Future of Scientific Computation?" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAQ-Y_IhBVzKWrntPuM9IOow4b84QNbQblxjEJffA4DNs/author-list" } ], "http://purl.org/ontology/bibo/pageEnd": [ { "@value": "1062" } ], "http://purl.org/ontology/bibo/pageStart": [ { "@value": "1061" } ] }, { "@id": "https://w3id.org/np/RAQ-Y_IhBVzKWrntPuM9IOow4b84QNbQblxjEJffA4DNs/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/05a28rw58" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/05a28rw58", "http://xmlns.com/foaf/0.1/name": [ { "@value": "ETH Zurich, Switzerland" } ] } ] }, { "@id": "https://w3id.org/np/RAq0uG42O-MMOCGkNehbwHTpiicWbF_X4xUpXgabE5lnU/assertion", "@graph": [ { "@id": "http://id.crossref.org/issn/2563-6316", "http://purl.org/dc/terms/title": [ { "@value": "JMIRx Med" } ] }, { "@id": "https://doi.org/10.2196/34979", "@type": [ "http://purl.org/spar/fabio/Article" ], "http://purl.org/dc/terms/abstract": [ { "@value": "Background: In the poorly studied field of physician suicide, various factors can contribute to misinformation or information distortion, which in turn can influence evidence-based policies and prevention of suicide in this unique population. Objective: The aim of this paper is to use nanopublications as a scientific publishing approach to establish a citation network of claims in peer-reviewed publications about the rate of suicide among US physicians. Methods: A list of articles from a previously published scoping literature review on physician suicide was used to identify those articles that commented on or investigated suicidal behaviors of physician populations, including students, postgraduate trainees, and practicing physicians. The included articles were from peer-reviewed publications and asserted a claim about the annual rate of physician suicide. Manual data extraction was performed to collect article (or resource) type, title, authors, digital object identifier or URI, publication year, claim (about annual physician suicide rate), data of last access of the article (eg, for a webpage), and citations supporting the claim. Additional articles, websites, or other links were only added to the set of claims if they were cited by a peer-reviewed article already included in the data set. A nanopublication was created for each article or resource using Nanobench with an investigator-developed literature-based claim nanopublication template. Results: A set of 49 claims concerning the rate of US physician suicide was represented as nanopublications. Analysis of the claim network revealed that (1) the network is not fully connected, (2) no single primary source of the claim could be identified, and (3) all end-point citations had a claim with no further citation, had no apparent claim, or could not be accessed to verify the claim. The nanopublication strategy also enabled the capture of variant claims published on a website. Conclusions: Nanopublications remain to be adopted in broader scientific publishing in medicine, especially in publishing about physician mental health and suicide. This proof-of-concept study highlights an opportunity for more coordinated research efforts in the subject of physician suicide. Our work integrates these various claims and enables the verification of nonauthoritative assertions, thereby better equipping researchers to advance evidence-based knowledge and to make informed statements in the advocacy of physician suicide prevention. Representing physician suicide rate claims as nanopublications can be extended and improved in future work." } ], "http://purl.org/dc/terms/date": [ { "@value": "2022-07-01" } ], "http://purl.org/dc/terms/isPartOf": [ { "@id": "http://id.crossref.org/issn/2563-6316" } ], "http://purl.org/dc/terms/title": [ { "@value": "Representing Physician Suicide Claims as Nanopublications: Proof-of-Concept Study Creating Claim Networks" } ], "http://purl.org/ontology/bibo/authorList": [ { "@id": "https://w3id.org/np/RAq0uG42O-MMOCGkNehbwHTpiicWbF_X4xUpXgabE5lnU/author-list" } ] }, { "@id": "https://w3id.org/np/RAq0uG42O-MMOCGkNehbwHTpiicWbF_X4xUpXgabE5lnU/author-list", "http://www.w3.org/1999/02/22-rdf-syntax-ns#_1": [ { "@id": "https://orcid.org/0000-0002-6007-4023" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_2": [ { "@id": "https://orcid.org/0000-0002-1267-0234" } ], "http://www.w3.org/1999/02/22-rdf-syntax-ns#_3": [ { "@id": "https://orcid.org/0000-0003-4727-9435" } ] }, { "@id": "https://orcid.org/0000-0002-1267-0234", "http://schema.org/affiliation": [ { "@id": "https://ror.org/008xxew50" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tobias Kuhn" } ] }, { "@id": "https://ror.org/008xxew50", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands" } ] }, { "@id": "https://orcid.org/0000-0002-6007-4023", "http://schema.org/affiliation": [ { "@id": "https://ror.org/02jz4aj89" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Tiffany I. Leung" } ] }, { "@id": "https://ror.org/02jz4aj89", "http://xmlns.com/foaf/0.1/name": [ { "@value": "Maastricht University" } ] }, { "@id": "https://orcid.org/0000-0003-4727-9435", "http://schema.org/affiliation": [ { "@id": "https://ror.org/02jz4aj89" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "Michel Dumontier" } ] } ] }, { "@id": "https://w3id.org/np/RAZNqNSF69adw8jiLs_bAJj9FEQkRuwaCdqGvLbJ4KHYI/assertion", "@graph": [ { "@id": "https://w3id.org/sciencelive/citex2026-abstract", "@type": [ "http://purl.org/spar/fabio/ScholarlyWork" ], "http://purl.org/spar/cito/cites": [ { "@id": "https://doi.org/10.1136/bmj.n71" } ] } ] } ]