The use and limits of scientific names in biological informatics

David Remsen

doi:10.3897/zookeys.550.9546

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

Beckett Sterner, Joeri Witteveen, Nico Franz (2020)
Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies. History and Philosophy of the Life Sciences 42: .

DOI: 10.1007/s40656-020-0300-z

Thierry Bourgoin, Nicolas Bailly, René Zaragueta, Régine Vignes-Lebbe (2021)
Complete formalization of taxa with their names, contents and descriptions improves taxonomic databases and access to the taxonomic knowledge they support. Systematics and Biodiversity 19: 738.

DOI: 10.1080/14772000.2021.1915895

Nico M. Franz, Naomi M. Pier, Deeann M. Reeder, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shawn Bowers, Bertram Ludäscher (2016)
Two Influential Primate Classifications Logically Aligned. Systematic Biology 65: 561.

DOI: 10.1093/sysbio/syw023

Thomas Pape (2017)
Editorial: BZN goes electronic-only. The Bulletin of Zoological Nomenclature 74: 4.

DOI: 10.21805/bzn.v74.a003

Beckett Sterner, Nathan Upham, Atriya Sen, Nico Franz (2020)
Avenues into Integration: Communicating taxonomic intelligence from sender to recipient. Biodiversity Information Science and Standards 4: .

DOI: 10.3897/biss.4.59006

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Shizhuo Yu, Bertram Ludäscher, Sergei L. Kosakovsky Pond (2019)
Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion. PLOS Computational Biology 15: e1006493.

DOI: 10.1371/journal.pcbi.1006493

Ross Mounce, Malin Rivers, Suzanne Sharrock, Paul Smith, Samuel Brockington (2018)
Comparing and contrasting threat assessments of plant species at the global and sub-global level. Biodiversity and Conservation 27: 907.

DOI: 10.1007/s10531-017-1472-z

Nico Franz, Edward Gilbert, Beckett Sterner (2019)
Distributed, but Global in Reach: Outline of a de-centralized paradigm for biodiversity data intelligence. Biodiversity Information Science and Standards 3: .

DOI: 10.3897/biss.3.37749

Dana L. Campbell, Anne E. Thessen, Leslie Ries (2020)
A novel curation system to facilitate data integration across regional citizen science survey programs. PeerJ 8: e9219.

DOI: 10.7717/peerj.9219

Beckett Sterner, Nathan Upham, Prashant Gupta, Caleb Powell, Nico Franz (2021)
Wanted: Standards for FAIR taxonomic concept representations and relationships . Biodiversity Information Science and Standards 5: .

DOI: 10.3897/biss.5.75587

Nico M. Franz, Chao Zhang, Joohyung Lee (2018)
A logic approach to modelling nomenclatural change. Cladistics 34: 336.

DOI: 10.1111/cla.12201

Brian Stucky, James Balhoff, Narayani Barve, Vijay Barve, Laura Brenskelle, Matthew Brush, Gregory Dahlem, James Gilbert, Akito Kawahara, Oliver Keller, Andrea Lucky, Peter Mayhew, David Plotkin, Katja Seltmann, Elijah Talamas, Gaurav Vaidya, Ramona Walls, Matt Yoder, Guanyang Zhang, Rob Guralnick (2019)
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. Biodiversity Data Journal 7: .

DOI: 10.3897/BDJ.7.e33303

J. W. Santos, R. A. Correia, A. C. M. Malhado, J. V. Campos‐Silva, D. Teles, P. Jepson, R. J. Ladle (2020)
Drivers of taxonomic bias in conservation research: a global analysis of terrestrial mammals. Animal Conservation 23: 679.

DOI: 10.1111/acv.12586

Matteo Conti, Pier Luigi Nimis, Stefano Martellos (2021)
Match Algorithms for Scientific Names in FlorItaly, the Portal to the Flora of Italy. Plants 10: 974.

DOI: 10.3390/plants10050974

Yi‐Yun Cheng, Nico Franz, Jodi Schneider, Shizhuo Yu, Thomas Rodenhausen, Bertram Ludäscher (2017)
Agreeing to disagree: Reconciling conflicting taxonomic views using a logic‐based approach. Proceedings of the Association for Information Science and Technology 54: 46.

DOI: 10.1002/pra2.2017.14505401006

Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A. Morris, Lyubomir Penev (2018)
OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system. Journal of Biomedical Semantics 9: .

DOI: 10.1186/s13326-017-0174-5

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

M. Andrew Johnston, Rolf Aalbu, Nico Franz (2018)
An updated checklist of the Tenebrionidae sec. Bousquet et al. 2018 of the Algodones Dunes of California, with comments on checklist data practices. Biodiversity Data Journal 6: e24927.

DOI: 10.3897/BDJ.6.e24927

Jessica Tam, Malgorzata Lagisz, Will Cornwell, Shinichi Nakagawa (2022)
Quantifying research interests in 7,521 mammalian species with h-index: a case study. GigaScience 11: .

DOI: 10.1093/gigascience/giac074

Ricardo A. Correia, Ivan Jarić, Paul Jepson, Ana C.M. Malhado, José A. Alves, Richard J. Ladle (2018)
Nomenclature instability in species culturomic assessments: Why synonyms matter. Ecological Indicators 90: 74.

DOI: 10.1016/j.ecolind.2018.02.059

Kari E. A. Norman, Scott Chamberlain, Carl Boettiger, Samantha Price (2020)
taxadb: A high‐performance local taxonomic database interface. Methods in Ecology and Evolution 11: 1153.

DOI: 10.1111/2041-210X.13440

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

Simon Scheider, Frank O. Ostermann, Benjamin Adams (2017)
Why good data analysts need to be critical synthesists. Determining the role of semantics in data analysis. Future Generation Computer Systems 72: 11.

DOI: 10.1016/j.future.2017.02.046

Nico Franz, Edward Gilbert, Bertram Ludäscher, Alan Weakley (2016)
Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal. Research Ideas and Outcomes 2: .

DOI: 10.3897/rio.2.e10610

Nico M. Franz, Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shawn Bowers, Alan S. Weakley, Bertram Ludäscher, Krysztof Janowicz, Benjamin Adams, Birgitta König-Ries, Deborah McGuinness, Mark Schildhauer (2016)
Names are not good enough: Reasoning over taxonomic change in the Andropogon complex1. Semantic Web 7: 645.

DOI: 10.3233/SW-160220

Beckett Sterner, Nico M. Franz (2017)
Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data. Biological Theory 12: 99.

DOI: 10.1007/s13752-017-0259-5

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 (2020)
Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes 6: .

DOI: 10.3897/rio.6.e57602

Cynthia S. Parr, Anne E. Thessen (2018)
Ecological Informatics. Chapter 17: 375.

DOI: 10.1007/978-3-319-59928-1_17