Synthesis of Systematic Resources

SYNTHESYS+ is a pan-European collections infrastructure project and the fourth iteration of the SYNTHESYS programme, funded by the European Commission. SYNTHESYS+ will commence on 1 February 2019 and run until 31 January 2023.

SYNTHESYS+ is the final iteration of the programme, which builds upon previous SYNTHESYS projects which ran from February 2004 -– July 2009; September 2009 – August 2013; and September 2013 – August 2017. All iterations of the SYNTHESYS programme have developed collections infrastructure with international partners, via discrete work packages coordinated under deliverables of Access, Networking, and Joint Research Activities.

SYNTHESYS+ will lay the foundations for the Distributed System of Scientific Collections (DiSSCO), a massive scientific infrastructure project, which will see 115 European Museums from 21 Countries position their collections at the centre of data-driven scientific excellence and innovation in environmental research, climate change, food security, one health and the bioeconomy.

eScience Lab involvement

eScience Lab is involved with making the Specimen Data Refinery (SDR), a workflow installation based on Galaxy that performs digitization and analysis of digital specimens using community standards including openDS, FAIR Digital Objects and RO-Crate.

  • WP8: JRA3: Specimen Data Refinery (lead: NHM)
    • (Task 8.2: Development of tools and services (lead: NHM))
      • (Subtask 8.2.6: Specimen Data Refinery Workflow and Tools Registry)
    • Task 8.3: Development of the SDR platform for executing data processing services (lead: UNIMAN)
    • D8.3: Cloud platform for tools and services (lead: UNIMAN)
    • MS61: Functional SDR registry (lead: UNIMAN)

Publications

Laurence Livermore, Paul Brack, Ben Scott, Stian Soiland-Reyes, Oliver Woolland (2022):
The Specimen Data Refinery: Using a scientific workflow approach for information extraction
Biodiversity Information Standards (TDWG 2022).
Biodiversity Information Science and Standards 6:e93500
https://doi.org/10.3897/biss.6.93500 [slides]

Oliver Woolland, Paul Brack, Stian Soiland-Reyes, Ben Scott, Laurence Livermore (2022):
Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e94349
https://doi.org/10.3897/rio.8.e94349 [poster]

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble (2022):
Ten Simple Rules for making a software tool workflow-ready.
PLOS Computational Biology 18(3):e1009823
https://doi.org/10.1371/journal.pcbi.1009823

Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes (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)
https://doi.org/10.1162/dint_a_00134

Peter Wittenburg, Ivonne Anders, Christophe Blanchi, Merret Buurman, Carole Goble, Jonas Grieb, Alex Hardisty, Sharif Islam, Thomas Jejkal, Tibor Kálmán, Christine Kirkpatrick, Laurence Lannom, Thomas Lauer, Giridhar Manepalli, Karsten Peters-von Gehlen, Andreas Pfeil, Robert Quick, Mark van de Sanden, Ulrich Schwardmann, Stian Soiland-Reyes, Rainer Stotzka, Zachary Trautt, Dieter Van Uytvanck, Claus Weiland, Philipp Wieder (2022):
FAIR Digital Object Demonstrators 2021.
Report, FAIR Digital Objects Forum. Zenodo
https://doi.org/10.5281/zenodo.5872645

Stephanie Walton, Laurence Livermore, Olaf Bánki, Robert W. N. Cubey, Robyn Drinkwater, Markus Englund, Carole Goble, Quentin Groom, Christopher Kermorvant, Isabel Rey, Celia M Santos, Ben Scott, Alan R. Williams, Zhengzhe Wu (2020):
Landscape Analysis for the Specimen Data Refinery.
Research Ideas and Outcomes 6:e57602
https://doi.org/10.3897/rio.6.e57602

Vincent Stuart Smith, Kristina Gorman, Wouter Addink, Christos Arvanitidis, Ana Casino, Katherine Dixey, Gabriele Dröge, Quentin Groom, Elspeth Margaret Haston, Donald Hobern, Sandra Knapp, Dimitrios Koureas, Laurence Livermore, Ole Seberg (2019):
SYNTHESYS+ Abridged Grant Proposal.
Research Ideas and Outcomes 5:e46404
https://doi.org/10.3897/rio.5.e46404