Stian Soiland-Reyes

Search results

• 2023

  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 othersKremer, 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 › Comment/debate › peer-review

  Open Access

  File

  • Documentation 100%
  • Specimen 100%
  • Sample 75%
  • Life 50%
  • Data Analysis 50%
  95 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 othersBonfils, 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., 9 Jan 2023, (Submitted) In: Data Science Journal. (submitted)

  Research output: Contribution to journal › Article

  • Data Management 100%
  • Research Infrastructure 50%
  • Service 33%
  • Networks 16%
  • Standards 16%
• 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.

  Research output: 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%
  • Standards 50%
  • Linked Data 33%
  • Metadata 33%
  • Contexts 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%
  • Data Analysis 33%
  • Workflows 33%
  • Research Environment 33%

• 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 othersStotzka, 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%
  • Service 14%
  • Specifications 14%
  • Testbed 14%
  • Software Component 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 othersSandström, 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, FAIRRS., 16 Mar 2022

  Research output: Book/Report › Other report

  Open Access

  • Application Software 100%
  • Guiding Principle 22%
  • Working Software 22%
  • Data Management 11%
  • Scientific Data 11%

• 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

  • Specimen 100%
  • Datum 83%
  • Refinery 66%
  • Building 50%
  • Workflows 50%

• 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., 7 Mar 2022, In: Data Intelligence. 4, 2

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

  Open Access

• 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, 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

  • Workflows 100%
  • Portability 25%
  • Standards 18%
  • Workflow System 18%
  • Domains 12%
  41 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

  • Metadata 100%
  • Annotation 66%
  • Artifacts 66%
  • Reproducibility 66%
  • Application Software 33%

• 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 › Article › peer-review

  Open Access

  • Workflows 100%
  • Application Software 42%
  • Data Analysis 14%
  • Computer 14%
  • Research Question 14%

• The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural science collections

  Hardisty, A., Brack, P., Goble, C., Livermore, L., Scott, B., Groom, Q., Owen, S. & Soiland-Reyes, S., 7 Mar 2022, In: Data Intelligence. 4, 2

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

  Open Access

  File

  • Workflows 100%
  • Digital Object 70%
  • Library Component 30%
  • Application 10%
  • Specifications 10%
  52 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

  • Workflows 100%
  • Records 33%
  • Evaluation 33%
  • Data Analysis 33%
  • User 33%

• Thoughts on FDO Collections

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

  Research output: Contribution to conference › Other

  Open Access

  • Digital 100%
  • Object 100%
  • Approach 50%
  • Review 25%
  • Aggregates 25%

• Updating Linked Data practices for FAIR Digital Object principles

  Soiland-reyes, S., Castro, L. J., Garijo, D., Portier, M., Goble, C. & Groth, P., 12 Oct 2022, In: Research Ideas and Outcomes. 8, e94501.

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

  • Linked Data 100%
  • Digital Object 66%
  • Research Infrastructure 33%
  • Great Potential 33%
  • Technology Stack 33%

• Using Research Objects to improve reproducibility: (working title)

  Soiland-Reyes, S., 18 Jul 2022, (In preparation) s11.no.

  Research output: Thesis › Doctoral Thesis

  • Reproducibility 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 othersMalawski, 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

  • Workflows 100%
  • Workflow System 28%
  • Education 14%
  • Standards 14%
  • Artificial Intelligence 14%

• 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

  • Workflows 100%
  • Tool 30%
  • Workflow Management System 20%
  • Testing 10%
  • Service 10%

• 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

  • Standards 100%
  • Standardization 60%
  • Research 40%
  • Project 40%
  • History 40%
  113 Downloads (Pure)

• Open PHACTS Linksets 2.1.1

  Soiland-Reyes, S., 1 Apr 2021

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

  Open Access

• Perspectives on automated composition of workflows in the life sciences: [version 1; peer review: 2 approved]

  Lamprecht, A-L., Palmblad, M., Ison, J., Schwämmle, V., Manir, M. S. A., Altintas, I., Amor, A. B. H., 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., Khanteymoori, A., Kuhn, T., & 10 othersMei, H., Ménager, H., Möller, S., Robert, V., Soiland-Reyes, S., Stevens, R., Szaniszlo, S., Verberne, S., Verhoeven, A. & Wolstencroft, K., 7 Sep 2021, In: F1000Research. 10, 897.

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

  Open Access

  • Workflows 100%
  • Application 11%
  • Semantic Technology 11%
  • Semantic Domain 11%
  • Domain Modeling 11%

• RO-Crate Metadata Specification 1.1.1

  Sefton, P., Carragáin, E. Ó., Soiland-Reyes, S., Corcho, O., Garijo, D., Palma, R., Coppens, F., Goble, C., Fernández, J. M., Chard, K., Gomez-Perez, J. M., Crusoe, M. R., Eguinoa, I., Juty, N., Holmes, K., Clark, J. A., Capella-Gutierrez, S., Gray, A. J. G., Owen, S., Williams, A. R., & 19 othersTartari, G., Bacall, F., Thelen, T., Ménager, H., Rodríguez-Navas, L., Walk, P., whitehead, B., Wilkinson, M., Groth, P., Bremer, E., Castro, LJ. G., Sebby, K., Kanitz, A., Trisovic, A., Kennedy, G., Graves, M., Koehorst, J., Leo, S. & Portier, M., 15 Feb 2021, researchobject.org.

  Research output: Book/Report › Book

  Open Access

  • Metadata 100%
  • Application Software 37%
  • Contexts 12%
  • Specifications 12%
  • Linked Data 12%

• Semantic micro-contributions with decentralized nanopublication services

  Kuhn, T., Taelman, R., Emonet, V., Antonatos, H., Soiland-Reyes, S. & Dumontier, M., 8 Mar 2021, In: PeerJ. 7, p. 1-23 23 p., e387.

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

  Open Access

  • Linked Data 100%
  • Service 80%
  • User 60%
  • Networks 40%
  • Semantics 40%

• Towards a Common Standard for Data and Specimen Provenance in Life Sciences

  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., Golebiewski, M., & 16 othersKisler, B., Kremer, A., 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., Zatloukal, K. & Geiger, J., 2021, 12 p. (Zenodo).

  Research output: Working paper › Preprint

  File

  • Standards 100%
  • Reproducibility 66%
  • Research Result 66%
  • Specimen 66%
  • Domains 33%
  34 Downloads (Pure)

• Workflows Community Summit: Bringing the Scientific Workflows Community Together.

  Silva, R. F. D., Casanova, H., Chard, K., Laney, D., Ahn, D., Jha, S., Goble, C. A., Ramakrishnan, L., Peterson, L., Enders, B., Thain, D., Altintas, I., Babuji, Y. N., Badia, R. M., Bonazzi, V., Coleman, T., Crusoe, M. R., Deelman, E., Natale, F. D., Tommaso, P. D., & 25 othersFahringer, T., Filgueira, R., Fursin, G., Ganose, A., Gruning, B., Katz, D. S., Kuchar, O., Kupresanin, A., Ludäscher, B., Maheshwari, K., Mattoso, M., Mehta, K., Munson, T., Ozik, J., Peterka, T., Pottier, L., Randles, T., Soiland-Reyes, S., Tovar, B., Turilli, M., Uram, T. D., Vahi, K., Wilde, M., Wolf, M. & Wozniak, J. M., 2021, Zenodo. 25 p.

  Research output: Book/Report › Other report

  Open Access

  • Workflows 100%
  • Workflow Management System 60%
  • User 20%
  • Scientific Workflow 20%
  • System Landscape 20%
• 2020

  IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020

  IEEE P2791 BioCompute Working Group (BCOWG), Mazumder, R. (ed.) & Simonyan, V. (ed.), 11 May 2020, IEEE. 16 p.

  Research output: Book/Report › Other report › peer-review

  Open Access

  File

  • Bioinformatics 100%
  • Communication 88%
  • Standards 66%
  • Workflows 22%
  • Interoperability 22%
  148 Downloads (Pure)

• RO-Crate Metadata Specification 1.1

  Sefton, P., Carragáin, E. Ó., Soiland-Reyes, S., Corcho, O., Garijo, D., Palma, R., Coppens, F., Goble, C., Fernández, J. M., Chard, K., Gomez-Perez, J. M., Crusoe, M. R., Eguinoa, I., Juty, N., Holmes, K., Clark, J. A., Capella-Gutierrez, S., Gray, A. J. G., Owen, S., Williams, A. R., & 18 othersTartari, G., Bacall, F., Thelen, T., Ménager, H., Rodríguez-Navas, L., Walk, P., whitehead, B., Wilkinson, M., Groth, P., Bremer, E., Castro, LJ. G., Sebby, K., Kanitz, A., Trisovic, A., Kennedy, G., Graves, M., Koehorst, J. & Leo, S., 30 Oct 2020, researchobject.org. 75 p.

  Research output: Book/Report › Book

  Open Access

  • Metadata 100%
  • Application Software 33%
  • Specifications 16%
  • Linked Data 16%
  • Formal Specification 16%

• The role of metadata in reproducible computational research

  Leipzig, J., Nüst, D., Hoyt, C. T., Soiland-Reyes, S., Ram, K. & Greenberg, J., 15 Jun 2020, 59 p.

  Research output: Working paper

  File
  131 Downloads (Pure)
• 2019

  A lightweight approach to research object data packaging

  Ó Carragáin, E., Goble, C., Sefton, P. & Soiland-Reyes, S., 24 Jun 2019.

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

  Open Access

  File

  • Annotation 100%
  • Application 50%
  • Application Software 50%
  • Domains 50%
  • Real World 50%
  164 Downloads (Pure)

• BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

  Andrio, P., Hospital, A., Conejero, J., Jordá, L., Del Pino, M., Codo, L., Soiland-reyes, S., Goble, C., Lezzi, D., Badia, R. M., Orozco, M. & Gelpi, J. L., 10 Sep 2019, In: Scientific Data. 6, 1, 8 p., 169.

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

  Open Access

  • Simulation 100%
  • Application Software 50%
  • Bioinformatics 50%
  • Workflows 33%
  • Container 33%

• Bioexcel building blocks test cases

  Andrio, P., Hospital, A., Conejero, J., Jordá, L., Del Pino, M., Codo, L., Soiland-Reyes, S., Goble, C., Lezzi, D., Badia, R., Orozco, M. & Gelpi, J. L., 18 Feb 2019

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

  Open Access

• FAIR Computational Workflows

  Goble, C., Cohen-Boulakia, S., Soiland-Reyes, S., Garijo, D., Gil, Y., Crusoe, M. R., Peters, K. & Schober, D., 1 Nov 2019, In: Data Intelligence. 2, 1, p. 108–121 14 p.

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

  Open Access

  File

  • Workflows 100%
  • Application Software 25%
  • Data Collection 25%
  • Metadata 25%
  • Modeling and Simulation 25%
  555 Downloads (Pure)

• Introducing RO-Crate: Research Object data packaging

  Sefton, P., Ó Carragáin, E., Goble, C. & Soiland-Reyes, S., 21 Aug 2019. 3 p.

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

  Open Access

  File

  • Specifications 100%
  • Standards 33%
  77 Downloads (Pure)

• RO-Crate: a lightweight approach to Research Object data packaging.

  Carragáin, E. Ó., Goble, C. A., Sefton, P. & Soiland-Reyes, S., 29 Jun 2019.

  Research output: Contribution to conference › Poster

  Open Access

• RO-Crate Metadata Specification 1.0

  Sefton, P., Carragáin, E. Ó., Soiland-Reyes, S., Corcho, O., Garijo, D., Palma, R., Coppens, F., Goble, C., González, J. M. F., Chard, K., Gomez-Perez, J. M., Crusoe, M. R., Eguinoa, I., Juty, N., Holmes, K., Clark, J. A., Capella-Gutierrez, S., Gray, A. J. G., Owen, S., Williams, A. R., & 3 othersTartari, G., Bacall, F. & Thelen, T., 15 Nov 2019, Zenodo.

  Research output: Other contribution

  Open Access

  • Metadata 100%
  • Application Software 33%
  • Specifications 16%
  • Linked Data 16%
  • Formal Specification 16%

• Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

  Khan, F. Z., Soiland-Reyes, S., Sinnott, R. O., Lonie, A., Goble, C. & Crusoe, M. R., 1 Nov 2019, In: GigaScience. 8, 11, 27 p., giz095.

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

  Open Access

  File

  • Workflows 100%
  • Standards 21%
  • Best Practice 14%
  • Automation 14%
  • Evaluation 7%
  212 Downloads (Pure)

• Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR

  Juty, N., Wimalaratne, S. M., Soiland-Reyes, S., Kunze, J., Goble, C. A. & Clark, T., 1 Nov 2019, In: Data Intelligence. 2, 1, p. 30–39 10 p.

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

  Open Access

  File

  • Design 100%
  • Identifier 100%
  • Unique Identifier 100%
  • Basic Principle 100%
  • Digital Artifact 100%
  105 Downloads (Pure)
• 2018

  Capturing interoperable reproducible workflows with Common Workflow Language

  Soiland-Reyes, S., Khan, F. Z., Sinnott, R., Lonie, A., Crusoe, M. R. & Goble, C., 29 Oct 2018.

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

  Open Access

  File

  • Workflows 100%
  124 Downloads (Pure)

• CWLProv - Interoperable Retrospective Provenance capture and its challenges

  Khan, F. Z., Soiland-Reyes, S., Crusoe, M. R., Lonie, A. & Sinnott, R., 27 Mar 2018, (Submitted). 14 p.

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

  File

  • Workflows 100%
  • Specifications 15%
  • Standards 15%
  • Automation 15%
  • Application 7%
  1 Downloads (Pure)

• CWL run of Alignment Workflow: CWLProv 0.6.0 Research Object

  Khan, F. Z. & Soiland-Reyes, S., 4 Dec 2018

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

  Open Access

  • Workflows 100%
  • Bioinformatics 25%
  • Case Study 25%
  • Utility Software 25%
  • Reference Genome 25%

• CWL run of RNA-seq Analysis Workflow: CWLProv 0.5.0 Research Object

  Khan, F. Z. & Soiland-Reyes, S., 4 Dec 2018

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

  Open Access

  • Workflows 100%
  • Reference Sequence 42%
  • Quantification 28%
  • Expression Level 28%
  • Precision Medicine 28%

• CWL run of Somatic Variant Calling Workflow: CWLProv 0.5.0 Research Object

  Khan, F. Z. & Soiland-Reyes, S., 4 Dec 2018

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

  Open Access

• Enabling precision medicine via standard communication of HTS provenance, analysis, and results

  Alterovitz, G., Dean, D., Goble, C., Crusoe, M. R., Soiland-Reyes, S., Bell, A., Hayes, A., Suresh, A., Purkayastha, A., King, C. H. S., Taylor, D., Johanson, E., Thompson, E. E., Donaldson, E., Morizono, H., Tsang, H., Vora, J. K., Goecks, J., Yao, J., Almeida, J. S., & 17 othersKeeney, J., Addepalli, K., Krampis, K., Smith, K. M., Guo, L., Walderhaug, M., Schito, M., Ezewudo, M., Guimera, N., Walsh, P., Kahsay, R., Gottipati, S., Rodwell, T. C., Bloom, T., Lai, Y., Simonyan, V. & Mazumder, R., 31 Dec 2018, In: PLoS Biology. 16, 12, 18 p., e3000099.

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

  Open Access

  • Precision Medicine 100%
  • Personalized Medicine 100%
  • Accuracy 100%
  • Domains 80%
  • Standard 80%
  21 Downloads (Pure)

• FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative

  Stanford, N., Bacall, F., Zamanzad Ghavidel, F., Golebiewski, M., Jonassen, I., Kleppe, R., Krebs, O., Leonov, H., Owen, S., Peterson, K., Rey, M., Soiland-Reyes, S., Tekle, K., Weiderman, A., Williams, A., Wittig, U., Wolstencroft, K., Goksøyr, A., Snoep, J., Vik, J. O., & 2 othersMüller, W. & Goble, C., 4 Sep 2018, (Accepted/In press). 4 p.

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

  Open Access

  File

  • Bioinformatics 100%
  • Data Management 100%
  • Data Sharing 66%
  • Research Infrastructure 33%
  • Application Software 33%
  253 Downloads (Pure)

• Research Object Community Update

  Goble, C., Soiland-Reyes, S. & Bechhofer, S., 29 Oct 2018. 4 p.

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

  Open Access

  • Research 100%
  • Object 75%
  • Containers 25%
  • Provenance 25%
  • Frame-work 25%

• stain/arcp-py: arcp 0.2.0: Create/parse arcp (Archive and Package) URIs in Python

  Soiland-Reyes, S., 5 Feb 2018

  Research output: Non-textual form › Software

• SWEET Ontology Suite v3.0.0: Development, Alignments and Use Cases

  Buttigieg, P. L., Mungall, C., Rueda, C., McGibbney, L., Cox, S., Duerr, R., Fils, D., Graybeal, J., Huffer, B., Narock, T., Ramachandran, B., Soiland-Reyes, S. & Whitehead, B., 8 Apr 2018.

  Research output: Contribution to conference › Abstract

  Open Access

  • Ontology 100%
  • Semantic Web 100%
  • Semantic Technology 37%
  • Domains 25%
  • Specific Domain 25%

• The Archive and Package (arcp) URI scheme: Internet-Draft

  Soiland-Reyes, S. & Cáceres, M., 17 Jan 2018, Internet Engineering Task Force, 21 p.

  Research output: Working paper › Discussion paper

  Open Access

  File

  • Hypermedia 100%
  • Multimedia 100%
  • References 100%
  • Application 50%
  • Content 50%
  61 Downloads (Pure)