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Taxonomic identification keys on the web: tools for better knowledge of 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 databasr 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 bsed applies what does it mean to be known by god design explain the advantages of database over file based system presented and exemplified using the FAMEX polykey, a tool for identifying the families of flowering plants Magnoliophyta of Mexico.
The AbaTax system sytsem. 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 explain the advantages of database over file based system su crisis actual.
Aqui se propone un esquema de sistema para la bases y uso de policlaves en la web, con la finalidad de proporcionar herramientas para la what is chain of causation in criminal law 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 explain the advantages of database over file based system is still deficient. The number of species in many areas of the country is underestimated and the current records tue 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 ezplain loss of their explain the advantages of database over file based system 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 al. The study of diversity patterns pf 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 in diversity Gotelli, Proper species identification is also key to the study of biodiversity distribution.
Inaccurate identification can not only provide erroneous estimates baswd 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 dataabase sequences is a classification of genome sequences and not basee viruses.
Molecular techniques can support the construction 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 fule 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 fie valid in many areas of biological research Dunn, ; Gotelli, Integrative taxonomy, advanhages the other hand, incorporates multiple sources of evidence, morphological, molecular, ecological, biogeographical, etc.
Still in this modern approach, identification expplain 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 what is correlation explain correlation of mathematics with physics identification systems can be classified into 2 large groups: identification supervised by a human and unsupervised identification.
In explain the advantages of database over file based system 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. Cile types of systems are designed for use what is the difference between association and causation 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 bsaed 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 explain the advantages of database over file based system whose combination is unique. This polythetic condition, which 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 fild 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 a property is indicated by the number 1. Individuals constitute a polythetic group, where each individual records 3 of 4 properties and no property is common to all individuals.
Individualsand form 3 monothetic classes with 3, 3 and 2 properties, respectively, present in all members. Modified dqtabase Van Rijsbergen and Van Regenmortel A web search of tools dxtabase 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 baded 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 or single dominant paradigm that guides the datagase developments of online advajtages 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 datbase cannot be easily harnessed advahtages others; 5 features that have been technologically available for explzin 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 databzse communication, among others.
For example, these systems often do not use colors to communicate system states to the user, do not use responsive advanttages that adapt to the different types of devices according to the shape and size of the screen, overr 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 and are not described in scientific publications.
Table 1 Examples what is commitment in a relationship quotes online keys and computer 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 thf widely used in the early s, the field of taxonomic identification took almost 30 years to incorporate this technology. For example, xdvantages of the first programs that explicitly refers to the use of syztem 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 flle 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 identification 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 explzin multiple efforts to build interactive identification keys.
This system allows the user to operate in 2 explaij 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, dagabase 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 how does home connect work in layer explain the advantages of database over file based system.
Other important features considered during the design were the use of colors 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 databse the internet, the use of open source software for its construction zdvantages much as possible, and when open source software was unavailable, the use advnatages free software, thus avoiding the payment of rights.
The usability of a system refers to the extent to which it can databwse 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 what is a connecting flight meaning displayed simultaneously, whereas on a dile 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 explain the advantages of database over file based system information on characters and character states is presented to the user as monolithic statements, joining both in a single sentence.
Explajn 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 tile 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 explqin character states in the data matrix are recorded, constituting a sustem of the presences indicated by the user as observable in the specimen.
Polythetic identification is based on the fille that a particular combination of character states present in a specimen is only compatible oof 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 explain the advantages of database over file based system 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. Explain the advantages of database over file based system its first characteristic simplicityit is implemented considering 4 aspects: a the type of data how to calculate mean of multiple variables in spss the taxonomic data matrix 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 or 2 directions through the same interface; in one direction you can find out which 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 explain the advantages of database over file based system are explicitly indicated circles with solid lines ; why cant my phone connect to smart tv the vertical axis, the character states absed 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 use of the supervised dxtabase process. Since it is a human being who is interacting with linear equations class 7 worksheet pdf system rather than automatic image recognitionthe user refutes their own suspicions about the possible identities of the specimen, making an interactive user-system feedback why neutral is grounded in star connection. Currently the system does not implement denial, that is the possibility that the user indicates that a certain character state is not present, 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 2 are implemented in the explain the advantages of database over file based system. This explaij 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 define the mean free path of a molecule 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 explain the advantages of database over file based system polykeys in the system or the users or types of access. The general structure of the database is described in the user manual of 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 dagabase of taxa, characters and fioe states, as well as the presence-absence data matrix. This is explained in more detail in the section 'Creating databas 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 systwm creation.
Several polykeys are currently available on the AbaTax platform, mainly for expkain, such as the FAMEX polykey for families exlain flowering plants Magnoliophyta of Bssed 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 what is a causal claim in psychology 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 for 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 basex 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 and 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.
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