Taxonomic identification keys on the web: tools for better knowledge of biodiversity

Autores/as

DOI:

https://doi.org/10.22201/ib.20078706e.2021.92.3592

Palabras clave:

AbaTax, Biodiversity informatics, Dynamic identification, FAMEX, Magnoliophyta, Polykeys

Resumen

Difficulty in correctly identifying species in biological collections is an important impediment in confronting the current biodiversity crisis. The development of tools to improve taxonomic knowledge would help reverse this deficiency. Here, we propose an informatics system for the creation and use of polykeys on the web as tools for the identification of taxa (species, genera, families, etc.). The design is based on 4 actions: the ease of use of the software (usability), polythetic identification, a theoretical model of dynamic identification, and the use of relational databases. A system that applies this design is presented and exemplified using the FAMEX polykey, a tool for identifying the families of flowering plants (Magnoliophyta) of Mexico. The AbaTax system (www.abatax.abaco2.org) allows the creation of polykeys that are published and made available to all web users. The system considers the use of responsive web design, which is adapted in real time so that the interface is properly displayed to the type of device from which it is accessed, be it a desktop computer, laptop, tablet or cell phone.

Citas

Abdulrahaman, A. A., Asaju, I. B., Arigbede M. O., & Oladel, F. A. (2010). Computerized system for identification of some savanna tree species in Nigeria. Journal of Horticulture and Forestry, 2, 112–116.

Attigala, L., De Silva, N. I., & Clark, L. G. (2016). Simple Web-Based Interactive Key Development Software (WEBiKEY) and an Example Key for Kuruna (Poaceae: Bambusoideae). Applications in Plant Sciences, 4, 1500128. https://doi.org/10.3732/apps.1500128

Bittrich, V., Souza, C. S. D., Coelho, R. L. G., Martins, M. V., Hopkins, M. J. G., & Amaral, M. C. E. (2012). An interactive key (Lucid) for the identifying of the genera of seed plants from the Ducke Reserve, Manaus, AM, Brazil. Rodriguésia, 63, 55–64.

Bevan, N., Carter, J., Earthy, J., Geis, T., & Harker, S. (2016). New ISO standards for usability, usability reports and usability measures. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 9731, 268–278. https://doi.org/10.1007/978-3-319-39510-4_25

Bonnet, P., Joly, A., Goëau, H., Champ, J., Vignau, C., Molino, J. F. et al. (2015). Plant identification: man vs. machine: LifeCLEF 2014 plant identification challenge. Multimedia Tools and Applications, 75, 1647–1665. https://doi.org/10.1007/s11042-015-2607-4

Bortolus, A. (2008). Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology. AMBIO: A Journal of the Human Environment, 37, 114–118. https://doi.org/10.1579/0044-7447(2008)37[114:ECITBS]2.0.CO;2

Chrétiennot-Dinet, M. J., Desreumaux, N., & Vignes-Lebbe, R. (2014). An interactive key to the Chrysochromulina species (Haptophyta) described in the literature. Phytokeys, 34, 47–60. https://doi.org/10.3897/phytokeys.34.6242

Codd, E. F. (1970). A relational model of data for large shared data banks. Communications of the Association for Computing Machinery, 13, 377–387.

Codd, E. F. (1990). The relational model for database management: version 2. Boston, Massachusetts: Addison-Wesley Longman Publishing Co., Inc.

Dallwitz, M. J. (1980). A general system for coding taxonomic descriptions. Taxon, 29, 41–46.

Dallwitz, M. J., Paine, T. A., & Zurcher, E. J. (1995). User’s guide to Intkey: a program for interactive identification and information retrieval. Available at: http://delta-intkey.com

Dallwitz, M. J., Paine, T. A., & Zurcher, E. J. (1998). Interactive keys. In P. R. Scott, P. Bridge, P. Jeffries, & D. Morse (Eds.), Information technology, plant pathology and biodiversity (pp. 201–212). Wallingford, United Kingdom: CAB International.

Dallwitz, M. J., Paine, T. A., & Zurcher, E. J. (2000). Principles of interactive keys. Available at: http://delta-intkey.com/www/interactivekeys.pdf

Dmitriev, D. A. (2006). 3I, a new program for creating Internet-accessible interactive keys and taxonomic databases and its application for taxonomy of Cicadina (Homoptera). Russian Entomological Journal, 15, 263–268.

Dubois, A. (2017). Diagnoses in zoological taxonomy and nomenclature. Bionomina, 12, 63–85.

Dunn, C. P. (2003). Keeping taxonomy based in morphology. Trends in Ecology & Evolution, 6, 270–271. https://doi.org/10.1016/S0169-5347(03)00094-6

Fowler, M. (2002). Patterns of enterprise application Architecture. Boston, Massachusetts: Addison-Wesley Longman Publishing Co., Inc.

Gaston, K. J., & O’Neill, M. A. (2004). Automated species identification: why not? Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 359, 655–667.

Gómez-Pompa, A., Krömer, T., & Castro-Cortés, R. (2010). Atlas de la flora de Veracruz: un patrimonio natural en peligro. Veracruz: Universidad Veracruzana/ Gobierno del Estado de Veracruz.

Gotelli, N. J. (2004). A taxonomic wish-list for community ecology. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 359, 585–597. https://doi.org/10.1098/rstb.2003.1443

Gries, C., Gilbert, E. E., & Franz, N. M. (2014). Symbiota - A virtual platform for creating voucher-based biodiversity information communities. Biodiversity Data Journal, 2, e1114. https://doi.org/10.3897/BDJ.2.e1114

Koleff, P., Soberón, J., Arita, H. T., Dávila, P., Flores-Villela. O., Golubov, J. et al (2008). Patrones de diversidad espacial en grupos selectos de especies. In Conabio (Ed.), Capital natural de México, Vol. II: estado de conservación y tendencias de cambio (pp. 323–364). México D.F.: Comisión Nacional para el Conocimiento y Uso de la Biodiversidad.

Marcotte, E. (2010). Responsive web design. París: A Book Apart. Available at: http://www.reprosol.be/sites/reprosol.beta.the-aim.be/files/responsive-webdesign(ethan-marcotte).pdf

Morse, L. E. (1975). Recent advances in the theory and practice of biological specimen identification. In R. J. Pankhurst (Ed.), Biological identification with computers (pp. 11–52). London and Orlando: Academic Press.

Murguía-Romero, M. (1987). FAMEX, policlave para la identificación de Magnoliophyta de México (Bachelor Thesis). Facultad de Ciencias, Universidad Nacional Autónoma de México. México D.F.

Murguía-Romero, M. (1992). Métodos en la identificación biológica automatizada (Master Thesis). Facultad de Ciencias, Universidad Nacional Autónoma de México. México D.F. http://132.248.9.195/pmig2017/0187269/Index.html

Murguía-Romero, M., & Villaseñor, J. L. (1992). La computadora en la identificación botánica. Ciencia y Desarrollo (México), 18, 130–137.

Murguía-Romero, M., & Villaseñor, J. L. (1993). FAMEX: Policlave para familias de plantas con flores (Magnoliophyta) de México. México D.F.: Asociación de Biólogos Amigos de la Computación, A.C.

Murguía-Romero, M., & Villaseñor, J. L. (1998). GENCOMEX: a computerized key for identify the genera of Asteraceae of Mexico. In P. R. Scott, P. Bridge, P. Jeffries, & D. Morse (Eds.), Information technology, plant pathology and biodiversity (pp. 305–314). Wallingford, United Kingdom: CAB International.

Nilsson, R. H., Ryberg, M., Kristiansson, E., Abarenkov, K., Larsson, K. H., & Kõljalg, U. (2006). Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. Plos One, 1, e59. https://doi.org/10.1371/journal.pone.0000059

Norton, G. A, Patterson, D. J., & Schneider, M. (2012). LucID: a multimedia educational tool for identification and diagnostics. International Journal of Innovation in Science and Mathematics Education, 4, 2000.

Pankhurst, R. J. (1991). Practical taxonomic computing. Cambridge, United Kingdom: Cambridge University Press.

Pankhurst, R. J. (1998). A historical review of identification by computer. In P. R. Scott, P. Bridge, P. Jeffries, & D. Morse (Eds.), Information technology, plant pathology and biodiversity (pp. 305–314). Wallingford, United Kingdom: CAB International.

Penev, L., Sharkey, M., Erwin, T., van Noort, S., Buffington, M., Seltmann, K. et al. (2009). Data publication and dissemination of interactive keys under the open access model. Zookeys, 21, 1–17. https://doi.org/10.3897/zookeys.21.274

Rajpoot, A., Kumar, V. P., Bahuguna, A., & Kumar, D. (2016). DNA barcoding and traditional taxonomy: an integrative approach. International Journal of Current Research, 8, 42025–42031.

Rojas-Cortés, Á. P. (2017). Manual de identificación con base en atributos foliares de los árboles de la estación de biología tropical Los Tuxtlas, Veracruz (Master Thesis). Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México. Morelia, Michoacán, México.

Scotland, R., Hughes, C., Bailey, D., & Wortley, A. (2003) The big machine and the much-maligned taxonomist DNA taxonomy and the web. Systematics and Biodiversity, 1, 139–143. https://doi.org/10.1017/S1477200003001178

Seltmann, K. (2004). Building Web-based interactive keys to the Hymenopteran families and superfamilies (Master Thesis). College of Agriculture, University of Kentucky. Lexington, Kentucky.

Sheth, B. P., & Thaker, V. S. (2017). DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation. Genome, 60, 618–628. https://doi.org/10.1139/gen-2015-0167

Sosa, V., & Dávila, P. (1994). Una evaluación del conocimiento florístico de México. Annals of the Missouri Botanical Garden, 81, 749–757.

Van Regenmortel, M. H. V. (2016). Classes, taxa and categories in hierarchical virus classification: a review of current debates on definitions and names of virus species. Bionomina, 10, 1–21.

Van Rijsbergen, K. (1979). Information retrieval. London: Butterworths.

Villaseñor, J. L. (2015). ¿La crisis de la biodiversidad es la crisis de la taxonomía? Botanical Sciences, 93, 3–14. https://doi.org/10.17129/botsci.456

Villaseñor, J. L. (2016). Checklist of the native vascular plants of Mexico. Revista Mexicana de Biodiversidad, 87, 559–902. https://doi.org/10.1016/j.rmb.2016.06.017

Villaseñor, J. L., Maeda, P., López, J. J. C., & Ortiz, E. (2005). Estimación de la riqueza de especies de Asteraceae mediante extrapolación a partir de datos de presencia-ausencia. Boletín de la Sociedad Botánica de México, 76, 5–18.

Walter, D. E., & Winterton, S. (2007). Keys and the crisis in taxonomy: extinction or reinvention? Annual Review of Entomology, 52, 193–208. https://doi.org/10.1146/annurev.ento.51.110104.151054

Watson, A. T, O’Neill, M. A., & Kitching, I. J. (2004). A qualitative study investigating automated identification of living macrolepidoptera using the Digital Automated Identification SYstem (DAISY). Systematics and Biodiversity, 1, 287–300.

Weeks, P., Gauld, I., Gaston, K., & O’Neill, M. (1997). Automating the identification of insects: A new solution to an old problem. Bulletin of Entomological Research, 87, 203–211. https://doi.org/10.1017/S000748530002736X

Will, K. W., & Rubinoff, D. (2004). Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics, 20, 47–55. https://doi.org/10.1111/j.1096-0031.2003.00008.x

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Publicado

2021-09-13

Número

Sección

TAXONOMÍA Y SISTEMÁTICA