Synthesis of systematic resources

Projektinformationen

SYNTHESYS PLUS

ID Finanzhilfevereinbarung: 823827

DOI

10.3030/823827

Projekt abgeschlossen

EK-Unterschriftsdatum 30 November 2018

Startdatum 1 Februar 2019

Enddatum 31 Juli 2023

Finanziert unter

• EXCELLENT SCIENCE - Research Infrastructures

Gesamtkosten

€ 11 342 333,77

EU-Beitrag

€ 10 000 000,00

Koordiniert durch

NATURAL HISTORY MUSEUM
United Kingdom

CORDIS bietet Links zu öffentlichen Ergebnissen und Veröffentlichungen von HORIZONT-Projekten.

Links zu Ergebnissen und Veröffentlichungen von RP7-Projekten sowie Links zu einigen Typen spezifischer Ergebnisse wie Datensätzen und Software werden dynamisch von OpenAIRE abgerufen.

Leistungen

Documents, reports (19)

Whitepaper on opportunities for increased alignment with other EU infrastructures

Whitepaper on opportunities for increased alignment and interoperability between SYNTHESYS and other EU infrastructures

Publication providing synthesis of cost-effective + scalable workflows for NH collections DNA sequencing

Peerreviewed publication providing synthesis of costeffective and scalable work flows for DNA sequencing NH collections

Report from engagement activities with taxonomic facilities in priority regions (non-Europe)

Report from engagement activities with taxonomic facilities in priority regions outside Europe

Landscape analysis and missing standards handbook
Evaluation and assessment of existing landscape

Evaluation and assessment of existing landscape, summarising the findings of task 8.1 “Evaluation and assessment of existing landscape”

Roadmap for integrated implementation of priority component areas

European roadmap for integrated implementation of priority component areas with focal areas for delivery by SYNTHESYS partners and other EU infrastructures

Best practice for usage of molecular collections handbook
Data use and exploitation of Specimen Data Refinery

Data delivery and exploitation of Specimen Data Refinery summarising the use cases for the delivery and exploitation of data generated through the specimen data refinery as part of task 84

Specification and requirements for integration with ELViS

Specification and requirements for integration of collections management systems with ELViS

Consolidated document on policy topics, related best practices + standards

Consolidated document on policy topics related best practices standards

Report from engagement with new user communities
Whitepaper on partnering with other infrastructures to ensure sustainable delivery of SYNTHESYS+ services

Whitepaper on partnering with other infrastructures to ensure sustainable delivery of services offered by SYNTHESYS partners to European research

Inventory and Analysis of Dataflows

Inventory and analysis of dataflows as part of the ELViS functional specifications

Paper on implementation, assessments and sustainability business plan of VA

Peer-reviewed paper on the implementation, assessment and sustainability business plan of VA

Identifier management for curators

A guide of best practices documentation for curatorial staff covering the maintenance of collections with persistent identifiers and documenting best practice in this domain, for example when collections are merged or specimens are deaccessioned.

Standards Report (Developing + extending standards in the biodiversity informatics domain)

Standards reports progress made on developing and extending standards in the biodiversity informatics domain built from the reports and standards created from meetings funded under task 412

Piloting Access through an AAI infrastructure
Results of pilot workflow integrations with ELViS
Implementation manual for IIIF and CETAF Identifiers in the NH collections community

An implementation manual for IIIF and CETAF Identifiers in the NH collections community

Demonstrators, pilots, prototypes (5)

Tools and services for extraction, enhancement and annotation

A set of automated and high throughput software services to extract, enhance and annotate NH specimen data

ELViS System for Unified Access
ELViS Helpdesk

ELViS Helpdesk: a unified helpdesk system support researchers access the collections and DoD services

Cloud platform for tools and services

An online platform to make services and workflows openly accessible together as a toolkit with an authentication and authorisation infrastructure

Data pipelines + standard workflows, enabling online access to complex digital content (3D scans)

Other (7)

Delivery of user days

User day delivery: Deliver a minimum of 7,235 user days

Final General Meeting

Final General Meeting: for all beneficiaries and other stakeholders

Periodic assessment (2) of VA by external board
Catalogue of training modules
Joint dashboard of collections assessment tools
Best practices for using the GGBN Data Standard to provide restriction and loan information handbook

Best practices for using the GGBN Data Standard to provide restriction and loan information handbook: Agreed guidelines for using the GGBN Data Standard in conjunction with OpenDS specification for restriction and loan information published via DiSSCo knowledge base. [month 48]

Periodic assessment (1) of VA by external board

Open Research Data Pilot (1)

Data Management Plan

Veröffentlichungen

Peer reviewed articles (22)

SYNTHESYS+ Virtual Access - Report on the Ideas Call (October to November 2019)

Autoren: Helen Hardy, Sandra Knapp, E. Louise Allan, Frederik Berger, Katherine Dixey, Bernadette Döme, Pierre-Yves Gagnier, Jiri Frank, Elspeth Haston, Joachim Holstein, Steffen Kiel, Maria Marschler, Patricia Mergen, Sarah Phillips, Rivka Rabinovich, Begoña Sanchez Chillón, Martin Sorensen, Marco Thines, Maarten Trekels, Robert Vogt, Scott Wilson, Karin Wiltschke-Schrotta
Veröffentlicht in: Research Ideas and Outcomes, Ausgabe 6, 2020, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.3897/rio.6.e50354

Towards a Roadmap for Advancing the Catalogue of the World’s Natural History Collections

Autoren: Donald Hobern; Laurence Livermore; Sarah Vincent; Tim Robertson; Joseph Miller; Quentin Groom; Marie Grosjean
Veröffentlicht in: Research Ideas and Outcomes, Ausgabe 7, 2022, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.3897/rio.8.e98593

Join the Dots: Adding collection assessment to collection descriptions

Autoren: Matt Woodburn, Sarah Vincent, Helen Hardy, Clare Valentine
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37200

Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

Autoren: Maurizio Mascarello, Mario Amalfi, Pieter Asselman, Erik Smets, Olivier J. Hardy, Hans Beeckman, Steven B. Janssens
Veröffentlicht in: PLoS ONE, Ausgabe 16: 6, 2021, ISSN 1932-6203
Herausgeber: Public Library of Science
DOI: 10.1371/journal.pone.0251655

A botanical demonstration of the potential of linking data using unique identifiers for people

Autoren: Anton Güntsch; Quentin Groom; Marcus Ernst; Jörg Holetschek; Andreas Plank; Dominik Röpert; David Fichtmüller; David Peter Shorthouse; Roger Hyam; Mathias Dillen; Maarten Trekels; Elspeth Haston; Heimo Rainer
Veröffentlicht in: PLoS ONE, Ausgabe 4, 2021, ISSN 1932-6203
Herausgeber: Public Library of Science
DOI: 10.1371/journal.pone.0261130

Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells

Autoren: Eva Chatzinikolaou, Kleoniki Keklikoglou, Panagiotis Grigoriou, Christos Arvanitidis
Veröffentlicht in: Biodiversity Data Journal, Ausgabe 9, 2021, ISSN 1314-2828
Herausgeber: Pensoft
DOI: 10.3897/bdj.9.e75358

The disambiguation of people names in biological collections

Autoren: Quentin Groom; Christian Bräuchler; Robert Cubey; Mathias Dillen; Pieter Huybrechts; Nicole Kearney; Niels Klazenga; Siobhan Leachman; Deborah L Paul; Heather Rogers; Joaquim Santos; David Shorthouse; Alison Vaughan; Sabine von Mering; Elspeth Haston
Veröffentlicht in: Biodiversity Data Journal, Ausgabe 10, 2022, ISSN 1314-2828
Herausgeber: Pensoft
DOI: 10.3897/bdj.10.e86089

10 Simple Rules for making a software tool workflow-ready

Autoren: 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
Veröffentlicht in: PLoS Computational Biology, Ausgabe 22, 2022, ISSN 1553-7358
Herausgeber: PLOS
DOI: 10.1371/journal.pcbi.1009823

Genetic characterization of a group of commercial African timber species: From genomics to barcoding

Autoren: Maurizio Mascarello, Olivier Lachenaud, Mario Amalfi, Erik Smets, Olivier J. Hardy, Hans Beeckman, Steven B. Janssens
Veröffentlicht in: PLoS ONE, Ausgabe 18: 4, 2023, ISSN 1932-6203
Herausgeber: Public Library of Science
DOI: 10.1371/journal.pone.0284732

Semantically Linking Specimens and Images

Autoren: Roger Hyam
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.35343

Target capture and genome skimming for plant diversity studies

Autoren: Flávia Fonseca Pezzini, Giada Ferrari, Laura L. Forrest, Michelle L. Hart, Kanae Nishii, Catherine A. Kidner
Veröffentlicht in: Applications in Plant Sciences, Ausgabe 11: 4, 2023, ISSN 2168-0450
Herausgeber: The Botanical Society of America
DOI: 10.1002/aps3.11537

Landscape Analysis for the Specimen Data Refinery

Autoren: Stephanie Walton, Laurence Livermore, Olaf Bánki, Robert Cubey, Robyn Drinkwater, Markus Englund, Carole Goble, Quentin Groom, Christopher Kermorvant, Isabel Rey, Celia Santos, Ben Scott, Alan Williams, Zhengzhe Wu
Veröffentlicht in: Research Ideas and Outcomes, Ausgabe 6, 2020, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.3897/rio.6.e57602

Collections Digitization and Assessment Dashboard, a Tool for Supporting Informed Decisions

Autoren: Ana Casino, Niels Raes, Wouter Addink, Matt Woodburn
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37505

Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards

Autoren: Stanley Blum, Katharine Barker, Steven J Baskauf, Walter G. Berendsohn, Pier Luigi Buttigieg, Markus Döring, Gabriele Droege, David Fichtmueller, Falko Glöckler, Anton Güntsch, Robert Guralnick, Jana Hoffmann, Niels Klazenga, James Macklin, Paul J. Morris, Deborah L Paul, Mareike Petersen, Tim Robertson, Joel Sachs, David Shorthouse, Ramona Walls, John Wieczorek, Paula F Zermoglio
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37491

Policies Handbook on Using Molecular Collections

Autoren: Astrid de Mestier, Daniel Mulcahy, David J. Harris, Nadja Korotkova, Sarah Long, Eva Häffner, Alan Paton, Edmund K. Schiller, Frederik Leliaert, Jacqueline Mackenzie-Dodds, Tim Fulcher, Gunilla Stahls, Thomas von Rintelen, María P. Martín, Robert Lücking, China Williams, Christopher H. C. Lyal, Anton Güntsch, Heléne Aronsson, Magalie Castelin, Anna Pielach, Peter Poczai, Yolanda Ruiz-León,
Veröffentlicht in: Research Ideas and Outcomes, Ausgabe 9, 2023, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.3897/rio.9.e102908

People are essential to linking biodiversity data

Autoren: Quentin Groom; Anton Güntsch; Pieter Huybrechts; Nicole Kearney; Siobhan Leachman; Nicky Nicolson; Roderic D. M. Page; David Shorthouse; Anne E. Thessen; Elspeth Haston
Veröffentlicht in: Database: The Journal of Biological Databases and Curation, Ausgabe 1, 2020, ISSN 1758-0463
Herausgeber: Oxford University Press
DOI: 10.1093/database/baaa072

Access to Natural History Collections – from SYNTHESYS to DiSSCo

Autoren: Sandra Knapp, Sarah Vincent, Christos Arvanitidis, Katherine Dixey, Patricia Mergen
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37149

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

Autoren: Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes
Veröffentlicht in: Data Intelligence, Ausgabe 4: 2, 2022, Seite(n) 320-341, ISSN 2641-435X
Herausgeber: MIT Press
DOI: 10.1162/dint_a_00134

SYNTHESYS+ Abridged Grant Proposal

Autoren: Vincent Smith, Kristina Gorman, Wouter Addink, Christos Arvanitidis, Ana Casino, Katherine Dixey, Gabriele Dröge, Quentin Groom, Elspeth Haston, Donald Hobern, Sandra Knapp, Dimitrios Koureas, Laurence Livermore, Ole Seberg
Veröffentlicht in: Research Ideas and Outcomes, Ausgabe 5, 2019, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.3897/rio.5.e46404

Biodiversity biobanks: a landscape analysis

Autoren: Carolina Corrales, Samantha Luciano, Jonas J. Astrin
Veröffentlicht in: Research Ideas and Outcomes, Ausgabe ARPHA Preprints, 2023, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.3897/arphapreprints.e103105

Documenting Natural History Collections in GBIF

Autoren: Tim Robertson, Marcos Gonzalez, Morten Høfft, Marie Grosjean
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37216

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Autoren: Giada Ferrari, Lore Esselens, Michelle L Hart, Steven Janssens, Catherine Kidner, Maurizio Mascarello, Joshua V Peñalba, Flávia Pezzini, Thomas von Rintelen, Gontran Sonet, Carl Vangestel, Massimiliano Virgilio, Peter M Hollingsworth
Veröffentlicht in: Biodiversity Data Journal, Ausgabe 11, 2023, ISSN 1314-2836
Herausgeber: Pensoft
DOI: 10.3897/bdj.11.e102317

Other (1)

Envisaging a global infrastructure to exploit the potential of digitised collections

Autoren: Quentin Groom,Mathias Dillen,Wouter Addink,Arturo H. Ariño,Christian Bölling,Pierre Bonnet,Lorenzo Cecchi,Elizabeth R. Ellwood,Rui Figueira,Pierre-Yves Gagnier,Olwen Grace,Anton Güntsch,Helen Hardy,Pieter Huybrechts,Roger Hyam,Alexis Joly,Isabel Larridon,Vamsi Krishna Kommineni,Laurence Livermore,Ricardo Jorge Lopes,Jeremy Miller,Sofie Meeus,Kenzo Milleville,Marc Pignal,Renato Panda,Jorrit H. P
Veröffentlicht in: Authorea, 2022
Herausgeber: Authorea
DOI: 10.22541/au.166678848.82362633/v2

Non-peer reviewed articles (1)

Uniquely Identifying Collectors of Specimens

Autoren: Quentin Groom, Mathias Dillen, Pieter Huybrechts
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37013

Conference proceedings (5)

Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

Autoren: Woolland, Oliver; Brack, Paul; Soiland-Reyes, Stian; Scott, Ben; Livermore, Laurence
Veröffentlicht in: Research Ideas and Outcomes 8: e94349, Ausgabe 25, 2022, ISSN 2367-7163
Herausgeber: Pensoft
DOI: 10.5281/zenodo.7224963

MIDS: The digitisation standard for Natural Science collections

Autoren: Elspeth M Haston, Cat Chapman
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 6, 2022
Herausgeber: Pensoft
DOI: 10.3897/biss.6.94604

Collections do not have to Remain Ambiguous Forever: Seven steps to getting the correct people into your data

Autoren: Groom, Quentin; Braeuchler, Christian; Cubey, Robert; Dillen, Mathias; Huybrechts, Pieter; Kearney, Nicole; Leachman, Siobhan; Paul, Deborah L; Rogers, Heather; Santos, Joaquim; Shorthouse, David; Vaughan, Alison; von Mering, Sabine; Haston, Elspeth
Veröffentlicht in: Biodiversity Information Science and Standards 6: e91194, Ausgabe 14, 2022
Herausgeber: Pensoft
DOI: 10.3897/biss.6.91194

Latimer Core: A new data standard for collection descriptions

Autoren: Matt Woodburn, Jutta Buschbom, Gabriele Droege, Sharon Grant, Quentin Groom, Janeen Jones, Maarten Trekels, Sarah Vincent, Kate Webbink
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 6, 2022
Herausgeber: Pensoft
DOI: 10.3897/biss.6.91159

Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project

Autoren: Christos Arvanitidis, Peter Hollingsworth, Patricia Mergen, Patrick Semal, Kleoniki Keklikoglou, Eva Chatzinikolaou, Wouter Addink, Vincent Smith, Dimitrios Koureas
Veröffentlicht in: Biodiversity Information Science and Standards, Ausgabe 3, 2019, ISSN 2535-0897
Herausgeber: Pensoft
DOI: 10.3897/biss.3.37290

Monographic books (1)

Biodiversity Biobanking – a Handbook on Protocols and Practices

Autoren: Carolina Corrales, Jonas J Astrin
Veröffentlicht in: Pensoft, Advanced Books, 2023
Herausgeber: Pensoft
DOI: 10.3897/ab.e101876