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Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

ABSTRACT: The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development.

SUBMITTER: Evans ML

PROVIDER: S-EPMC11305395 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

Evans Matthew L ML Bergsma Johan J Merkys Andrius A Andersen Casper W CW Andersson Oskar B OB Beltrán Daniel D Blokhin Evgeny E Boland Tara M TM Castañeda Balderas Rubén R Choudhary Kamal K Díaz Díaz Alberto A Domínguez García Rodrigo R Eckert Hagen H Eimre Kristjan K Fuentes Montero María Elena ME Krajewski Adam M AM Mortensen Jens Jørgen JJ Nápoles Duarte José Manuel JM Pietryga Jacob J Qi Ji J Trejo Carrillo Felipe de Jesús FJ Vaitkus Antanas A Yu Jusong J Zettel Adam A de Castro Pedro Baptista PB Carlsson Johan J Cerqueira Tiago F T TFT Divilov Simon S Hajiyani Hamidreza H Hanke Felix F Jose Kevin K Oses Corey C Riebesell Janosh J Schmidt Jonathan J Winston Donald D Xie Christen C Yang Xiaoyu X Bonella Sara S Botti Silvana S Curtarolo Stefano S Draxl Claudia C Fuentes Cobas Luis Edmundo LE Hospital Adam A Liu Zi-Kui ZK Marques Miguel A L MAL Marzari Nicola N Morris Andrew J AJ Ong Shyue Ping SP Orozco Modesto M Persson Kristin A KA Thygesen Kristian S KS Wolverton Chris C Scheidgen Markus M Toher Cormac C Conduit Gareth J GJ Pizzi Giovanni G Gražulis Saulius S Rignanese Gian-Marco GM Armiento Rickard R

Digital discovery 20240418 8

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the AP ...[more]

PMID: 39118978

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Project description:BackgroundThe complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.DescriptionSADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.ConclusionsSADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.

Dataset Information

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

Publications

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

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