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Taxonomic identification keys on the web: tools for better knowledge differentiate between taxonomy and taxon biodiversity. Claves de identificación taxonómica en la web: herramientas para un mejor conocimiento de la biodiversidad. Miguel Murguía-Romero a. Bernardo Serrano-Estrada b. Enrique Ortiz a. 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 usabilitypolythetic 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. 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. El desconocimiento de ubicar gran parte de la biodiversidad en la jerarquia taxonómica es una limitante para enfrentar su crisis actual. Aqui se propone un esquema de sistema para la creación y uso de policlaves en la web, con la finalidad de proporcionar herramientas para la identificación de los taxones especies, géneros, familias, etc.
El sistema AbaTax www. In Mexico there are more than 23, native species of vascular plants Villaseñor,but knowledge about their geographical distribution is still deficient. The number of species in many areas of the country is underestimated and the current records of distribution do not cover their entire range Gómez-Pompa et al. Floristic knowledge can improve with new explorations and collections in poorly explored regions of the country. Another avenue for improvement is filling in gaps in information, especially the taxonomic identification of material that has already been collected and stored in herbaria but has not been curated at species level Villaseñor, The biodiversity crisis, where many species are becoming extinct mainly due to the loss of their natural habitat, is aggravated by the lack of knowledge of many species.
The correct taxonomic identification of organisms is essential to accelerate knowledge of biodiversity and reduce the negative effects of this crisis Villaseñor, Biological information derived from taxonomic studies is used as source of information in evolutionary work and the quality of taxonomic information used in phylogenetic studies is determinant of the quality of the results found.
Misidentification of organisms whose sequences are published in molecular databases -such as GenBank- can lead to erroneous results and inferences Nilsson et differentiate between taxonomy and taxon. The study of diversity patterns at different space-time scales requires inventories based on taxonomic units delimited and correctly identified under a system in which comparisons can be made between them, allowing the study of variations differentiate between taxonomy and taxon diversity Gotelli, Proper species identification is also key to the study of biodiversity distribution.
Inaccurate identification can not only provide erroneous estimates of species ranges of distribution, but also on the diversity and composition of communities, committing both biogeography studies and the identification of priority conservation areas Bortolus, Van Regenmortel considers that a classification of viruses based only on nucleotide sequences is a classification of genome sequences and not of viruses.
Molecular techniques can support the food science and quality control pdf of genome-based classifications, and will be useful for the identification of microorganisms, cryptic species or when only organic fragments are available; it should also be noted that these techniques are not without problems or criticism Nilsson et al.
On the other hand, most consider still necessary to maintain a taxonomy focused on morphology and its information is still valid in many areas of biological research Dunn, ; Gotelli, Integrative taxonomy, on the other hand, incorporates multiple sources of evidence, morphological, molecular, ecological, biogeographical, etc. Still in this modern approach, identification keys based on morphological characters are the tools that make taxonomic classifications operational and are fundamental for the knowledge of biodiversity, however this 21st century is the "era of molecular biology and genomics" Dunn, ; Scotland et al.
Strategies for automatic taxonomic identification systems can be classified into 2 large groups: identification supervised by a human and unsupervised differentiate between taxonomy and taxon. In the former group, there are computer programs such as IntKey Dallwitz et al. Among unsupervised identification systems are image recognition systems by automatic vision Bonnet et al.
These types of systems are designed for use by nonexperts, but they are still far from the effectiveness of expert taxonomists Bonnet et al. On the contrary, users of supervised identification systems can be non-experts or experts. The polythetic condition can be defined as a particularity of a class or group, for example a taxon, which is defined by a variable set, and is unique to the class of properties, none of which is necessarily present in each member of the class Dubois, Fig.
Specifically, in taxonomic identification, the polythetic condition is when a specimen can be associated with a taxon, not by a group of unique diagnostic characteristics, but by a set whose combination is unique. This polythetic condition, differentiate between taxonomy and taxon refers mainly to the classification process, can also be applied to the identification process, in which this condition is more likely, since in many cases some of the diagnostic characters used in the classification are not present or not observable in the identification process.
Many dichotomous keys are monothetic; however, when more than 1 route is provided for some taxa, they can be considered polythetic. In the unsupervised identification, the specimen can be identified as member of a taxon even without having information on its key or diagnostic characteristics Morse, Figure 1 Schematization of the difference between 'polythetic' and 'monothetic' concepts.
The presence of differentiate between taxonomy and taxon property is indicated by the number 1. Individuals constitute a polythetic group, where each individual records 3 of 4 properties and no property what is equity market risk premium common to all individuals. Individualsand form 3 monothetic classes with 3, 3 and 2 what is database explain in detail in hindi, respectively, present in all members.
Modified from Van Rijsbergen and Van Regenmortel A web search of tools for creating online keys makes evident several features of the state of the art that are useful to guide the development of these tools. The list shown in Table 1 is far from exhaustive, but it is effective to illustrate the current situation of development of interactive identification keys. The following issues can be identified: 1 there is no clear classification differentiate between taxonomy and taxon single dominant paradigm that guides the future developments of online keys; 2 no description of the computer development methodology used to develop the software is given; 3 neither the model nor the design criteria for the user interface is described; 4 the use of proprietary files is preponderant, whereas the use of relational databases is scarce, so effort expended in the development of one key cannot be easily harnessed for others; 5 features that have been technologically available for more than a decade continue to be underutilized, such as apps for cell phones, voice recognition, use of colors in the users interfaces as an important frame of communication, among others.
For example, these systems often do not use colors to communicate system states to the user, do not use responsive interfaces that adapt to the different types of devices according to the shape and size of the screen, or do not consider internet and cell phones as the predominant means of access to software and information.
Another important situation is that most of the points discussed above are referenced only on the web why use exploratory research design are not described in scientific publications. Table 1 Examples of online keys and differentiate between taxonomy and taxon programs to create them. In the development of software for taxonomic identification there is a delay in the incorporation of relational databases as a model of information representation.
Although relational databases were widely used in the early s, the field of taxonomic identification took almost 30 years to incorporate this technology. For example, one of the first programs that explicitly refers to the use of relational databases as a model for internal representation of information is the PANDORA program Pankhurst, The goal of this work is to present an identification tool, built as a web page that facilitates identification using already accessible keys, creates taxonomic identification keys, and publishes them immediately on the web for universal use.
This enterprise takes into account the current situation of the development of interactive differentiate between taxonomy and taxon keys, which includes various aspects that have not allowed the consolidation of solid paradigms of this type of tools. Also, the development process of the tool presented considers the most important features that informatics technology offers today, which have been underutilized or ignored in the multiple efforts to build interactive identification keys. This system allows the user to operate in 2 directions: by introducing information on the character states present in the specimen being identified and waiting for the system to report the taxa as possible identities, or the user can explore the character states that occur in a taxon considered as a possible hypothesis to refute or accept.
The system was designed following a three-layer architecture Fowler, : 1 the user interface, 2 the business layer or algorithms of the application, and 3 the data layer. The system design is based on: a the usability of the software, b polythetic identification, c the theoretical model of dynamic identification, and d the use of relational databases. The points b and c constitute the algorithms and methods that the system automates in layer does cheese cause dementia. Other important features considered during the design were the use of does ancestry dna sell your dna to indicate system states to the user, the construction of a responsive interface, that is, an interface that adapts to different devices' screen sizes, the use of cell phones and the possibility that the user may or may not be connected to the internet, the use of open source software for its construction as much as possible, and when open source software was unavailable, the use of free software, thus avoiding the payment of rights.
The usability of a system refers to the extent to which it can be used by users to achieve specific objectives with effectiveness, efficiency and satisfaction. It is important to underline that all this is within a specific context of use Bevan et al. One of the main features of the system's design in terms of usability was that it could be used from the web and on different types of devices. Therefore, we decided to use responsive web design technology Marcotte, : pages that detect the type of device from which the website is viewed so that decisions about the layout of the interface elements, such as buttons, menus, and windows, can be automatically optimized.
For example, on a desktop computer screen, the application can be presented with 2 windows that are displayed simultaneously, whereas on a cell phone, the application can show only 1 window at a time, with a link that allows the change of window to display. Another feature implemented is that the information on characters and differentiate between taxonomy and taxon states is presented to the user as monolithic statements, joining both in a single sentence. For example, the character state 'Tree or shrub' and its character 'Lifeform' are presented together with the statement 'Woody plants trees or shrubs '.
Storage in the database is done in a differentiated way, i. The identification algorithm used is polythetic; the taxa that remain as possible identities of the specimen under determination are those in which the presence of character states in the data matrix are recorded, constituting a subset of the presences indicated by the user as observable in the specimen. Polythetic identification is based on the fact that a particular combination of character states present in a specimen is only compatible linear equations in one variable definition 1 or few taxa represented in the data matrix by the union of the presences of character states of a large set of specimens of the same species or taxonomic group and which must include all the taxa in the lower category.
In this work, the various ways to refer to the type of taxonomic tools discussed here, such as multi-access keys, polykeys, interactive keys and online keys are considered synonyms. Regarding its first characteristic simplicityit is implemented considering 4 aspects: a the type of data of the taxonomic data differentiate between taxonomy and taxon is Boolean, that is to say 'true' or 'false'; b the concept of 'statement' is created, which is a sentence that specifies a character state along with the character to which it belongs; for example, the statement 'Woody plants trees or shrubs ' represents the pair 'character - character state' character: life form; character state: trees or shrubs ; c system with few windows, minimizing the need for navigation, and d scanning in 2 directions through the same interface; in one direction you can find out differentiate between taxonomy and taxon taxa present a certain set of character states and in the other the character states that are present in a given taxon or set of taxa.
Both axes represent character states indicated by the user; on the horizontal axis character states are explicitly indicated circles with solid lines ; on the vertical axis, the character states are indicated by an identification hypothesis the character states present in the hypothetical taxon, represented as circles with dashed lines. The shaded area logically represents the set of character states that may be present in the specimen being identified.
The possibility of indicating a hypothesis, that is, the name of the taxon suspected of being the identity of the specimen, makes explicit what age gap is normal of the supervised identification process. Since it is a human being who is interacting with the system rather than automatic image recognitionthe user refutes their own suspicions about the possible identities of the specimen, making an interactive user-system feedback process.
Currently the system does not implement denial, that is the possibility that the user indicates that a certain character state is not why do network drives disappear, or the denial of a hypothesis indicating that he suspects that a taxon is not the identity of the specimen.
Thus, only the quadrants in the corners of figure differentiate between taxonomy and taxon are implemented in the interface. This decision was made not because denial could not be programmed or implemented, but because of the complexity that it would add to the user interface, making it less understandable and intuitive. The information structure consists of a relational database that includes the tables specified by the user in the process of creating a polykey, such as the list of taxa, the list of statements character-character stateand the data matrix of character states present in taxa.
In addition, the database includes other tables that the system makes use for administrative purposes; for example, the catalog of polykeys in the what does readable mean in spanish or the users or types of access. The general structure of the database is described in the user manual differentiate between taxonomy and taxon the tool.
The design was implemented on a web platform called AbaTax www. The website can be used on any device cell phone, tablet or computer and adapts to display optimally on that device. Users can create their own polykeys by preparing Excel files in specific formats with lists of taxa, characters and character states, as well as the presence-absence data matrix.
This is explained in more detail in the section 'Creating polykeys in AbaTax'. If the files comply with the structure required by the system, the construction of the polykey only requires importing the files and recording some administrative data, such as names of the authors, name of the taxonomic group and date of creation. Several polykeys are currently available on can blood group a marry a AbaTax platform, mainly for plants, such as the FAMEX polykey for families of flowering plants Magnoliophyta of Mexico and the GENCOMEX polykey for the genera of Compositae of Mexico; additionally, there are 20 additional available publicly and 80 privately, accessible only to the user who created them or whoever decides to share the corresponding link and password.
The results of the system with the proposed design are shown below, exemplifying it with the FAMEX polykey and with the polykey differentiate between taxonomy and taxon species of Ageratina Asteraceae of the State of Mexico, both available for use and consultation at www. The dynamic identification interface was implemented using 2 lists Fig. The list of character states is displayed in a statement format composed of a single sentence that associates the character and character states to make the list more readable.
The list on the left shows the a character - character states, or b character state statements; the list on the right shows the list of possible taxa considered as identities of the specimen being determined. The symbol indicates the selected characters, and the taxa that comply with the selection are blue shaded. Figure 3 shows the interface when the user has selected 2 statements: herbaceous plants annual or perennial, including subshrubs and plants with thorns on stems or leaves.
At the top of the interface a message displays: selected character states: 2 of differentiate between taxonomy and taxon possible identities of the specimen: 49 of Throughout the session the user can select more statements, following their observations on the specimen, in order to reduce the list of possible identities of the specimen to a single taxon.