Synthesis of systematic resources

Risultati finali

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

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)

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

Data Management Plan

Pubblicazioni

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

Autori: 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
Pubblicato in: Research Ideas and Outcomes, Numero 6, 2020, ISSN 2367-7163
Editore: Pensoft
DOI: 10.3897/rio.6.e50354

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

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

Join the Dots: Adding collection assessment to collection descriptions

Autori: Matt Woodburn, Sarah Vincent, Helen Hardy, Clare Valentine
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: Pensoft
DOI: 10.3897/biss.3.37200

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

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

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

Autori: 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
Pubblicato in: PLoS ONE, Numero 4, 2021, ISSN 1932-6203
Editore: 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

Autori: Eva Chatzinikolaou, Kleoniki Keklikoglou, Panagiotis Grigoriou, Christos Arvanitidis
Pubblicato in: Biodiversity Data Journal, Numero 9, 2021, ISSN 1314-2828
Editore: Pensoft
DOI: 10.3897/bdj.9.e75358

The disambiguation of people names in biological collections

Autori: 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
Pubblicato in: Biodiversity Data Journal, Numero 10, 2022, ISSN 1314-2828
Editore: Pensoft
DOI: 10.3897/bdj.10.e86089

10 Simple Rules for making a software tool workflow-ready

Autori: 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
Pubblicato in: PLoS Computational Biology, Numero 22, 2022, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1009823

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

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

Semantically Linking Specimens and Images

Autori: Roger Hyam
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: Pensoft
DOI: 10.3897/biss.3.35343

Target capture and genome skimming for plant diversity studies

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

Landscape Analysis for the Specimen Data Refinery

Autori: 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
Pubblicato in: Research Ideas and Outcomes, Numero 6, 2020, ISSN 2367-7163
Editore: Pensoft
DOI: 10.3897/rio.6.e57602

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

Autori: Ana Casino, Niels Raes, Wouter Addink, Matt Woodburn
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: Pensoft
DOI: 10.3897/biss.3.37505

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

Autori: 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
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: Pensoft
DOI: 10.3897/biss.3.37491

Policies Handbook on Using Molecular Collections

Autori: 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,
Pubblicato in: Research Ideas and Outcomes, Numero 9, 2023, ISSN 2367-7163
Editore: Pensoft
DOI: 10.3897/rio.9.e102908

People are essential to linking biodiversity data

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

Access to Natural History Collections – from SYNTHESYS to DiSSCo

Autori: Sandra Knapp, Sarah Vincent, Christos Arvanitidis, Katherine Dixey, Patricia Mergen
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: 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

Autori: Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes
Pubblicato in: Data Intelligence, Numero 4: 2, 2022, Pagina/e 320-341, ISSN 2641-435X
Editore: MIT Press
DOI: 10.1162/dint_a_00134

SYNTHESYS+ Abridged Grant Proposal

Autori: 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
Pubblicato in: Research Ideas and Outcomes, Numero 5, 2019, ISSN 2367-7163
Editore: Pensoft
DOI: 10.3897/rio.5.e46404

Biodiversity biobanks: a landscape analysis

Autori: Carolina Corrales, Samantha Luciano, Jonas J. Astrin
Pubblicato in: Research Ideas and Outcomes, Numero ARPHA Preprints, 2023, ISSN 2367-7163
Editore: Pensoft
DOI: 10.3897/arphapreprints.e103105

Documenting Natural History Collections in GBIF

Autori: Tim Robertson, Marcos Gonzalez, Morten Høfft, Marie Grosjean
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: Pensoft
DOI: 10.3897/biss.3.37216

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Autori: 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
Pubblicato in: Biodiversity Data Journal, Numero 11, 2023, ISSN 1314-2836
Editore: Pensoft
DOI: 10.3897/bdj.11.e102317

Envisaging a global infrastructure to exploit the potential of digitised collections

Autori: 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
Pubblicato in: Authorea, 2022
Editore: Authorea
DOI: 10.22541/au.166678848.82362633/v2

Uniquely Identifying Collectors of Specimens

Autori: Quentin Groom, Mathias Dillen, Pieter Huybrechts
Pubblicato in: Biodiversity Information Science and Standards, Numero 3, 2019, ISSN 2535-0897
Editore: Pensoft
DOI: 10.3897/biss.3.37013

Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

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

MIDS: The digitisation standard for Natural Science collections

Autori: Elspeth M Haston, Cat Chapman
Pubblicato in: Biodiversity Information Science and Standards, Numero 6, 2022
Editore: 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

Autori: 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
Pubblicato in: Biodiversity Information Science and Standards 6: e91194, Numero 14, 2022
Editore: Pensoft
DOI: 10.3897/biss.6.91194

Latimer Core: A new data standard for collection descriptions

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

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

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

Biodiversity Biobanking – a Handbook on Protocols and Practices

Autori: Carolina Corrales, Jonas J Astrin
Pubblicato in: Pensoft, Advanced Books, 2023
Editore: Pensoft
DOI: 10.3897/ab.e101876

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