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Soiland-Reyes, S., Sefton, P., Crosas, M., Castro, L. J., Coppens, F., Fernández, J. M., Garijo, D., Grüning, B., La Rosa, M., Leo, S., Ó Carragáin, E., Portier, M., Trisovic, A., RO-Crate Community, Groth, P., & Goble, C. (2022). Packaging research artefacts with RO-Crate. Data Science, 5(2), 97-138. https://doi.org/10.3233/DS-210053[details]
Brack, P., Crowther, P., Soiland-Reyes, S., Owen, S., Lowe, D., Williams, A. R., Groom, Q., Dillen, M., Coppens, F., Grüning, B., Eguinoa, I., Ewels, P., & Goble, C. (2022). Ten Simple Rules for making a software tool workflow-ready. PLoS Computational Biology, 18(3), [e1009823]. https://doi.org/10.5281/zenodo.5636487, https://doi.org/10.1371/journal.pcbi.1009823[details]
Crusoe, M. R., Abeln, S., Iosup, A., Amstutz, P., Chilton, J., Tijanić, N., Ménager, H., Soiland-Reyes, S., Gavrilović, B., Goble, C. A., & CWL Community (2022). Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Communications of the ACM, 65(6), 54-63. https://doi.org/10.1145/3486897
Hardisty, A., Brack, P., Goble, C., Livermore, L., Scott, B., Groom, Q., Owen, S., & Soiland-Reyes, S. (2022). The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections. Data Intelligence, 4(2), 320–341. https://doi.org/10.1162/dint_a_00134[details]
Soiland-Reyes, S., Sefton, P., Crosas, M., Castro, L. J., Coppens, F., Fernández, J. M., Garijo, D., Grüning, B., La Rosa, M., Leo, S., Ó Carragáin, E., Portier, M., Trisovic, A., RO-Crate Community, Groth, P., & Goble, C. (2022). Packaging research artefacts with RO-Crate. Data Science, 5(2), 97-138. https://doi.org/10.3233/DS-210053[details]
Ferreira da Silva, R., Casanova, H., Chard, K., Altintas, I., Badia, R. M., Balis, B., Coleman, T., Coppens, F., Di Natale, F., Enders, B., Fahringer, T., Filgueira, R., Fursin, G., Garijo, D., Goble, C., Howell, D., Jha, S., Katz, D. S., Laney, D., ... Wolf, M. (2021). A Community Roadmap for Scientific Workflows Research and Development. In 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS 2021): St. Louis, Missouri, USA, 15 November 2021 (pp. 81-90). IEEE. https://doi.org/10.1109/WORKS54523.2021.00016[details]
Lamprecht, A-L., Palmblad, M., Ison, J., Schwämmle, V., Al Manir, M. S., Altintas, I., Baker, C. J. O., Ben Hadj Amor, A., Capella-Gutierrez, S., Charonyktakis, P., Crusoe, M. R., Gil, Y., Goble, C., Griffin, T. J., Groth, P., Ienasescu, H., Jagtap, P., Kalaš, M., Kasalica, V., ... Wolstencroft, K. (2021). Perspectives on automated composition of workflows in the life sciences. F1000Research, 10, [897]. https://doi.org/10.12688/f1000research.54159.1[details]
Wittner, R., Holub, P., Müller, H., Geiger, J., Goble, C., Soiland-Reyes, S., Pireddu, L., Frexia, F., Mascia, C., Fairweather, E., Swedlow, J. R., Moore, J., Strambio, C., Grunwald, D., & Nakae, H. (2021). ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data. In B. Glavic, V. Braganholo, & D. Koop (Eds.), Provenance and Annotation of Data and Processes: 8th and 9th International Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021, virtual event, July 19–22, 2021 : proceedings (pp. 222-225). (Lecture Notes in Computer Science; Vol. 12839). Springer. https://doi.org/10.5281/zenodo.5004842, https://doi.org/10.1007/978-3-030-80960-7_16[details]
David, R., Richard, A. S., Connellan, C., Lauer, K. B., Chiusano, M. L., Goble, C., Houde, M., Kemmer, I., Keppler, A., Lieutaud, P., Ohmann, C., Panagiotopoulou, M., Raza Khan, S., Rybina, A., Soiland-Reyes, S., Wit, C., Wittner, R., Andrade Buono, R., Marsh, S. A., ... Ewbank, J. (2023). Umbrella Data Management Plans to integrate FAIR data: Lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness. https://doi.org/10.5281/zenodo.7998443
Soiland-Reyes, S., Goble, C., & Groth, P. (2023). Evaluating FAIR Digital Object and Linked Data as distributed object systems. (v1 ed.) ArXiv. https://doi.org/10.48550/arXiv.2306.07436
Wittner, R., Holub, P., Mascia, C., Frexia, F., Müller, H., Plass, M., Allocca, C., Betsou, F., Burdett, T., Cancio, I., Chapman, A., Chapman, M., Courtot, M., Curcin, V., Eder, J., Elliot, M., Exter, K., Goble, C., Golebiewski, M., ... Geiger, J. (2023). Toward a common standard for data and specimen provenance in life sciences. Learning Health Systems, [e10365]. https://doi.org/10.1002/lrh2.10365
2022
Arend, D., Beier, S., bouri, L., Brandizi, M., Hobern, D., Le Floch, E., Mühlhaus, T., Pommier, C., Owen, S., Rocca-Serra, P., Rosnet, T., & Soiland-Reyes, S. (2022). BioHackEU22 Project 22: Plant data exchange and standard interoperability. BioHackrXiv. https://doi.org/10.37044/osf.io/c724r
Geest, P. D., Coppens, F., Soiland-Reyes, S., Eguinoa, I., & Leo, S. (2022). Enhancing RDM in Galaxy by integrating RO-Crate. Research Ideas and Outcomes, 8, [e95164]. https://doi.org/10.3897/rio.8.e95164
Soiland-Reyes, S., Castro, L. J., Garijo, D., Portier, M., Goble, C., & Groth, P. (2022). Updating Linked Data practices for FAIR Digital Object principles. Research Ideas and Outcomes, 8, [e94501]. https://doi.org/10.3897/rio.8.e94501
Soiland-Reyes, S., Sefton, P., Castro, L. J., Coppens, F., Garijo, D., Leo, S., Portier, M., & Groth, P. (2022). Creating lightweight FAIR Digital Objects with RO-Crate. Research Ideas and Outcomes, 8, [e93937]. https://doi.org/10.3897/rio.8.e93937
Woolland, O., Brack, P., Soiland-Reyes, S., Scott, B., & Livermore, L. (2022). Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows. Research Ideas and Outcomes, 8, [e94349]. https://doi.org/10.3897/rio.8.e94349
2021
Holub, P., Wittner, R., Mascia, C., Frexia, F., Müller, H., Plass, M., Allocca, C., Betsou, F., Burdett, T., Cancio, I., Chapman, A., Chapman, M., Courtot, M., Curcin, V., Eder, J., Elliot, M., Exter, K., Fairweather, E., Goble, C., ... Geiger, J. (2021). Towards a Common Standard for Data and Specimen Provenance in Life Sciences. (v1 ed.) Zenodo. https://doi.org/10.5281/zenodo.5093125
2022
Soiland-Reyes, S., Sefton, P., Castro, L. J., Coppens, F., Garijo, D., Leo, S., Portier, M., Groth, P., & Goble, C. (2022). Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting. Poster session presented at 1st International Conference on FAIR Digital Objects , Leiden, Netherlands. https://doi.org/10.5281/zenodo.7245315
Woolland, O., Brack, P., Soiland-Reyes, S., Scott, B., & Livermore, L. (2022). Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows. Poster session presented at 1st International Conference on FAIR Digital Objects , Leiden, Netherlands. https://doi.org/10.5281/zenodo.7233688
Soiland-Reyes, S. (speaker) (17-6-2021). Capturing Just Enough Data, Software and Metadata with RO-Crate, DataVerse Community Meeting. https://youtu.be/LJq-mzT9v8o?t=1731
2021
Goble, C., Soiland-Reyes, S., Bacall, F., Owen, S., Williams, A., Eguinoa, I., Droesbeke, B., Leo, S., Pireddu, L., Rodríguez-Navas, L., Fernández, J. M., Capella-Gutierrez, S., Ménager, H., Grüning, B., Serrano-Solano, B., Ewels, P., & Coppens, F. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. Zenodo. https://doi.org/10.5281/zenodo.4605654
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