We describe our pragmatic approach for aligning parallel scientific processes through the implementation of Fair Digital Objects (FDOs), as RO-Crates. Our work is grounded in the Biodiversity domains, but may be extrapolated to be useful more generally in other scientific domains

Brown, Tom

Juty, Nick

Shaw, Felix

Soiland-Reyes, Stian

Vos, Rutger

English

The University of Manchester - Institutional Repository

The University of Manchester ResearchRO-Crates as a practical implementation of FAIR DigitalObject to align biodiversity genomics work streamsDocument VersionSubmitted manuscriptLink to publication record in Manchester Research ExplorerCitation for published version (APA):Brown, T., Juty, N., Soiland-Reyes, S., Shaw, F., & Vos, R. (2023). RO-Crates as a practical implementation ofFAIR Digital Object to align biodiversity genomics work streams. Abstract from International FAIR Digital ObjectsImplementation Summit 2024, Berlin, Berlin, Germany.Citing this paperPlease note that where the full-text provided on Manchester Research Explorer is the Author Accepted Manuscriptor Proof version this may differ from the final Published version. If citing, it is advised that you check and use thepublisher's definitive version.General rightsCopyright and moral rights for the publications made accessible in the Research Explorer are retained by theauthors and/or other copyright owners and it is a condition of accessing publications that users recognise andabide by the legal requirements associated with these rights.Takedown policyIf you believe that this document breaches copyright please refer to the University of Manchester’s TakedownProcedures [http://man.ac.uk/04Y6Bo] or contact uml.scholarlycommunications@manchester.ac.uk providingrelevant details, so we can investigate your claim.Download date:08. Feb. 2024RO-Crates as a practical implementation of FAIRDigital Object to align biodiversity genomics workstreamsAuthors:● Tom Brown (Leibniz Institute for Zoo & Wildlife Research, ERGA, BGE)● Nick Juty (The University of Manchester, Bioschemas, ELIXIR-UK, FAIRplus, BY-COVID,FAIR-IMPACT, BGE)● Stian Soiland-Reyes (The University of Manchester, University of Amsterdam, RO-Crate lead,ELIXIR-UK, BY-COVID, FAIR-IMPACT, EOSC-Life, EuroScienceGateway, BGE)● Felix Shaw (Earlham Institute, BGE)● Rutger Vos (Leiden University, Naturalis Biodiversity Center, BGE)Category:● Science● Technology● FAIRKeywords: FDO, Data management, metadata, biodiversitySummaryWe describe our pragmatic approach for aligning parallel scientific processes through theimplementation of Fair Digital Objects (FDOs), as RO-crates. Our work is grounded in theBiodiversity domains, but may be extrapolated to be useful more generally in other scientificdomains.Proposed topic (2 pages)ERGA streamThe European Reference Genome Atlas (ERGA) is a pan-European scientific response to threats tobiodiversity, with the aim of producing reference genomes for all eukaryotic species in Europe via adistributed model of sampling, sequencing, and generating genome assemblies. This process involvesa number of distinct sets of data, metadata, and workflows, which must be linked and published in aconnected manner. Existing infrastructure such as provided by the INSDC (ENA, BioSamples,GenBank, DDBJ [Arita et al., 2021]), COPO [Shaw et al., 2020], and WorkflowHub [Goble et al., 2023]are currently used to collect raw sequencing data, sample metadata, genome assemblies, andworkflows, respectively, yet the nature and clarity of their inter-connectedness remains a challenge.For research outputs of ERGA to remain FAIR [Wilkinson et al., 2016], the genomics field requires thedevelopment of resources such as RO-crate [Soiland-Reyes 2023], where the provenance andinterconnectedness of research objects can be explicitly stated and maintained throughout the life ofa genome assembly project. Supporting RO-crate for submission to public nucleotide archives such asENA or NCBI would facilitate the attachment of associated metadata, data, and workflows toresearch outputs, and ensure the relations between these objects are explicit.iBOL streamBIOSCAN is the second tranche of bundled activity within the DNA barcoding community, operatingunder the aegis of the iBOL consortium, to achieve a step change in the number of publicly available,high-quality reference DNA barcode sequences used for species identification, delimitation, andsystematics. DNA barcoding refers to the concept of sequencing single-copy, single-inheritance,genetic markers whose constant substitution rate is such that they have low variation within speciesbut sufficient variation between species to allow for discrimination among them [Hebert et al.,2003]. The BIOSCAN ‘stream’ (slated to be renamed iBOL Europe) is the practical implementation ofthis step change within the context of the Biodiversity Genomics Europe project. The implementationinvolves a number of work processes starting with specimen collection (both in the wild and fromnatural history collection), sampling, DNA extraction, library preparation, sequencing, bioinformatics,quality assurance, and data publishing to BOLD [Ratnasingham & Hebert, 2007], the centralrepository for DNA barcodes. Due to the variation in the sample sources - fresh or preserved - thechain includes some branching depending on whether the DNA extracts are amplicon sequenced orgenome skimmed, with downstream impacts on bioinformatics and QA. The complexity of theprocesses and their distributed nature complicate provenance tracking and FAIRness, which isnevertheless essential for the credibility of the resulting data products. To address this, the BIOSCANstream adopts RO-crate technology as the common framework.RO-CrateRO-Crate [Soiland-Reyes 2023] is a community effort to practically achieve FAIR packaging ofresearch objects (digital objects like data, methods, and software) with structured metadata.RO-Crate uses well-established web standards and FAIR principles. For common metadatarepresentations, RO-Crate builds on schema.org, a mature and general mark-up vocabulary used bysearch engines including Google Dataset Search. RO-Crate is adapted by many EU/EOSC projects as apragmatic implementation of the FAIR Digital Objects [De Smedt et al., 2020] vision. This paperbrings together representatives of existing Biodiversity ‘pipelines’ in an effort to identify andharmonise processes and (meta)data that are currently parallel but equivalent. We envisageconvergence on a common, or at least more integrated, scientific and computational workflow where(meta)data are better interrelated both within a workstream and across them. The mechanism bywhich we will achieve this is the RO-Crate implementation of FDOs. This work is relevant tobiodiversity projects and community-driven efforts but also serves as a practical solution tocomparable issues which will exist in other domains, by analogy.Implementation strategyFaced with the opportunities provided by the RO-crate framework, both ERGA and BIOSCAN aredeveloping approaches towards its adoption and implementation. Along the respective streams,various technologies can be leveraged to achieve this. In some parts of the streams, this may requiremore custom development. For example, both streams struggle with tracking physical specimens andsamples as they are being collected, lab-processed, and sequenced. The metadata about the physicalobjects and their status can be expressed and negotiated among participants in the stream usingsimple spreadsheets, but the problems these pose in terms of inadvertent data modification (e.g.date parsing) and vague semantics may drive the development of FDO solutions. Further down thestream, technological developments make RO-crate adoption easier. Once sequenced, the data fromboth streams is processed by various analysis pipelines. Some of the workflow management systemsin which these pipelines are implemented provide RO-crate functionality ‘out of the box’, forexample, Galaxy [Galaxy 2022] or NextFlow [Nextflow 2017], while others (such as SnakeMake[Snakemake 2021]) have less well-developed support, which influences workflow managementtechnology choices. How tracking of physical objects and pipeline provenance as FDO is, in the end,integrated and attached to data submissions is likewise a topic that is still being explored by theconsortium.References[Arita et al., 2021] Masanori Arita, Ilene Karsch-Mizrachi, Guy Cochrane (2021):The international nucleotide sequence database collaboration.Nucleic Acids Research 49(D1)https://doi.org/10.1093/nar/gkaa967[De Smedt et al., 2020] Koenraad De Smedt, Dimitris Koureas, Peter Wittenburg (2020):FAIR Digital Objects for Science: From Data Pieces to Actionable Knowledge Units.Publications 8(2)https://doi.org/10.3390/publications8020021[Goble 2023] Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, BertDroesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Björn Grüning, Simone Leo,Luca Pireddu, Michael Crusoe, Johan Gustafsson, Salvador Capella-Gutierrez, Frederik Coppens(2023): EOSC-Life Workflow Collaboratory for the Life Sciences.Proceedings of the Conference on Research Data Infrastructure 1https://doi.org/10.52825/cordi.v1i.352[Hebert et al., 2003] Paul D. N. Hebert, Alina Cywinska, Shelley L. Ball and Jeremy R. deWaard (2003):Biological identifications through DNA barcodes.Proceedings of the Royal Society B 270(1512)https://doi.org/10.1098/rspb.2002.2218[Ratnasingham & Hebert, 2007] Sujeevan Ratnasingham, Paul D. N. Hebert (2007):BOLD: The Barcode of Life Data System (http://www.barcodinglife.org)Molecular Ecology Notes 7(3)https://doi.org/10.1111/j.1471-8286.2007.01678.x[Shaw et al., 2020] Felix Shaw, Anthony Etuk, Alice Minotto, Alejandra Gonzalez-Beltran, DavidJohnson, Phillipe Rocca-Serra, Marie-Angélique Laporte, Elizabeth Arnaud, Medha Devare, Paul J.Kersey, Susanna-Assunta Sansone, Robert P. Davey (2020):COPO: a metadata platform for brokering FAIR data in the life sciences.F1000 research 9(495)https://doi.org/10.12688/f1000research.23889.1[Soiland-Reyes 2023] Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, FrederikCoppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan ÓCarragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022):Packaging research artefacts with RO-Crate.Data Science 5(2)https://doi.org/10.3233/DS-210053[Wilkinson et al., 2016] Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, GabrielleAppleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos,Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, OlivierDumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray,Paul Groth, Carole Goble, Jeffrey S. 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P., Palumbo, E., & Notredame, C.(2017):Nextflow enables reproducible computational workflows.Nature Biotechnology, 35(4)https://doi.org/10.1038/nbt.3820[Snakemake 2021] Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V.,Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S.,Köster, J.Sustainable data analysis with Snakemake.F1000Research 2021, 10:33https://doi.org/10.12688/f1000research.29032.2

RO-Crates as a practical implementation of FAIR Digital Object to align biodiversity genomics work streams

https://pure.manchester.ac.uk/ws/files/291308873/2023-12-01_RO-Crate_FDO_2024.pdf

RO-Crates as a practical implementation of FAIR Digital Object to align biodiversity genomics work streams

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