Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data

Robert P. Guralnick; Nico Cellinese; John Deck; Richard L. Pyle; John Kunze; Lyubomir Penev; Ramona Walls; Gregor Hagedorn; Donat Agosti; John Wieczorek; Terry Catapano; Roderic Page

doi:10.3897/zookeys.494.9352

Roderic Page (2016)
Towards a biodiversity knowledge graph. Research Ideas and Outcomes 2: e8767.

Patrick W. Sweeney, Binil Starly, Paul J. Morris, Yiming Xu, Aimee Jones, Sridhar Radhakrishnan, Christopher J. Grassa, Charles C. Davis (2018)
Large–scale digitization of herbarium specimens: Development and usage of an automated, high–throughput conveyor system. TAXON 67: 165.

DOI: 10.12705/671.10

James Lendemer, Barbara Thiers, Anna K Monfils, Jennifer Zaspel, Elizabeth R Ellwood, Andrew Bentley, Katherine LeVan, John Bates, David Jennings, Dori Contreras, Laura Lagomarsino, Paula Mabee, Linda S Ford, Robert Guralnick, Robert E Gropp, Marcy Revelez, Neil Cobb, Katja Seltmann, M Catherine Aime (2020)
The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education. BioScience 70: 23.

DOI: 10.1093/biosci/biz140

F. Andres Rivera-Quiroz, Booppa Petcharad, Jeremy A. Miller (2020)
Mining data from legacy taxonomic literature and application for sampling spiders of the Teutamus group (Araneae; Liocranidae) in Southeast Asia. Scientific Reports 10: .

DOI: 10.1038/s41598-020-72549-8

Brenda Daly, Fhatani Ranwashe (2023)
South Africa’s initiative toward an integrated biodiversity data portal. Frontiers in Ecology and Evolution 11: .

DOI: 10.3389/fevo.2023.1124928

Aurélien Miralles, Teddy Bruy, Katherine Wolcott, Mark D Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim W Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne S Renner, Miguel Vences, Matt Friedman (2020)
Repositories for Taxonomic Data: Where We Are and What is Missing. Systematic Biology 69: 1231.

DOI: 10.1093/sysbio/syaa026

Susanne S Renner, Mark D Scherz, Conrad L Schoch, Marc Gottschling, Miguel Vences, Alexandre Antonelli (2024)
Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains. Systematic Biology 73: 486.

DOI: 10.1093/sysbio/syad068

Shobha Sharma, Stacy Ciufo, Elena Starchenko, Dakshesh Darji, Larry Chlumsky, Ilene Karsch-Mizrachi, Conrad L Schoch (2018)
The NCBI BioCollections Database. Database 2018: .

DOI: 10.1093/database/bay006

Klaus Riede (2018)
Acoustic profiling of Orthoptera: present state and future needs. Journal of Orthoptera Research 27: 203.

DOI: 10.3897/jor.27.23700

Joan E. Damerow, Charuleka Varadharajan, Kristin Boye, Eoin L. Brodie, Madison Burrus, K. Dana Chadwick, Robert Crystal-Ornelas, Hesham Elbashandy, Ricardo J. Eloy Alves, Kim S. Ely, Amy E. Goldman, Ted Haberman, Valerie Hendrix, Zarine Kakalia, Kenneth M. Kemner, Annie B. Kersting, Nancy Merino, Fianna O'Brien, Zach Perzan, Emily Robles, Patrick Sorensen, James C. Stegen, Ramona L. Walls, Pamela Weisenhorn, Mavrik Zavarin, Deborah Agarwal (2021)
Sample Identifiers and Metadata to Support Data Management and Reuse in Multidisciplinary Ecosystem Sciences. Data Science Journal 20: 11.

DOI: 10.5334/dsj-2021-011

Roderic D. M. Page (2016)
DNA barcoding and taxonomy: dark taxa and dark texts. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150334.

DOI: 10.1098/rstb.2015.0334

Vivek Navale, Michele Ji, Olga Vovk, Leonie Misquitta, Tsega Gebremichael, Alison Garcia, Yang Fann, Matthew McAuliffe (2019)
Development of an informatics system for accelerating biomedical research.. F1000Research 8: 1430.

DOI: 10.12688/f1000research.19161.1

Ryan A. Folk, Carolina M. Siniscalchi (2021)
Biodiversity at the global scale: the synthesis continues. American Journal of Botany 108: 912.

DOI: 10.1002/ajb2.1694

Cristian Hernandez, Elham Aslankoohi, Pavel Frolikov, Houpu Li, Sri Kurniawan, Marco Rolandi, Shadab Alam (2023)
Implementing QR codes in academia to improve sample tracking, data accessibility, and traceability in multicampus interdisciplinary collaborations. PLOS ONE 18: e0282783.

DOI: 10.1371/journal.pone.0282783

Robert P. Guralnick, Paula F. Zermoglio, John Wieczorek, Raphael LaFrance, David Bloom, Laura Russell (2016)
The importance of digitized biocollections as a source of trait data and a new VertNet resource. Database 2016: baw158.

DOI: 10.1093/database/baw158

W. Daniel Kissling, Jorge A. Ahumada, Anne Bowser, Miguel Fernandez, Néstor Fernández, Enrique Alonso García, Robert P. Guralnick, Nick J. B. Isaac, Steve Kelling, Wouter Los, Louise McRae, Jean‐Baptiste Mihoub, Matthias Obst, Monica Santamaria, Andrew K. Skidmore, Kristen J. Williams, Donat Agosti, Daniel Amariles, Christos Arvanitidis, Lucy Bastin, Francesca De Leo, Willi Egloff, Jane Elith, Donald Hobern, David Martin, Henrique M. Pereira, Graziano Pesole, Johannes Peterseil, Hannu Saarenmaa, Dmitry Schigel, Dirk S. Schmeller, Nicola Segata, Eren Turak, Paul F. Uhlir, Brian Wee, Alex R. Hardisty (2018)
Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biological Reviews 93: 600.

DOI: 10.1111/brv.12359

Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R. McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L. Snoep, Stian Soiland-Reyes, Natalie J. Stanford, Neil Swainston, Nicole Washington, Alan R. Williams, Sarala M. Wimalaratne, Lilly M. Winfree, Katherine Wolstencroft, Carole Goble, Christopher J. Mungall, Melissa A. Haendel, Helen Parkinson (2017)
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLOS Biology 15: e2001414.

DOI: 10.1371/journal.pbio.2001414

Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov (2019)
OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science. Publications 7: 38.

DOI: 10.3390/publications7020038

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 (2019)
SYNTHESYS+ Abridged Grant Proposal. Research Ideas and Outcomes 5: .

DOI: 10.3897/rio.5.e46404

D. Edge-Garza, K. Evans, E.M. Ross, S. Jung, D. Main, C. Hardner (2023)
A strategy for aggregating multi-source historical phenotypic and genotypic data sets containing homonyms for global genomic prediction in apple (Malus domestica). Acta Horticulturae : 123.

DOI: 10.17660/ActaHortic.2023.1362.17

Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Donald Hobern, Olaf Banki, Wouter Addink, Urmas Kõljalg, Kyle Copas, Patricia Mergen, Anton Güntsch, Laurence Benichou, Jose Benito Gonzalez Lopez, Patrick Ruch, Corinne Martin, Boris Barov, Iliyana Demirova, Kristina Hristova (2022)
Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: .

DOI: 10.3897/rio.8.e81136

Xiao Feng, Brian J. Enquist, Daniel S. Park, Brad Boyle, David D. Breshears, Rachael V. Gallagher, Aaron Lien, Erica A. Newman, Joseph R. Burger, Brian S. Maitner, Cory Merow, Yaoqi Li, Kimberly M. Huynh, Kacey Ernst, Elizabeth Baldwin, Wendy Foden, Lee Hannah, Peter M. Jørgensen, Nathan J. B. Kraft, Jon C. Lovett, Pablo A. Marquet, Brian J. McGill, Naia Morueta‐Holme, Danilo M. Neves, Mauricio M. Núñez‐Regueiro, Ary T. Oliveira‐Filho, Robert K. Peet, Michiel Pillet, Patrick R. Roehrdanz, Brody Sandel, Josep M. Serra‐Diaz, Irena Šímová, Jens‐Christian Svenning, Cyrille Violle, Trang D. Weitemier, Susan Wiser, Laura López‐Hoffman (2022)
A review of the heterogeneous landscape of biodiversity databases: Opportunities and challenges for a synthesized biodiversity knowledge base. Global Ecology and Biogeography 31: 1242.

DOI: 10.1111/geb.13497

Jens Klump, Robert Huber (2017)
20 Years of Persistent Identifiers – Which Systems are Here to Stay?. Data Science Journal 16: .

DOI: 10.5334/dsj-2017-009

Jeremy Miller, Donat Agosti, Lyubomir Penev, Guido Sautter, Teodor Georgiev, Terry Catapano, David Patterson, David King, Serrano Pereira, Rutger Vos, Soraya Sierra (2015)
Integrating and visualizing primary data from prospective and legacy taxonomic literature. Biodiversity Data Journal 3: e5063.

DOI: 10.3897/BDJ.3.e5063

David Patterson, Dmitry Mozzherin, David Shorthouse, Anne Thessen (2016)
Challenges with using names to link digital biodiversity information. Biodiversity Data Journal 4: e8080.

DOI: 10.3897/BDJ.4.e8080

Joakim Philipson, Alejandra Gonzalez-Beltran, Alejandra Gonzalez-Beltran, Francesco Osborne, Silvio Peroni, Sahar Vahdati (2019)
Identifying PIDs playing FAIR. Data Science 2: 229.

DOI: 10.3233/DS-190024

Anton Güntsch, Roger Hyam, Gregor Hagedorn, Simon Chagnoux, Dominik Röpert, Ana Casino, Gabi Droege, Falko Glöckler, Karsten Gödderz, Quentin Groom, Jana Hoffmann, Ayco Holleman, Matúš Kempa, Hanna Koivula, Karol Marhold, Nicky Nicolson, Vincent S. Smith, Dagmar Triebel (2017)
Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects. Database 2017: .

DOI: 10.1093/database/bax003

M Rabone, T Horton, D O B Jones, E Simon-Lledó, A G Glover (2023)
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade. Database 2023: .

DOI: 10.1093/database/baad013

Birgit Gemeinholzer, Miguel Vences, Bank Beszteri, Teddy Bruy, Janine Felden, Ivaylo Kostadinov, Aurélien Miralles, Tim W. Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Tanja Schuster, Tanja Weibulat, Thomas Wilke, Susanne S. Renner (2020)
Data storage and data re-use in taxonomy—the need for improved storage and accessibility of heterogeneous data. Organisms Diversity & Evolution 20: 1.

DOI: 10.1007/s13127-019-00428-w

Torsten Dikow, Donat Agosti (2015)
Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae). Biodiversity Data Journal 3: e5707.

DOI: 10.3897/BDJ.3.e5707

Vítězslav Moudrý, Rodolphe Devillers (2020)
Quality and usability challenges of global marine biodiversity databases: An example for marine mammal data. Ecological Informatics 56: 101051.

DOI: 10.1016/j.ecoinf.2020.101051

Emily M. Braker (2022)
Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia). ZooKeys 1134: 185.

DOI: 10.3897/zookeys.1134.96103

Sharif Islam, Alex Hardisty, Wouter Addink, Claus Weiland, Falko Glöckler (2020)
Incorporating RDA Outputs in the Design of a European Research Infrastructure for Natural Science Collections. Data Science Journal 19: .

DOI: 10.5334/dsj-2020-050

Fran Humphries, Muriel Rabone, Marcel Jaspars (2021)
Traceability Approaches for Marine Genetic Resources Under the Proposed Ocean (BBNJ) Treaty. Frontiers in Marine Science 8: .

DOI: 10.3389/fmars.2021.661313

Gil Nelson, Patrick Sweeney, Edward Gilbert (2018)
Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens. Applications in Plant Sciences 6: .

DOI: 10.1002/aps3.1027

Viktor Senderov, Lyubomir Penev (2016)
The Open Biodiversity Knowledge Management System in Scholarly Publishing. Research Ideas and Outcomes 2: e7757.

DOI: 10.3897/rio.2.e7757

Donat Agosti, Laurence Benichou, Wouter Addink, Christos Arvanitidis, Terence Catapano, Guy Cochrane, Mathias Dillen, Markus Döring, Teodor Georgiev, Isabelle Gérard, Quentin Groom, Puneet Kishor, Andreas Kroh, Jiří Kvaček, Patricia Mergen, Daniel Mietchen, Joana Pauperio, Guido Sautter, Lyubomir Penev (2022)
Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing. Research Ideas and Outcomes 8: .

DOI: 10.3897/rio.8.e97374

Dagmar Triebel, Wolfgang Reichert, Simone Bosert, Martin Feulner, Daniel Osieko Okach, Abderachid Slimani, Gerhard Rambold (2018)
A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing. Database 2018: .

DOI: 10.1093/database/bax096

Min Hyung Cho, Kwang-Hwi Cho, Kyoung Tai No (2023)
PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing. BMC Bioinformatics 24: .

DOI: 10.1186/s12859-023-05588-3

Michelle J. LeFebvre, Laura Brenskelle, John Wieczorek, Sarah Whitcher Kansa, Eric C. Kansa, Neill J. Wallis, Jessica N. King, Kitty F. Emery, Robert Guralnick, Sergi Lozano (2019)
ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks. PLOS ONE 14: e0215369.

DOI: 10.1371/journal.pone.0215369

Weijia Xu, Ruizhu Huang, Maria Esteva, Jawon Song, Ramona Walls (2016)
Content-based comparison for collections identification. 2016 IEEE International Conference on Big Data (Big Data) : 3283.

DOI: 10.1109/BigData.2016.7840987

Joakim Philipson (2018)
Semantics, Analytics, Visualization. Chapter 3: 33.

DOI: 10.1007/978-3-030-01379-0_3

Robert Guralnick, Robert A. Morris (2024)
Encyclopedia of Biodiversity. : 308.

DOI: 10.1016/B978-0-12-822562-2.00329-7