Stian Soiland-Reyes

Search results

• 2024

  Applying the FAIR Principles to Computational Workflows

  Wilkinson, S. R., Aloqalaa, M., Belhajjame, K., Crusoe, M. R., Kinoshita, B. D. P., Gadelha, L., Garijo, D., Gustafsson, O. J. R., Juty, N., Kanwal, S., Khan, F. Z., Köster, J., Gehlen, K.P.-V., Pouchard, L., Rannow, R. K., Soiland-Reyes, S., Soranzo, N., Sufi, S., Sun, Z. & Vilne, B. & 3 others, Wouters, M. A., Yuen, D. & Goble, C., 4 Oct 2024, arXiv.

  Research output: Preprint/Working paper › Preprint

  Open Access

  File

  • Reproducibility 100%
  • Digital Object 100%
  • System Developer 100%
  • Workflow Management System 100%
  • System Provider 100%
  18 Downloads (Pure)

• BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate

  Fernández, J. M., Iborra, P., Moretti, S., Isaac, A., De Geest, P. & Soiland-Reyes, S., 1 Mar 2024, Open Science Framework, (BioHackrXiv).

  Research output: Preprint/Working paper › Preprint

  • Workflow Execution 100%
  • Research Community 33%
  • Research Question 33%
  • Data Source 33%
  • Project Funding 33%

• BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas

  Soiland-Reyes, S., Castro, L. J., Ravinder, R., Weiland, C., Grieb, J., Rogers, A., Blanchi, C. & Van de Sompel, H., 9 Jan 2024, BioHackrXiv, (BioHackrXiv).

  Research output: Preprint/Working paper › Preprint

  Open Access

  • Digital Object 100%
  • Browser Extension 50%

• BY-COVID D4.3 Provenance model for infectious diseases

  Wittner, R., Soiland-Reyes, S., Leo, S., Meurisse, M. & Hermjakob, H., 3 Apr 2024, Zenodo. 60 p.

  Research output: Book/Report › Other report

  Open Access

  • Reproducibility 100%
  • Data Generation 100%
  • Data Source 50%
  • Granularity 50%
  • Information Model 50%

• D4.4 - Guidelines for recommended metadata standard for research software within EOSC

  Gruenpeter, M., Granger, S., Monteil, A., Chue Hong, N., Breitmoser, E., Antonioletti, M., Garijo, D., González Guardia, E., Gonzalez Beltran, A., Goble, C., Soiland-Reyes, S., Juty, N. & Mejias, G., 6 Mar 2024, Zenodo. 53 p.

  Research output: Book/Report › Other report

  Open Access

  • Scholarly Infrastructure 100%
  • Self-Archive 100%
  • European Board 100%

• EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows

  Soiland-Reyes, S., Chadwick, E., Bacall, F., Fernández, J. M., Grüning, B. & Bayındır, H., 28 Aug 2024, Zenodo. 47 p.

  Research output: Book/Report › Other report

  Open Access

  • Workflow System 100%
  • Digital Object 100%
  • Best Practice 33%
  • Workflow Execution 33%
  • System Analysis 33%

• Evaluating FAIR Digital Object and Linked Data as distributed object systems

  Soiland-Reyes, S., Goble, C. & Groth, P., 30 Apr 2024, In: PeerJ Computer Science. 10, p. 1-45 45 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Linked Data 100%
  • Digital Object 100%
  • Distributed Object 100%
  • Interoperability 14%
  • Semantic Web 14%
  286 Downloads (Pure)

• FAIR Research Objects and Computational Workflows – A Linked Data Approach

  Soiland-Reyes, S., 21 Aug 2024, (Accepted/In press) 348 p.

  Research output: Thesis › Doctoral Thesis

  Open Access

  • Information Relationship 100%

• FAIR Signposting: Exposing the Topology of Digital Objects on the Web

  Van De Sompel, H. & Soiland-Reyes, S., 13 Jan 2024, (Submitted) International FAIR Digital Objects Implementation Summit 2024. TIB Open Publishing

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  File
  72 Downloads (Pure)

• Five Safes RO-Crate: FAIR Digital Objects for Trusted Research Environments

  Soiland-Reyes, S., Wheater, S., Giles, T., Quinlan, P. & Goble, C., 4 Mar 2024, (Accepted/In press) International FAIR Digital Objects Implementation Summit 2024. TIB Open Publishing, 1 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  File

  • Research Environment 100%
  • Digital Object 100%
  • Research Infrastructure 9%
  • Exchange Service 9%
  • Data Services 9%
  174 Downloads (Pure)

• Five ways RO-Crate data packages are important for repositories

  Sefton, P. & Soiland-Reyes, S., 1 Jun 2024.

  Research output: Contribution to conference › Abstract › peer-review

  Open Access

  File

  • Linked Data 100%
  • Interoperability 50%
  • Data Structure 50%
  • Software Repository 50%
  • Explain Briefly 50%
  130 Downloads (Pure)

• Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned

  Soiland-Reyes, S., Sefton, P., Leo, S., Castro, L. J., Weiland, C. & Van De Sompel, H., 19 Apr 2024, (Submitted) Open Conference Proceedings: International FAIR Digital Objects Implementation Summit 2024. TIB Open Publishing, Vol. 4.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  File

  • Research Output 100%
  • Data Infrastructure 100%
  • Digital Object 100%
  • Development Community 100%
  • Object Principle 100%
  135 Downloads (Pure)

• Recording provenance of workflow runs with RO-Crate

  Leo, S., Crusoe, M. R., Rodríguez-Navas, L., Sirvent, R., Kanitz, A., Geest, P. D., Wittner, R., Pireddu, L., Garijo, D., Fernández, J. M., Colonnelli, I., Gallo, M., Ohta, T., Suetake, H., Capella-Gutierrez, S., Wit, R. D., Kinoshita, B. P. & Soiland-Reyes, S., 10 Sept 2024, In: PLoS ONE. 19, 9, e0309210.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Workflow Management System 100%
  • Image Analysis 50%
  • Use Case 50%
  • Input/Output 50%
  • Granularity 50%
  38 Downloads (Pure)

• Report on FAIR Signposting and its Uptake by the Community: EOSC Task Force on FAIR Metrics and Data Quality

  Wilkinson, M., Sansone, S.-A., Grootveld, M., Dennis, R., Hecker, D., Huber, R., Soiland-Reyes, S., Van de Sompel, H., Czerniak, A., Thurston, M., Lister, A. & Gaignard, A., 11 Jan 2024, Zenodo. 22 p.

  Research output: Book/Report › Commissioned report

  Open Access

• RO-Crate: package your research outputs with their metadata

  Chadwick, E. & Soiland-Reyes, S., 3 Sept 2024.

  Research output: Contribution to conference › Poster › peer-review

  Open Access

  File

  • Research Output 100%
  • Linked Data 50%
  • Data Type 50%
  • Use Case 50%
  • Data Provenance 50%
  27 Downloads (Pure)

• RO-Crate community update 2024

  RO-Crate community, Soiland-Reyes, S., Sefton, P., Leo, S., Castro, L. J. & Weiland, C., 13 Jan 2024, (Submitted) International FAIR Digital Objects Implementation Summit 2024. TIB Open Publishing

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  File

  • Digital Object 100%
  • Development Community 100%
  115 Downloads (Pure)

• Using Webby FDOs to Integrate AI Taxon Identification and Citizen Science

  Grieb, J., Weiland, C., Wolodkin, A., Castro, L. J., Soiland-Reyes, S., Beukes, M. & Jansen, M., 15 Aug 2024, In: Biodiversity Information Science and Standards. 8, e134757.

  Research output: Contribution to journal › Meeting Abstract › peer-review

  Open Access

• WorkflowHub: a registry for computational workflows

  Gustafsson, O. J. R., Wilkinson, S. R., Bacall, F., Pireddu, L., Soiland-Reyes, S., Leo, S., Owen, S., Juty, N., Fernández, J. M., Grüning, B., Brown, T., Ménager, H., Capella-Gutierrez, S., Coppens, F. & Goble, C., 9 Oct 2024, arXiv.

  Research output: Preprint/Working paper › Preprint

  Open Access

  File

  • Diverse Platform 100%
  11 Downloads (Pure)

• WorkflowHub Knowledge Graph

  Hambley, A., Chadwick, E., Woolland, O., Soiland-Reyes, S. & Savchenko, V., 22 Aug 2024

  Research output: Non-textual form › Data set/Database

  Open Access

• Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows

  Ferreira da Silva, R., Bard, D., Chard, K., Shaun, D. W., Foster, I. T., Gibbs, T., Goble, C., Godoy, W., Gustafsson, J., Haus, U.-U., Hudson, S., Jha, S., Los, L., Paine, D., Suter, F., Ward, L., Wilkinson, S., Amaris, M., Babuji, Y. & Bader, J. & 91 others, Balin, R., Balouek, D., Beecroft, S., Belhajjame, K., Bhattarai, R., Brewer, W., Brunk, P., Caino-Lores, S., Casanova, H., Cassol, D., Coleman, J., Coleman, T., Colonnelli, I., Da Silva, A. A., de Oliveira, D., Elahi, P., Elfaramawy, N., Elwasif, W., Etz, B., Fahringer, T., Ferreira, W., Filgueira, R., Fosso Tande, J., Gadelha, L., Gallo, A., Garijo, D., Georgiou, Y., Gritsch, P., Grubel, P., Gueroudji, A., Guilloteau, Q., Hamalainen, C., Hong Enriquez, R., Huet, L., Hunter Kesling, K., Iborra, P., Jahangiri, S., Janssen, J., Jordan, J., Kanwal, S., Kunstmann, L., Lehmann, F., Leser, U., Li, C., Liu, P., Luettgau, J., Lupat, R., M. Fernandez, J., Maheshwari, K., Malik, T., Marquez, J., Matsuda, M., Medic, D., Mohammadi, S., Mulone, A., Navarro, J.-L., Ng, K. W., Noelp, K., P. Kinoshita, B., Prout, R., R. Crusoe, M., Ristov, S., Robila, S., Rosendo, D., Rowell, B., Rybicki, J., Sanchez, H., Saurabh, N., Saurav, S. K., Scogland, T., Senanayake, D., Shin, W., Sirvent, R., Skluzacek, T., Sly-Delgado, B., Soiland-Reyes, S., Souza, A., Souza, R., Talia, D., Tallent, N., Thamsen, L., Titov, M., Tovar, B., Vahi, K., Vardar-Irrgang, E., Vartina, E., Wang, Y., Wouters, M., Yu, Q., Al Bkhetan, Z. & Zulfiqar, M., 19 Oct 2024, arXiv.

  Research output: Book/Report › Other report

  Open Access

  • Cloud Service Model 100%
• 2023

  BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates

  Eguinoa, I., Suchánek, M., Knaisl, V., Slifka, J., Geest, P. D., López, D., Gruning, B., Leo, S. & Soiland-Reyes, S., 1 Jul 2023, Open Science Framework, (BioHackrXiv).

  Research output: Preprint/Working paper › Preprint

  Open Access

  • Data Stewardship 100%
  • Data Management 100%
  • Crates 100%
  • Stewardship 100%
  • Data Sharing 66%

• BY-COVID D3.3.1: COVID-19 Data Portal

  Hermjakob, H., Kleemola, M., Ventouratou, M., Lister, A., Sansone, S.-A., David, R., Lischke, J., Navest, R., Belien, J., Juty, N., Soiland-Reyes, S. & Goble, C., 28 Sept 2023, Zenodo. 20 p.

  Research output: Book/Report › Other report

  Open Access

  • Data Source 100%
  • Field Research 100%
  • Metadata Standard 100%
  • Critical Resource 100%
  • Discovery System 100%

• EOSC-Life Implementation of a mechanism for publishing and sharing workflows across instances of the environment

  Goble, C., Soiland-Reyes, S., Bacall, F., Owen, S., Pireddu, L. & Leo, S., 2 May 2023, Zenodo. 39 p.

  Research output: Book/Report › Other report

  • Interoperability 100%
  • Digital Object 100%
  • Access Point 50%
  • Developer Tool 50%
  • Reproducibility 50%

• EOSC-Life Workflow Collaboratory for the Life Sciences

  Goble, C., Bacall, F., Soiland-Reyes, S., Owen, S., Eguinoa, I., Droesbeke, B., Ménager, H., Rodriguez-Navas, L., Fernández, J. M., Grüning, B., Leo, S., Pireddu, L., Crusoe, M., Gustafsson, J., Capella-Gutierrez, S. & Coppens, F., 7 Sept 2023, Proceedings of the Conference on Research Data Infrastructure: 1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities . TIB Open Publishing, Vol. 1. (Proceedings of the Conference on Research Data Infrastructure).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  Open Access

  • Research Infrastructure 100%
  • Data Analytics 50%
  • Collaborative Space 50%
  • Digital Object 50%
  • Data Cleaning 50%

• Federated causal inference based on real-world observational data sources: Application to a SARS-CoV-2 vaccine effectiveness assessment

  Meurisse, M., Estupiñán-Romero, F., González-Galindo, J., Martínez-Lizaga, N., Royo-Sierra, S., Saldner, S., Dolanski-Aghamanoukjan, L., Degelsegger-Marquez, A., Soiland-Reyes, S., Van Goethem, N. & Bernal-Delgado, E., 23 Oct 2023, In: BMC Medical Research Methodology . 23, 1, 248.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Data Source 100%
  • Source Application 100%
  • Observational Data 100%
  • SARS Coronavirus 100%
  • Research Question 50%
  126 Downloads (Pure)

• Linking provenance and its metadata in multi-organizational environments

  Wittner, R., Gallo, M., Frexia, F., Leo, S., Pireddu, L., Mascia, C., Plass, M., Soiland-Reyes, S., Müller, H., Geiger, J. & Holub, P., 12 Dec 2023, (Submitted).

  Research output: Preprint/Working paper › Preprint

  File

  • Use Case 100%
  • Reproducibility 100%
  • Organizational Process 100%
  • Digital Signature 100%
  • Cryptographic Technique 100%
  174 Downloads (Pure)

• ro-crate-py 0.8.0: RO-Crate metadata generator/parser

  De Geest, P. (Developer), Droesbeke, B. (Developer), Eguinoa, I. (Developer), Gaignard, A. (Developer), Huber, S. (Developer), Kinoshita, B. (Developer), Leo, S. (Developer), Pireddu, L. (Developer), Rodríguez-Navas, L. (Developer), Sirvent, R. (Developer) & Soiland-Reyes, S. (Developer), 5 Jun 2023

  Research output: Non-textual form › Software

  Open Access

  • Crates 100%
  • Parser Generator 100%
  • Python 20%
  • Pythonidae 20%

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

  Brown, T., Juty, N., Soiland-Reyes, S., Shaw, F. & Vos, R., 13 Dec 2023, (Submitted).

  Research output: Contribution to conference › Abstract

  File

  • Crates 100%
  97 Downloads (Pure)

• RO-Crates Meets FAIR Digital Objects

  Castro, L. J., Soiland-Reyes, S. & Rebholz-Schuhmann, D., 7 Sept 2023, Proceedings of the Conference on Research Data Infrastructure: 1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities . TIB Open Publishing, Vol. 1. (Proceedings of the Conference on Research Data Infrastructure).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  Open Access

  • Digital Object 100%
  • Linked Data 33%
  • Best Practice 33%
  • Persistent Identifier 33%

• Towards a common standard for data and specimen provenance in life sciences

  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. & Kisler, B. & 16 others, Kremer, A., Leo, S., Lin-Gibson, S., Marsano, A., Mattavelli, M., Moore, J., Nakae, H., Perseil, I., Salman, A., Sluka, J., Soiland-Reyes, S., Strambio-De-Castillia, C., Sussman, M., Swedlow, J. R., Zatloukal, K. & Geiger, J., 18 Apr 2023, (E-pub ahead of print) In: Learning Health Systems. e10365.

  Research output: Contribution to journal › Commentary/debate › peer-review

  Open Access

  File

  • Analytical Procedure 100%
  • Nonrepudiation 100%
  • Data Lineage 100%
  • Data Processing 100%
  • Research Results 100%
  184 Downloads (Pure)

• Umbrella Data Management Plans to integrate FAIR data: Lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness

  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. & Audergon, P. & 25 others, Bonfils, D., Carazo, J.-M., Charrel, R., Coppens, F., Fecke, W., Filippone, C., Garcia Alvarez, E., Gul, S., Hermjakob, H., Herzog, K., Holub, P., Kozera, L., Lister, A. L., López-Coronado, J., Madon, B., Majcen, K., Martin, W., Müller, W., Papadopoulou, E., Prat, C. M. A., Romano, P., Sansone, S.-A., Saunders, G., Blomberg, N. & Ewbank, J., 18 Aug 2023, In: Data Science Journal. 22

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Data Management 100%
  • DMP 100%
  • Step Process 100%
  • Research Infrastructure 60%
  • Data Reuse 20%
• 2022

  BioHackEU22 Project 22: Plant data exchange and standard interoperability

  Arend, D., Beier, S., bouri, L., Brandizi, M., Hobern, D., Floch, E. L., Mühlhaus, T., Pommier, C., Owen, S., Rocca-Serra, P., Rosnet, T. & Soiland-Reyes, S., 18 Dec 2022, Open Science Framework, (BioHackrXiv).

  Research output: Preprint/Working paper › Preprint

  Open Access

• Creating lightweight FAIR Digital Objects with RO-Crate

  Soiland-Reyes, S., Sefton, P., Castro, L. J., Coppens, F., Garijo, D., Leo, S., Portier, M. & Groth, P., 12 Oct 2022, In: Research Ideas and Outcomes. 8, e93937.

  Research output: Contribution to journal › Conference article › peer-review

  Open Access

  • Digital Object 100%
  • Linked Data 33%
  • Best Practice 16%
  • Interoperability 16%
  • Research Output 16%

• Enhancing RDM in Galaxy by integrating RO-Crate

  De Geest, P., Coppens, F., Soiland-reyes, S., Eguinoa, I. & Leo, S., 12 Oct 2022, In: Research Ideas and Outcomes. 8, e95164.

  Research output: Contribution to journal › Conference article › peer-review

  Open Access

  • Galaxies 100%
  • Digital Object 66%
  • Clouds 33%
  • Environment 33%
  • Research Environment 33%

• EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version

  Bietrix, F., Carazo, J. M., Capella-Gutierrez, S., Coppens, F., Chiusano, M. L., David, R., Fernández, J. M., Fratelli, M., Heriche, J.-K., Goble, C., Gribbon, P., Holub, P., P. Joosten, R., Leo, S., Owen, S., Parkinson, H., Pieruschka, R., Pireddu, L., Porcu, L. & Raess, M. & 5 others, Rodriguez-Navas, L., Scherer, A., Soiland-Reyes, S., Tang, J. & Saunders, G., 30 Sept 2022, Zenodo. 23 p.

  Research output: Book/Report › Other report

  Open Access

  • Training Data 100%
  • Meta-Analysis 100%
  • Benchmarking 100%
  • Data Bank 100%
  • Open Data 100%

• FAIR Digital Object Demonstrators 2021

  Wittenburg, P., Anders, I., Blanchi, C., Buurman, M., Goble, C., Grieb, J., Hardisty, A., Islam, S., Jejkal, T., Kálmán, T., Kirkpatrick, C., Lannom, L., Lauer, T., Manepalli, G., Peters-von Gehlen, K., Pfeil, A., Quick, R., van de Sanden, M., Schwardmann, U. & Soiland-Reyes, S. & 5 others, Stotzka, R., Trautt, Z., Van Uytvanck, D., Weiland, C. & Wieder, P., 18 Jan 2022, Zenodo. 19 p.

  Research output: Book/Report › Other report

  Open Access

  • Digital Object 100%
  • Infrastructure 14%
  • Software Component 14%
  • Space Data 14%
  • Pilot Project 14%

• FAIR Principles for Research Software (FAIR4RS Principles)

  Hong, N. P. C., Katz, D. S., Barker, M., Lamprecht, A.-L., Martinez, C., Psomopoulos, F. E., Harrow, J., Castro, L. J., Gruenpeter, M., Martinez, P. A., Honeyman, T., Struck, A., Lee, A., Loewe, A., Werkhoven, B. V., Garijo, D., Plomp, E., Genova, F., Shanahan, H. & Hellström, M. & 46 others, Sandström, M., Sinha, M., Kuzak, M., Herterich, P., Islam, S., Sansone, S.-A., Pollard, T., Atmojo, U. D., Williams, A., Czerniak, A., Niehues, A., Fouilloux, A. C., Desinghu, B., Goble, C., Richard, C., Gray, C., Erdmann, C., Nüst, D., Tartarini, D., Ranguelova, E., Anzt, H., Todorov, I., McNally, J., Burnett, J., Garrido-Sánchez, J., Belhajjame, K., Sesink, L., Hwang, L., Tovani-Palone, M. R., Wilkinson, M. D., Servillat, M., Liffers, M., Fox, M., Miljković, N., Lynch, N., Lavanchy, P. M., Gesing, S., Stevens, S., Cuesta, S. M., Peroni, S., Soiland-Reyes, S., Bakker, T., Rabemanantsoa, T., Sochat, V., Yehudi, Y. & WG, F., 16 Mar 2022

  Research output: Book/Report › Other report

  Open Access

  • Guiding Principle 100%
  • Working Software 100%
  • Scientific Data 50%
  • Data Stewardship 50%
  • Continuous Evolution 50%

• Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

  Woolland, O., Brack, P., Soiland-reyes, S., Scott, B. & Livermore, L., 12 Oct 2022, In: Research Ideas and Outcomes. 8, e94349.

  Research output: Contribution to journal › Conference article › peer-review

  Open Access

  • Digital Object 100%
  • Digital Twin 33%
  • Workflow System 33%

• Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

  Soiland-Reyes, S., Bayarri, G., Andrio, P., Long, R., Lowe, D., Niewielska, A., Hospital, A. & Groth, P., 1 Apr 2022, In: Data Intelligence. 4, 2, p. 342-357 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Building-Blocks 100%
  • Interoperability 33%
  • System Manager 33%
  • Widespread Adoption 33%
  • Computational Method 33%

• Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

  Crusoe, M. R., Abeln, S., Iosup, A., Amstutz, P., Chilton, J., Tijanić, N., Ménager, H., Soiland-Reyes, S., Gavrilović, B., Goble, C. A. & The CWL Community (Collaborator), 20 May 2022, In: Communications of the ACM. 65, 6, p. 54–63 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Workflow System 100%
  • Image Analysis 33%
  • Open Standard 33%
  • Command Line Tool 33%
  • Computing Environment 33%
  172 Downloads (Pure)

• Packaging research artefacts with RO-Crate

  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., 20 Jul 2022, In: Data Science. 5, 2, p. 97-138 42 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Annotation 100%
  • Reproducibility 100%
  • Linked Data 50%
  • Best Practice 50%
  • Research Output 50%

• Ten Simple Rules for making a software tool workflow-ready

  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., 24 Mar 2022, In: PLoS computational biology. 18, 3, e1009823.

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

  • Software Development Tool 100%
  • Research Question 33%
  • Research Output 33%
  • Research Quality 33%
  • Workflow Tool 33%

• The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

  Hardisty, A., Brack, P., Goble, C., Livermore, L., Scott, B., Groom, Q., Owen, S. & Soiland-Reyes, S., 1 Apr 2022, In: Data Intelligence. 4, 2, p. 320-341 22 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Digital Object 100%
  • Named Entity Recognition 33%
  • Library Component 33%
  • Optical Character Recognition 33%
  • Translation (Languages) 33%
  99 Downloads (Pure)

• The Specimen Data Refinery: Using a scientific workflow approach for information extraction

  Livermore, L., Brack, P., Scott, B., Soiland-reyes, S. & Woolland, O., 23 Aug 2022, In: Biodiversity Information Science and Standards (BISS). 6, e93500.

  Research output: Contribution to journal › Meeting Abstract › peer-review

  Open Access

  • Open Source 100%
  • Information Extraction 100%
  • Natural Language Processing 100%
  • Interoperability 100%
  • Application Platform 100%

• Thoughts on FDO Collections

  Soiland-Reyes, S. & Van De Sompel, H., 26 Oct 2022.

  Research output: Contribution to conference › Other

  Open Access

  • Digital 100%
  • Review 25%

• Updating Linked Data practices for FAIR Digital Object principles

  Soiland-reyes, S., Castro, L. J., Garijo, D., Portier, M., Goble, C. & Groth, P., Dec 2022, In: Research Ideas and Outcomes. 8, e94501.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Type Identifier 100%
• 2021

  A Community Roadmap for Scientific Workflows Research and Development

  Da Silva, R. F., 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. & Leser, U. & 9 others, Malawski, M., Mehta, K., Pottier, L., Ozik, J., Peterson, J. L., Ramakrishnan, L., Soiland-reyes, S., Thain, D. & Wolf, M., 28 Dec 2021, p. 81-90. 10 p.

  Research output: Contribution to conference › Paper › peer-review

  Open Access

  • Workflow System 100%
  • Scientific Workflow 100%
  • Artificial Intelligence 50%
  • Interoperability 50%
  • Scientific Application 50%

• Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

  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., 1 Mar 2021, In: Zenodo.

  Research output: Contribution to journal › Article

  Open Access

  • Digital Object 100%
  • Workflow Management System 100%
  • Benchmarking 50%
  • Support Integration 50%
  • Common Practice 50%

• Implementing FAIR for research software: attitudes, advantages and challenges

  Castro, L. J., Álvarez, D. A., Soiland-Reyes, S., Markus, T., Harrison, S., Diblen, F., Dasgupta, A., Gruenpeter, M. & Martinez, P. A., 20 Apr 2021

  Research output: Other contribution

  Open Access

• ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

  Wittner, R., Holub, P., Müller, H., Geiger, J., Goble, C., Soiland-Reyes, S., Pirredu, L., Frexia, F., Mascia, C., Fairweather, E., Swedlow, J. R., Moore, J., Strambio, C., Zanetti, G., Grunwald, D. & Nakae, H., 9 Jul 2021, Lecture Notes in Computer Science. Springer Nature, Vol. 12839. p. 222-225 4 p. (Lecture Notes in Computer Science).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

  Open Access

  File

  • Information Model 100%
  • Data Processing 100%
  • Standardization Activity 100%
  • Future Development 50%
  • And-States 50%
  185 Downloads (Pure)