Ontology-based knowledge graph infrastructure for interoperable atomistic simulation data

Ontology-based knowledge graph infrastructure for interoperable atomistic simulation data | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Ontology-based knowledge graph infrastructure for interoperable atomistic simulation data Abril Azocar Guzman, Sarath Menon, Tilmann Hickel, Stefan Sandfeld This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9337379/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The reuse of atomistic simulation data is often limited by heterogeneous formats, incomplete metadata, and a lack of standardized representations of workflows and provenance. Here we present an ontology-based infrastructure for representing and integrating atomistic simulation data as a knowledge graph. The approach combines domain ontologies with a software framework that enables data capture both from existing datasets and directly from simulation workflows at the point of generation. Heterogeneous data from multiple sources are normalized into a common, ontology-aligned representation, enabling consistent querying and analysis across datasets. We demonstrate these capabilities through the integration of grain boundary data, cross-dataset analysis of material properties, and extraction of derived thermodynamic quantities from existing simulations. In addition, workflows are represented in a machine-readable form, enabling both forward provenance tracking and partial reconstruction of computational procedures. The resulting knowledge graph contains over 750,000 triples describing nearly 8,000 computational samples. This work provides a practical framework for improving the findability, interoperability, and reuse of atomistic simulation data. Materials Theory and Modeling Knowledge graphs Ontology engineering Atomistic simulations Materials science data FAIR data Provenance Semantic interoperability Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9337379","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":618468520,"identity":"3a057650-7142-41b0-8cb7-00a9da776cff","order_by":0,"name":"Abril Azocar Guzman","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0001-7564-7990","institution":"Forschungszentrum Juelich","correspondingAuthor":true,"prefix":"","firstName":"Abril","middleName":"Azocar","lastName":"Guzman","suffix":""},{"id":618470689,"identity":"aa63c33d-f2e1-4fce-bffb-d9db13323f56","order_by":1,"name":"Sarath Menon","email":"","orcid":"","institution":"Ruhr University Bochum","correspondingAuthor":false,"prefix":"","firstName":"Sarath","middleName":"","lastName":"Menon","suffix":""},{"id":618470690,"identity":"2dc12d28-0ba3-40fa-9b44-c323444f5512","order_by":2,"name":"Tilmann Hickel","email":"","orcid":"","institution":"Bundesanstalt fur Materialforschung und -prufung","correspondingAuthor":false,"prefix":"","firstName":"Tilmann","middleName":"","lastName":"Hickel","suffix":""},{"id":618470691,"identity":"2c2208c7-ca98-4f6c-b646-63e59439235d","order_by":3,"name":"Stefan Sandfeld","email":"","orcid":"","institution":"Forschungszentrum Juelich","correspondingAuthor":false,"prefix":"","firstName":"Stefan","middleName":"","lastName":"Sandfeld","suffix":""}],"badges":[],"createdAt":"2026-04-06 21:48:33","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-9337379/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9337379/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":106724777,"identity":"7dac9a7a-320a-435a-9d11-4105c90c2ec7","added_by":"auto","created_at":"2026-04-12 18:29:41","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4819624,"visible":true,"origin":"","legend":"","description":"","filename":"ontologyAAG.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9337379/v1_covered_094de322-ec63-44c6-9c7b-39263a02e219.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eOntology-based knowledge graph infrastructure for interoperable atomistic simulation data\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Forschungszentrum Jülich","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Knowledge graphs, Ontology engineering, Atomistic simulations, Materials science data, FAIR data, Provenance, Semantic interoperability","lastPublishedDoi":"10.21203/rs.3.rs-9337379/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9337379/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe reuse of atomistic simulation data is often limited by heterogeneous formats, incomplete metadata, and a lack of standardized representations of workflows and provenance. 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