An Xper3 reference guide for taxonomists: a collaborative system for identification keys and descriptive data
Abstract
The Xper3 software enables collaborative management of descriptive data on taxa. This paper focuses on the essential information about the knowledge model that underlies the software, its features and user interface which has been evolving since 2014. The best practices for representing taxonomic descriptions, managing polymorphism and missing data in a consistent way are also presented. Its ease of use and the versatility of its data model mean that the software can be used to create and distribute identification keys for all types of taxa.
References
Abdellahoum Z., Nebbak A., Lafri I., Kaced A., Bouhenna M.M., Bachari K., Boumegoura A., Agred R., Boudchicha R.H., Smadi M.A., Maurin M. & Bitam I. 2022. Identification of Algerian field-caught mosquito vectors by MALDI-TOF MS. Veterinary Parasitology: Regional Studies and Reports 31: 100735. https://doi.org/10.1016/j.vprsr.2022.100735
Agathokleous E., Saitanis C.J., Fang C. & Yu Z. 2023. Use of ChatGPT: What does it mean for biology and environmental science? Science of The Total Environment 888: 164154. https://doi.org/10.1016/j.scitotenv.2023.164154
Aide T.M., Corrada-Bravo C., Campos-Cerqueira M., Milan C., Vega G. & Alvarez R. 2013. Real-time bioacoustics monitoring and automated species identification. PeerJ 1: e103. https://doi.org/10.7717/peerj.103
Bartlett P., Eberhardt U. & Beker H.J. 2022. Demystifying Hebeloma: introducing hebeloma.org and its database. IMA Fungus 13 (1): 18. https://doi.org/10.1186/s43008-022-00105-2
Beentje H. 2010. The Kew Plant Glossary: An Illustrated Dictionary of Plant Terms. Royal Botanic Gardens Kew, UK.
Bodin S.C., Scheel-Ybert R., Beauchêne J., Molino J.-F. & Bremond L. 2019. CharKey: an electronic identification key for wood charcoals of French Guiana. IAWA Journal 40 (1): 75-S20. https://doi.org/10.1163/22941932-40190227
Burguiere T., Causse F., Ung V. & Vignes-Lebbe R. 2013. IKey+: a new single-access key generation web service. Systematic Biology 62 (1): 157–161. https://doi.org/10.1093/sysbio/sys069
Dallwitz M.J. 1980. A general system for coding taxonomic descriptions. TAXON 29 (1): 41–46. https://doi.org/10.2307/1219595
Dallwitz M.J., Paine T.A. & Zurcher E.J. 2018. Principles of interactive keys. Available from https://www.delta-intkey.com/www/interactivekeys.htm [accessed on 25 May 2023].
Darmoni S.J., Lebbe J., Vignes R. & Poynard T. 1993. MAKEY : génération automatique d’un algorithme clinique pour aider le diagnostic sérologique de l’hépatite virale aiguë. Informatique et Santé 15: 49–55.
Del Rio C., Stull G.W. & De Franceschi D. 2020. Survey of the fruits and endocarps of Icacinaceae (Lamiids, Icacinales). European Journal of Taxonomy 645: 1–130. https://doi.org/10.5852/ejt.2020.645
Dubuisson J.-Y., Bouquin S. & Vignes Lebbe R. 2018. Computer assisted identification: Xper and orchids of France. L’Orchidophile 219: 311–318.
Gautam N. & Sidhu M.C. 2023. An alternative key for identifying three prostrate species of the genus Euphorbia. Botanica 29 (1): 21–27. https://doi.org/10.35513/Botlit.2023.1.3
Gérard D. & Vignes Lebbe R. 2010. MyKey: a server-side software to create customized decision trees. In: Nimis P.L. & Vignes Lebbe R. (eds) Tools for Identifying Biodiversity: Progress and Problems: 107–112. Trieste.
Goëau H., Bonnet P. & Joly A. 2021. AI-based identification of plant photographs from herbarium specimens. Biodiversity Information Science and Standards 5: e73751. https://doi.org/10.3897/biss.5.73751
Goharimanesh M., Stöhr S., Mirshamsi O., Ghassemzadeh F. & Adriaens D. 2021. Interactive identification key to all brittle star families (Echinodermata; Ophiuroidea) leads to revised morphological descriptions. European Journal of Taxonomy 766: 1–63. https://doi.org/10.5852/ejt.2021.766.1483
Gourraud A., Vignes Lebbe R., Kerner A. & Pignal M. 2021. Architectural pattern: study of orchid architecture using tools to take quick measurements of virtual specimens. Biodiversity Information Science and Standards 5: e75752. https://doi.org/10.3897/biss.5.75752
Hagedorn G. 2007. Structuring descriptive data of organisms — Requirement analysis and information models (Strukturierung organismischer Beschreibungsdaten – Anforderungsanalyse und Informationsmodelle). Universität Bayreuth.
Hagedorn G., Rambold G. & Martellos S. 2010. Types of identification keys. In: Nimis P.L. & Vignes Lebbe R. (eds) Tools for Identifying Biodiversity: Progress and Problems: 59–64.
Hays L.-M. & Kerner A. 2020. Virtual systematics with annotate: the Mexican archaeocyaths example. Biodiversity Information Science and Standards 4: e59106. https://doi.org/10.3897/biss.4.59106
Hebert P.D.N. & Gregory T.R. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54 (5): 852–859. https://doi.org/10.1080/10635150500354886
Hilgenhof R., Gagnon E., Knapp S., Aubriot X., Tepe E.J., Bohs L., Giacomin L.L., Gouvêa Y.F., Martine C.T., Orejuela A., Orozco C.I., Peralta I.E. & Särkinen T. 2023. Morphological trait evolution in Solanum (Solanaceae): evolutionary lability of key taxonomic characters. Taxon 72 (4): 811–847. https://doi.org/10.1002/tax.12990
Jouveau S., Delaunay M., Vignes-Lebbe R. & Nattier R. 2018. A multi-access identification key based on colour patterns in ladybirds (Coleoptera, Coccinellidae). ZooKeys 758: 55–73. https://doi.org/10.3897/zookeys.758.22171
Kerner A. 2022. De rat de bibliothèque à pro de la souris. In: Paléontologie d’aujourd’hui: 122–123. EDP Sciences.
Kerner A. & Levy C. 2023. E-taxonomy, Open Science, and FAIR Principles: a comparison of how taxon descriptions are computerized. Biodiversity Information Science and Standards 7: e110459. https://doi.org/10.3897/biss.7.110459
Kerner A. & Vignes Lebbe R. 2016. Knowledge base with XPER3 in palaeontology: calculated descriptors offer new functionalities. TDWG 2016 Santa Clara de San Carlos, Costa Rica.
Kerner A. & Vignes Lebbe R. 2019. Multi-context knowledge base using calculated descriptors from Xper3: the archaeocyaths knowledge base example. Biodiversity Information Science and Standards 3: e37083. https://doi.org/10.3897/biss.3.37083
Kerner A., Bouquin S., Portier R. & Vignes Lebbe R. 2021. The 8 years of existence of Xper3: state of the art and future developments of the platform. Biodiversity Information Science and Standards 5: e74250. https://doi.org/10.3897/biss.5.74250
Klopfstein S., Broad G.R., Urfer K., Vårdal H. & Haraldseide H. 2022. An interactive key to the European genera of Campopleginae (Hymenoptera, Ichneumonidae) and 20 new species for Sweden. Entomologisk Tidskrift 143: 121–156.
Koch W. 2023. Capturing and using taxonomic knowledge for species identification. Biodiversity Information Science and Standards 7: e110957. https://doi.org/10.3897/biss.7.110957
Lebbe J. 1991. Représentation des concepts en biologie et en médecine : introduction à l’analyse des connaissances et à l’identification assistée par ordinateur. Université Pierre et Marie Curie.
Lebbe J. & Vignes R. 1991. Génération de graphes d’identification à partir de descriptions de concepts. In: Induction symbolique et numérique à partir de données. Cepadues: 193–239. Cepadues, Toulouse, France.
Lebbe J., Vignes R. & Dedet J.P. 1989. Computer-aided identification of insect vectors. Parasitology Today 5 (9): 301–304. https://doi.org/10.1016/0169-4758(89)90025-2
Linchamps P., Avery D.M., Cornette R., Denys C., Matthews T. & Stoetzel E. 2023. Quaternary rodents of South Africa: A companion guide for cranio-dental identification. PLoS ONE 18 (11): e0289812. https://doi.org/10.1371/journal.pone.0289812
Lombard N., Le Roux M.M. & van Wyk B.-E. 2021. Electronic identification keys for species with cryptic morphological characters: a feasibility study using some Thesium species. PhytoKeys 172: 97–119. https://doi.org/10.3897/phytokeys.172.53484
Maddison D.R., Swofford D.L. & Maddison W.P. 1997. Nexus: an extensible file format for systematic information. Systematic Biology 46 (4): 590–621. https://doi.org/10.1093/sysbio/46.4.590
Nimis P.L. & Vignes-Lebbe R. 2010. Tools for Identifying Biodiversity: Progress and Problems. Universita di Trieste, Trieste, Italy.
Norton G.A., Patterson D.J. & Schneider M. 2000. LucID: a multimedia educational tool for identification and diagnostics. International Journal of Innovation in Science and Mathematics Education 4 (1): 15–22.
Open Science 2023. Trends and best practices in open science. Available from https://openscience.eu/ [accessed on 15 May 2024].
Palomares-Rius J.E., León-Ropero G., Clavero-Camacho I., Archidona-Yuste A., Cantalapiedra-Navarrete C. & Castillo P. 2022. A new interactive web-based polytomous key for species identification of pin nematodes of the genus Paratylenchus Micoletzky, 1922 (Nematoda: Paratylenchinae) with the use of ribosomal and mitochondrial genes. Journal of Zoological Systematics and Evolutionary Research 2022: 6216266. https://doi.org/10.1155/2022/6216266
Pankhurst R.J. 1970. Key generation by computer. Nature 227 (5264): 1269–1270. https://doi.org/10.1038/2271269a0
Pellen F., Bouquin S., Mougenot I. & Vignes-Lebbe R. 2018. Building an OWL ontology with Xper3. Biodiversity Information Science and Standards 2: e25614. https://doi.org/10.3897/biss.2.25614
Picek L., Šulc M., Patel Y. & Matas J. 2022. Plant recognition by AI: deep neural nets, transformers, and kNN in deep embeddings. Frontiers in Plant Science 13: 787527. https://doi.org/10.3389/fpls.2022.787527
Pignal M., Laudereau C. & Laudereau P.-L. 2023. Liste annotée des Goodyerinae Klotzsch (Orchidaceae) de Nouvelle-Calédonie avec la description de deux nouvelles espèces. Adansonia 45 (19): 307–325. https://doi.org/10.5252/adansonia2023v45a19
Pignal M., Bertin G., Chupin L., Perez Pimparé E., Klasnja S., Vignes Lebbe R. & Dusoulier F. 2024. Récolnat Annotate-On: a tool to improve your experience with virtual collections. Adansonia 46 (13): 133–148. https://doi.org/10.5252/adansonia2024v46a13
Pinel A., Bouquin S., Bourdon E., Kerner A. & Vignes-Lebbe R. 2017. Three years of Xper3 assessment: towards sharing semantic taxonomic content of identification keys. Proceedings of TDWG 1: e20382. https://doi.org/10.3897/tdwgproceedings.1.20382
Porcher M.-L. 2022. Terminologie associée au processus de diagnose des espèces : un service de formalisation pour l’interopérabilité sémantique. Master 2 thesis, Sorbonne Université-MNHN.
Saïd A.H., Hennequin S., Rouhan G. & Dubuisson J.-Y. 2017. Disentangling the diversity and taxonomy of Hymenophyllaceae (Hymenophyllales, Polypodiidae) in the Comoros. European Journal of Taxonomy 313: 1–53. https://doi.org/10.5852/ejt.2017.313
Santos Neves M.S.A., Motta M.A., Maciel-De-Freitas R., Da Silva Xavier A., Lourenço-De-Oliveira R. & Silva-Do-Nascimento T.F. 2024. Illustrated identification key to females of the genus Sabethes Robineau-Desvoidy recorded from Brazil (Diptera: Culicidae), in dichotomous and interactive formats, including an updated list of species and new records for the states. Zootaxa 5406 (2): 253–287. https://doi.org/10.11646/zootaxa.5406.2.3
Saucède T., Eléaume M., Jossart Q., Moreau C., Downey R., Bax N., Sands C., Mercado B., Gallut C. & Vignes-Lebbe R. 2021. Taxonomy 2.0: computer-aided identification tools to assist Antarctic biologists in the field and in the laboratory. Antarctic Science 33 (1): 39–51.
Schneider C., Minor M.A. & D’Haese C.A. 2023. A new group of species of the genus Megalothorax (Collembola, Neelidae) with Gondwanan distribution, and introducing an open interactive identification key of Megalothoraxspecies. Zootaxa 5228 (2): 101–121. https://doi.org/10.11646/zootaxa.5228.2.1
Structure of Descriptive Data Subgroup 2005. Structured Descriptive Data (SDD). Biodiversity Information Standards (TDWG). Available from https://www.tdwg.org/standards/sdd/ [accessed on 15 May 2024].
Taberlet P., Coissac E., Pompanon F., Brochmann C. & Willerslev E. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology 21 (8): 2045–2050. https://doi.org/10.1111/j.1365-294X.2012.05470.x
Vignes Lebbe R., Chesselet P. & Diep Thi M.H. 2016. Xper3: nouveaux outils pour le travail collaboratif, la formation et la transmission des connaissances sur les phénotypes végétaux. In: Botanists of the Twenty First Century: Roles, Challenges and Opportunities: Based on the Proceedings of UNESCO International Conference, 22–25 September 2014, Paris, France. UNESCO: 228–239. UNESCO, Paris, France.
Wilkinson M.D., Dumontier M., Aalbersberg I.J., Appleton G., Axton M., Baak A., Blomberg N., Boiten J.-W., Da Silva Santos L.B., Bourne P.E., Bouwman J., Brookes A.J., Clark T., Crosas M., Dillo I., Dumon O., Edmunds S., Evelo C.T., Finkers R., Gonzalez-Beltran A., Gray A.J.G., Groth P., Goble C., Grethe J.S., Heringa J., ’T Hoen P.A.C., Hooft R., Kuhn T., Kok R., Kok J., Lusher S.J., Martone M.E., Mons A., Packer A.L., Persson B., Rocca-Serra P., Roos M., Van Schaik R., Sansone S.-A., Schultes E., Sengstag T., Slater T., Strawn G., Swertz M.A., Thompson M., Van Der Lei J., Van Mulligen E., Velterop J., Waagmeester A., Wittenburg P., Wolstencroft K., Zhao J. & Mons B. 2016.
The FAIR guiding principles for scientific data management and stewardship. Scientific Data 3 (1): 160018. https://doi.org/10.1038/sdata.2016.18
Copyright (c) 2025 Adeline Kerner, Elie Mario Saliba, Sylvain Bouquin, Rémy Portier, Régine Vignes-Lebbe
This work is licensed under a Creative Commons Attribution 4.0 International License.
Creative Commons Copyright Notices
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License (CC BY 4.0) that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are NOT PERMITTED to post their submitted work online (e.g., in institutional repositories or on personal websites) prior to publication, as it may lead to nomenclatural issues.
