User's Manual

version 5 Building taxanomic keys on the web User’s Manual Abatax. User’s Manual www.abatax.abaco2.org AbaTax v5. Bulding taxonomic keys on the web User’s Manual Miguel Murguía Romero Unidad de Informática para la Biodiversidad (UNIBIO), Instituto de Biología, UNAM www.unibio.abaco2.org Asociación de Biólogos Amigos de la Computación A.C. www.abaco2.org Bernardo Serrano Estrada SERES Sistemas Especializados. www.seresespecializados.com © SERES Sistemas Especializados © Asociación de Biólogos Amigos de la Computación A.C. México, 2021 How to cite: Murguía-Romero, M & B Serrano-Estrada. 2021. AbaTax version 5. Building taxonomic keys on the web. User’s Maual. Revista ABACo. January 2021. Mexico City. http://www.abacoac.org/revista/ Page 2 / 45 Abatax. User’s Manual Index 1\ Objectives of AbaTax .......................................................................................................................... 4 2\ The AbaTax web page ......................................................................................................................... 5 3\ Basic use of an AbaTax polykey ........................................................................................................ 9 4\ The dynamic identification model .................................................................................................. 13 5\ The dinanic identification environment AID ............................................................................... 15 6 \ Find out the character states of a taxon ......................................................................................... 21 7 \ Images in the AID ............................................................................................................................. 23 8 \ Generating taxonomic descriptions ............................................................................................... 24 9 \ Browse a polykey database.............................................................................................................. 25 10 \ Reports and statistics of a polikey ................................................................................................ 26 11 \ Creation of polykeys in AbaTax .................................................................................................... 27 12 \ Public keys and private keys ........................................................................................................... 33 13 \ Documentation associated with a polikey ................................................................................... 34 14 \ Collaborative work with policlaves ............................................................................................. 35 15 \ Improving the quality of taxonomic descriptions ..................................................................... 36 16 \ AbaTax App for Cell Phones ........................................................................................................ 39 17 \ Tools linked to AbaTax .................................................................................................................. 41 18 \ Interactive lists: other uses of AID ............................................................................................... 42 References ................................................................................................................................................. 43 Glossary ................................................................................................................................................... 44 Page 3 / 45 Abatax. User’s Manual 1\ Objectives of AbaTax 1.1\ What is AbaTax? AbaTax is a web page for the creation and use of taxonomic identification keys. For the user who wishes to identify an organism, it provides an agile and easy way to indicate the characteristics observed in it in order to obtain a list of possible identities, and in the best of cases the taxon to which it belongs. For the taxonomist who wants to create an identification polykey, AbaTax provides an easy way to generate it and make it available on the web. 1.2\ New characteristics of AbaTax 5 In version 5 of AbaTax, improvements have been incorporated, both for the user who wishes to identify a biological organism, and for the taxonomist who wishes to create a key. In the first case, the option of a new way of displaying the characteristics and states of an alternative character to that of the "statement" that AbaTax has traditionally provided has been incorporated: now both formats are available at the user's choice, both in the form of the “character-character state” paradigm, like the usual and integrative list of “statements” that the interface has always shown. In the second case, that is, whoever wants to create a key in AbaTax, an agile way is provided to import from Excel sheets the specification of the various elements of the polykey; Another important new facility is the way to edit the data matrix, with simple checkboxes and an easy way to navigate. 1.3\ The biodiversity crisis This new version 5 will help promote the use and creation of keys on the web and thereby contribute to the study and knowledge of biodiversity, objectives today so important in the face of the biodiversity crisis in which humans have caused a massive extinction of species at a higher rate than we can get to know something about them. Page 4 / 45 Abatax. User’s Manual 2\ The AbaTax web page 2.1\ Home page When entering the AbaTax address www.abatax.abaco2.org in the web browser, the home screen is displayed (Figure 2.1). This interface provides a "level 1 navigation", that is, the user does not have to navigate through labyrinthine options, but rather a single control panel is provided. Figure 2.1\ AbaTax home page From the home page you can consult a key to run it, or create a new key. The functionality of the elements of the AbaTax home interface is described in Table 2.1. Page 5 / 45 Abatax. User’s Manual Table 2.1\ Functionality of the AbaTax home interface elements. Icon Name Functionality “Home” button Returns to the list of key Hamburguer menu Displays options with information about the system Login/Logout Allows to enter (or quit) to a session with a user account User’s ID First letters of the user’s name. It identifies that the user is on a session Select language Identifies or select the actual language: Spanish, English or Italian Left window Menu with contextual options depending on the content of the right window, for example, “List of keys”, “Dynamic Interface”, “Matrix edition”, ... Right window Presents the relevant information: for example, “List of keys”, “Dynamic Interface”, “Matrix edition”, … Hide left window Allows to display only the right window, or both at the same time. Useful when using in a mobile. Pagination of Defines the number of rows per page to visualize results in the list, and forward or backward between pages Filter rows Activates the filter for specific values in the list of keys Upper band Header that shows the name of the software and its logo Menu bar Contains functional icons and presents the name of the active key Lower band Years of the first and last version, and name of the creators Page 6 / 45 Abatax. User’s Manual 2.2\ Using a key To use a key, just click on the name of the desired one, for example, “FAMEX”. The contents of both windows will change and the name of the active key will be indicated in the menu bar. The right window will contain the "Dynamic identification environment", that is, the polikey itself, through which the user can indicate the characteristics of the specimen under identification. This environment is explained in detail in chapter “5\ The dynamic identification environment” (AID, for its initials in Spanish). In the left window a menu will be displayed with options that lead to viewing or modifying information on the active key, as well as tools for its analysis. 2.3\ User’s registration The public keys can be used without registering in AbaTax. Some other operations, such as creating a polikey or collaborating with other users, will require registration in order to create a user. Depending on the permissions assigned by the owner of each key, they may or may not be accessible. To create a user and register as an AbaTax user, select the login/logout icon at the top right (Figure 2.1); A menu will be displayed from which you have to select “Register”, which in turn will show a window to enter the registration data (Figure 2.2). Figure 2.2\ Aspect of the registration page Page 7 / 45 Abatax. User’s Manual 2.4\ Operations that require login The use of AbaTax can be done by entering the page directly and without the need for a user. This form of entry allows the use of all public keys. When it is required to build or edit a key, it is necessary to login and enter with username and password. It is necessary because it is the way in which the system identifies which are the user's keys or in which they have been registered as a collaborator. Thus, when logging in with username and password, the left window shows the option "MyKeys" which when selected shows the list of keys of which the user is the author or contributor. 2.5\ I forgot my password Through the option "I forgot my password" from the user menu, people can reset their password by entering the email with which they registered and a link will be sent (with 10 minutes expiration) to enter the new password (Figure 2.3) . a) b) Figure 2.3\ “I forgot my password”. a) User menu where the

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