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/

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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

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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.

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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.

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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

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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

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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 option "Forgot password" is displayed; b) "Forgot password" dialog.

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3\ Basic use of an AbaTax polykey

This chapter explains the steps to use a polykey in the way most commonly required by a user:

Step 1. Access AbaTax Step 2. Choose the desired key Step 3. Indicate the list of character states observed in the specimen Step 4. Verify the description of the taxon possible identity Step 5. Deselect the states and start a new session

3.1\ Step 1. Access AbaTax

AbaTax is a tool for free and universal use, so to access it, simply enter the following address in any web browser: www.abatax.abaco2.org

In general, AbaTax runs adequately on any web browser, as the developers have tested it on the most used ones, such as MS Edge, Firefox, Opera, Chrome and Safari. However, the Internet environment constantly makes new restrictions, so AbaTax is constantly updated and it is possible that at a certain point, with a certain version of a browser, it stops working, such is the case of Microsoft's Internet Explorer that has been replaced by the Edge browser, so the first one is no longer maintained and therefore the AbaTax developers will not be testing that it works properly in this already discontinued browser.

3.2\ Step 2. Choose the desired key

After entering the AbaTax web address, the browser establishes contact with the server where the AbaTax system resides, and two groups of information are read and transferred through the internet: i) the graphic elements of the interface, and ii) the elements of the AbaTax database, such as the list of public keys. It is then that the user can see the environment on his screen with the left menu and the list of public keys in the right window (Figure 2.3).

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Figure 2.3\ Appearance of the AbaTax initial screen. It is displayed the list of public keys.

To start using a polikey, just click on its name. AbaTax will show the dynamic identification environment that is made up of two windows, the left contains the list of character states that the user can select, and the right with the list of possible taxon identities of the specimen under taxonomic determination.

3.3\ Step 3. Indicate the list of character states observed in the specimen

The user indicates the character states observed in the specimen under determination. The interface will report in the upper part of each window: the number of states selected by the user (upper part of the left window), and the number of taxa possible identities of the specimen (upper part of the right window).

3.4\ Step 4. Verify the description of the taxon possible identity

It is common that the list of possible taxa to contain more than one element, so the user must find out which of these is the correct identity. One possibility is to see the taxonomic description that AbaTax generates automatically when clicking on the taxon and select the option "Generate description" from the contextual window.

3.5\ Paso 5. Deselect the states and start a new session

To deselect all the character states (or statements) indicated in a work session in order to start a new one, you must click on the trash icon (first button on the top ribbon of buttons).

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a)

b)

Figure 2.4\ Appearance of the interface in AbaTax after selecting a key. a) Format "Character - Character States"; b) "Statements" format.

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Figure 2.5\ Dynamic Identification interface in AbaTax in an identification session. The button “Show the statement of the character status” (fourth button) on the upper ribbon has been activated, as well as the last button “Show the taxa of the selected states”.

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4\ The dynamic identification model

The AbaTax program was designed based on a theoretical proposal that we call the “Dynamic identification model” (Murguía-Romero, 1992; Murguía-Romero & Villaseñor, 1998). The purpose of this model is to clarify which are the actors and objects and the interaction between them when in a computer identification session. Thus, the model helps not only to define the elements to be considered when programming a taxonomic identification software, but also guides the logic of its operation.

Figure 4.1\ Schematization of the dynamic identification model. Both circles represent the sets of character states: the left to those of the specimen under identification and the right to the character states of the hypotheses. The cases in which the intersection is not empty (green color) represent congruence between both sets, while the cases in which the intersection is empty (white color) represent incongruities.

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The two central elements are the identification key and the person who identifies, and between them two an interaction is established whose objective is the correct identification of the specimen under determination. On the one hand, the program provides an information matrix with which it can help the user, on the other, the user indicates to the program two types of information: a) the characteristics observed in the specimen under identification, and b) the list of hypothetical taxa, that is, the taxa that she/he suspects are the correct identity of the specimen. The set of hypotheses has its counterpart expressed in character states: all the character states that are present in those taxa. The program can then confront both sets of character states: those that belong to the hypothesis and those that the user has observed in the specimen under determination (Figure 2.3).

The hypotheses may then be congruent or incongruous with respect to the characteristics observed in the sample, the program will communicate it to the user, who in turn will be able to obtain feedback and review what is causing said incongruity in order to take the necessary actions (discard hypotheses or review the information of the specimen under determination) to reestablish the congruence between both lists.

Based on this model, the user interface known as the “Dynamic Identification Environment” (AID, for its initials in Spanish) is designed, which is explained in the next section.

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5\ The dinanic identification environment AID

5.1\ The AID interface

We call “Dynamic identification environment” (AID, for its initials im Spanish) to the interface implemented by the program for interaction with the user, which, as explained in the previous section, has its theoretical foundation in the “dynamic identification model”.

Figure 5.1\ Dynamic identification environment (AID). The left window displays the character states (or statements) that the user can select, and the right window displays the list of taxa possible identities of the specimen under determination.

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The AID (Figure 5.1) is made up of two windows where two lists are displayed. In the left list the “statements” are shown (an alternative representation to that of the characters and character states); the true statements for the specimen under determination are shown in a green checkbox. The right list shows the taxa; in blue those that may belong to the specimen under determination.

The buttons on the top bar are grouped into three sets (Table 2.1): buttons from the list of "character states", buttons from the list of "hypotheses", and a button in the middle of these two groups that allows to switch between the view of "Statements" or the view of "Character - Character States" (Figure 5.2).

a) b)

Figure 5.2\ Two views of the Dynamic Identification Environment (AID). a) View “Character-Character states”; b) "Statements" view. The fourth button on the top bar "Show Character-Character States" is enabled in a), while in b) it is disabled.

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Table 5.1 \ Groups of buttons of the dynamic identification environment. Disabled buttons Area of influence Enabled buttons

List of character states

List of character states

List of taxa (hypothesis)

The buttons (Table 5.2) allow the user-program interaction to be carried out in a "level 1 navigation", that is, the user must not navigate hierarchically through structured paths that are hierarchically, but instead always have a single screen with the same control elements, analogous to a control board.

There are two selectable items to control an identification session: - the checkboxes for each of the elements of the list of character states and of the taxa list (identified with a small gray square , which turn green when selected ), and - the buttons above the lists of character states and taxa.

With these two types of elements (checkboxes and buttons) the user can control the identification session.

5.2\ Identification based on presences

By means of the checkboxes of the character states , the user can indicate the states observed in the specimen under determination. Character states with unselected checkboxes that remain in gray, indicate a neutral situation, that is, they do not represent a negation, such as "this character state is not present in this instance", they only indicate that the user is still has not expressed evidence that the specimen presents such a state of character. 2

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Although the dynamic identification model refers to the logical “negation”, for simplicity reasons it has been decided not to implement it in the AID, so the identification process and the data matrix of the polykeys in AbaTax are built based on presences and not on absences. The absences are only evident or explicit when you want to know the list of character states of a taxon (section "6 Finding the character states of a taxon").

5.3\ Functions of buttons in the Dynamic Identification Environment

The main actions that control the buttons above the lists of character states and taxa are: - Deselect all items in the lists - Filter items from lists - Change view type between “Character-character states” view and “Statements” view - Activate/deactivate the advanced view that allows specifying hypotheses

Table 5.2\ Buttons of the Dynamic Identification Environment Button Functionality

Buttons of the left side: Deselect character states (or statements) selected by the user

Show only the character states (or statements) you select

Shows only the character states (or statements) of the selected hypotheses Switches between the views of "Character - Character States" or "Statements" Button at the midle: Activates/deactivates the advanced view that allows to indicate identification hypotheses Buttons of the right side: Deselect the selected taxa as hypotheses

Shows only the taxa selected as hypotheses

Shows only the taxa of the selected states (possible identities)

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5.3 \ Indicate characters of the specimen under determination

When the polykey is executed, in the left list the character states (or statements) considered by the data matrix of that polikey is presented to the user (Figure 4.1). Each character state has on its left a checkbox by means of which the user can indicate the presence of the corresponding character state in the specimen under determination.

As the user indicates new character states observed in the specimen, the AID interface updates two important pieces of information: the number of taxa that are compatible with said character states, and the list of names of said taxa, that is, the possible identities of the specimen; the way to indicate it is to color them on a blue background. For example, in figure 4.1 two character states have been indicated, which correspond to taxa compatible with such selection, since at the top of the list of taxa it is indicated “Possible identities of the specimen: 49 of 264”, while the list shows that the names "Acanthaceae", "Agavaceae", etc. are colored in a blue background: if the user were to browse through the list of taxa names, he would find that 49 of these are colored with a blue background.

5.5 \ Deselect all items in lists

If the user wants to start a new identification session, she/he will want to do it "from scratch", that is, delete the information he entered from the previous instance. The button with the trash icon de-deselects all the character states (or statements) that have been indicated by the corresponding checkboxes located to the left of each one (Figure 5.3).

Similarly, the button with the trash icon located above the list of taxa allows deselecting all the taxa indicated as identification hypotheses (see next chapter “6. Finding out the character states of a taxon”).

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Figure 5.3 \ Two states of the “Character states” list of an identification session. Left: Two character states have been selected; right: after having pressed the button "Deselect states"

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6 \ Find out the character states of a taxon

6.1 \ List of character states of a taxon

As the data matrix of a polykey contains information on what characteristics taxa have, then it is possible to obtain a list of these for a given taxon. This is precisely why we decided to include in the AbaTax AID a way in which the user can easily obtain these lists.

When starting the identification session, by default the AID shows the “Basic view”, in which only the elements of the left list (the character states or statements) are selectable. If the "Advanced View" button is pressed, it will change to yellow with a red background and the list of taxa will be updated, now showing a checkbox on the left side of each taxon.

6.2 \ The identification hypotheses

In addition to being able to get to know the taxa in a key better by exploring their list of characteristics, the list of characteristics of a taxon is used in another way in the AID: to establish identification hypotheses.

The user can indicate her/his suspicions of the identity of the specimen when selecting a taxon (Figure 6.1), which in the interface translates into greening the character states of that hypothesis. In this way, in the identification session the user can see if his selections of character states are compatible with the hypothesis she/he proposed.

The user can indicate more than one hypothesis if she/he suspects that the specimen belongs to any of these taxa. If so, the interpretation is a union, a logical OR of all characteristics together.

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Figure 6.1 \ Appearance of the AID when the user indicates Acanthaceae as an identification hypothesis in the FAMEX polykey. Top: the Acanthaeae family has been selected in the right window as the identification hypothesis; the list of statements colors in green background those compatible with the hypothesis. Bottom: In addition, the button "Show hypothesis statements" has been selected, which filters to display only those compatible with the hypothesis. In both cases, the "Advanced view" button has been selected.

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7 \ Images in the AID

Both character states and taxa can be associated with images; To see them, just click on the element and it will display a contextual menu indicating whether or not there are associated images (Figure 7.1). In the first case the message “No images” is displayed, while in the second “See images”.

101 / 5000

Figure 7.1 \ Image of the genus Ferocactus displayed using the right button on the CacTeh key.

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8 \ Generating taxonomic descriptions

It is always possible to generate a taxonomic description of any taxon included in a polyclave in AbaTax. The quality of the description depends on the way in which the character states have been structured and written and also on the way in which they were grouped in the list of "Groups" of the key.

To generate a description, simply select the desired taxon with the left click; A contextual menu will appear with two options: "View images" and "Generate description" (Figure 7.1).

Figure 8.1 \ Taxonomic description (in Spanish) automatically generated in AbaTax of the key “The genus Ageratina in central Mexico”.

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9 \ Browse a polykey database

When selecting a key to use, the left menu presents options to explore or edit its information (Figure 9.1).

The information of each polykey is stored in five different tables: "Groups", “Characters", "Character states", "Taxa", and "Matrix (Presence/Absence)", which correspond to the options in the left menu to explore it. The structure in terms of the columns that these files contain is explained in chapter “11 Creating polykeys in AbaTax”.

Figure 9.1 \ Left menu showing the options to explore the data matrix of the FAMEX polykey.

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10 \ Reports and statistics of a polikey

In the menu on the left window, you can select the “Reports” section (Figure 10.1), which in turn displays four other options to know the total number of visits to the key per day, month or year, as well as the total number of downloads of the documents associated with the key that have been published in its "Documents" section.

The user who creates the key is the one who assigns the permissions to view the usage reports and statistics, being able to choose between a universal one or reserve it only for private viewing.

Figure 10.1 \ Left menu showing the options for reporting the use of the FAMEX polykey. In the right window, the total number of views of the key per day is displayed.

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11 \ Creation of polykeys in AbaTax

There are two alternatives for creating a polykey in AbaTax. The first is by importing Excel files and the other is by editing on the web interface. Here is a brief description of how to create polykeys in AbaTax.

11.1 \ Creation by importing Excel files

This method is the most recommended when creating a polykey for the first time. You need to specify five Excel files, each with one sheet: cat_taxa: List of taxa. cat_caracter: List of characters. cat_estado: List of character states associated with each character. For each one, a statement is defined, which is the one displayed on the interface of the polykey. cat_group: Groups to which each character belongs, they are used to organize the automatic generation of taxonomic descriptions. cat_matriz: Matrix of presence-absence of each character state for each taxon.

Figure 11.1 \ Dialog to select the Excel file corresponding to the list of "Groups" of characters in the new key.

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These Excel files can be created directly by the user, or generated by exporting a taxonomic database created in AbaTaxEdit, a system based on Microsoft Access® specifically for this purpose, also available on the AbaTax website.

Under the option "Tutorial of use" of the left window the label "Formats to upload key" is included. These formats contain five Excel files in the format required to create a key. The important thing about these formats is the name of the columns and their order. The easiest way to create a key is to copy these files and replace the key information in each one without modifying the column titles or their order.

11.2 \ Relationship between the lists "Groups" and "Characters"

As described in the previous section, of the five Excel files that must be uploaded to build a key, there are three that correspond to the list of characteristics; the other two contain the list of taxa and the data matrix. The following figure explains how each of the three types of information is used by AbaTax.

Figure 11.2 \ Schematization of the use by AbaTax of the “Groups”, “Characters” and “Character States” tables. The tables "Groups” and “Character States" are used to generate the taxonomic descriptions, while the tables "Characteres” and “Character states" are used in the identification interface.

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“Groups” Sheet id_grupo grupo 10 Plantas 20 Hoja 30 Invólucro 40 Brácteas involucrales 50 Pedúnculos 60 Lóbulos de la corola 70 Cerdas del vilano

“Characters” Sheet id_caracter caracter caracter_dsc id_grupo orden 100 Forma de vida Forma de vida 10 1 200 Filotaxia Filotaxia 20 2 300 Venación Venación 20 3 400 Forma hoja Forma hoja 20 4 500 Base Base 20 5 600 Márgen Márgen 20 6 700 Prescencia o ausencia pecíolos Prescencia o ausencia pecíolos 20 7 800 Tamaño pecíolos Tamaño pecíolos 20 8 900 Forma involucro Forma involucro 30 9 1000 Tamaño involucro Tamaño involucro 30 10 1100 Pubescencia brácteas involucrales Pubescencia brácteas involucrales 40 11 1200 Pubescencia pedúnculo Pubescencia pedúnculo 50 12 1300 Pubescencia lóbulos de la corola Pubescencia lóbulos de la corola 60 13 1400 Tamaño cerdas del vilano Tamaño cerdas del vilano 70 14 1500 Número de series Número de series 70 15

“Character states” Sheet id_estado id_caracter estado estado_dsc orden id_grupo 10 100 arbóreas Arboles 10 10 20 100 arbustivas Arbustos 20 10 30 100 sufrútices Sufrútices 30 10 40 100 hierbas perennes Hierbas perennes 40 10 45 100 trepadoras Trepadora 45 10 50 200 alternas Hojas alternas 50 20 60 200 opuestas Hojas opuestas 60 20 70 300 pinnado-nervadas Hojas pinnado-nervadas 70 20 80 300 ado-nervadas, las venas originándose en lalmado-nervadas, las venas originándose e 80 20 90 300 -nervadas, las venas originándose arriba ddo-nervadas, las venas originándose arrib 90 20

Figure 11.3 \ Portion of the contents of three Excel files of the key "The Ageratina genus in the state of Mexico".

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11.3\ Key creation via web interface

The use of the web interface is recommended to make modifications to existing polykeys created by importing Excel files. Through this interface, both the presence-absence data matrix, as well as the list of characters, character states, and taxa can be modified (Figure 11.4).

Figure 11.4 \ Menu in the left window to edit the five elements of a key. The options to edit "Groups", "Character", "Character states", "Taxa" and the "Data matrix" are displayed.

Figure 11.5 \ Dialog to add a new “Character state” through the web interface.

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In order to have access to the edition of the data of a polykey, it is necessary to make login entering the username and password, and then choose the key to edit.

A Group -> Character -> Character status hierarchy is followed, so to edit or add a character the Group to which it will be assigned must already exist. Similarly, when editing or adding a Character state, the Character to which it belongs must exist.

In the case of States and Taxa, it is possible to associate images (Figure 11.5). }

The data matrix is made up of all combinations of character states by taxa. The way it is presented to the user for editing is through a checkbox for each of these combinations (Figure 11.6). The interface allows navigation forward or backward in rows or columns by means of a vertical and horizontal pagination control. Another facility is that the interface can exchange the format of the taxa matrix as columns or as rows, by selecting the button that is in the upper left cell next to the “States/Taxa” label.

Figure 11.6 \ Web interface to edit the “Data Matrix”.

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11.4 \ Metadata of a polikey

The data entered in the "Metadata" section (Table 11.1) are those presented in the "List of Keys". That is why it is important to describe the key in a short and descriptive way.

Table 11.1 \ Fields in "Metadata" of a polykey. Field Description Name Name of the polykey, for example "FAMEX" Kingdom Biological kingdom Taxonomic group Name of lower taxonomic category to the kingdom. Language Language in which the key characters are written Authors Names of the creators of the key Description Brief explanation of the key Has it been validated At the authors' discretion it indicates whether an authority in the by an expert? taxonomic group reviewed the key Type of display Private or public Creation date Date the key was created Attach logo To date has no use

11.5 \ Permissions of a polikey

The Figure 11.1 shows the appearance of the row in the user interface with the FAMEX metadata and a hypothetical example of a private polykey. You can see the different icons for each type of key: "Public" (an open eye), "Private" (a closed padlock).

Figure 11.1 \ Row of the FAMEX polykey in the List of keys. The data displayed are those captured in the "Metadata" tab (Figure 12.1).

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12 \ Public keys and private keys

AbaTax incorporates two options in relation to the access and visualization of each polykey. The user can publish his taxonomic key created within the system in the following way: 1. Private. Only the user has access to view their own password. This option is an alternative when the specialist is still working and making modifications. 2. Public. The password is made available to everyone, allowing any user to access it as a query.

Figure 12.1 \ "Metadata" of the FAMEX polykey. The "Display Type" has been set to "Public", the option is "Private".

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13 \ Documentation associated with a polikey

All keys are associated with a "Documents" section that is displayed in the left window once you have chosen to work with it (Figure 13.1). Depending on the authors of the key, there may or may not be associated documentation. It is recommended that the author associate a descriptive document with each key that helps the user to put the polykey into context, both taxonomically and geographically. For example, you can specify the systematic criteria as well as the inclusion and exclusion criteria of the taxa in the key, such as indicating whether or not exotic taxa are included.

Figure 13.1 \ List of documents associated with the FAMEX polykey. The list of documents associated with a polykey is displayed with the "Documents" option in the left window menu.

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14 \ Collaborative work with policlaves

Working collectively between specialists is an important point that AbaTax has considered within its functionalities, therefore it offers the possibility of inviting more users to collaborate within the same polikey, allowing to establish different types of access, such as only for review (read-only) or also for editing.

Through the option "Collaborators" (Figure 13.1), the user who created a polykey in AbaTax can invite other users to modify or update the key. It can be specifyed the permissions for each one of the sections of the menu of the left window of a polykey, such as "MyKeys" o "Database".

Figure 14.1 \ “Permissions” section in the “Collaborators” option.

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15 \ Improving the quality of taxonomic descriptions

15.1 \ Key fields for the generation of taxonomic descriptions

The data required to create a polykey in AbaTax is grouped into five tables: Groups.- Names of the way to group characters. Characters.- Character names Character states.- Names of the character and text states of the statements that are presented in the identification interface. Taxa.- Names of the taxa included in the key Data matrix.- Presence-absence data of the character states for each taxon.

Of these groups, only the "Characters" table is not used for the automatic generation of taxonomic descriptions. Of the remaining four, two are central to forming the structure of the syntactic form of descriptions: the "Groups" table and the "Character states" table. In fact, the information in the "Groups" table is only used in the process of generating taxonomic descriptions but not in the identification process. For this reason, it is in these two tables that attention must be paid and adjustments must be made so that the descriptions have a coherent wording.

15.2 \ Tips for recording character states

Note the first part of the following description automatically generated in AbaTax:

A. adenophora: Plantas arbustivas o hierbas perennes. Hojas opuestas; palmado- nervadas, las venas originándose en la base; lanceoladas u ovadas. Invólucro campanulado; largo, cubriendo más de la mitad o todas la corolas.

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The following observations can be made: - There are three groups: "Plants", "Leaves", "Involuntary" - Character states are separated by "or", ";". - Each sentence begins with the name of a Group and ends with a period “.”.

Note the first sentence:

Plantas arbustivas o hierbas perennes. the words "bush" and "perennial herbs" are states of the same character. While in this sentence:

Hojas opuestas; palmado-nervadas the words "opposite" and "palmate-ribbed" are states of different character. The database then contains, among other things, the following information:

Character status Character Group shrubby life form Plants herbs-perennials life form Plants opposite arrangement of leaves Leaves palmate-veined venation Leaves veins originating at the base venation Leaves lanceolate shape of the leaves Leaves ovate shape of the leaves Leaves

It is appreciated that the information in the Character column is not used in the generation of the description.

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15.3 \ Balance between specification and post-editing

The natural language that humans talk or write is generated based on syntactic rules, so it is possible that computers can generate sentences in natural language. However, natural language does not always follow the rules at the bottom of the letter and in fact part of its richness is breaking the same rules. For this reason, it is very difficult to build programs that generate texts in natural language that are always coherent or satisfactory.

In the case of taxonomic descriptions, the creator of a data matrix in AbaTax can write the texts of the "Character status" and "Groups" tables so that the descriptions generated by AbaTax are as "natural" as possible. However, from what has already been explained about the rules and exceptions in natural language, it will be highly unlikely that automatic descriptions will be generated that fully satisfy the taxonomist requirements for all sections and for all taxa. For this reason, the best way to design the contents of the tables of character states and Groups is keeping in mind that the generated descriptions will have to be edited later by making small adjustments.

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16 \ AbaTax App for Cell Phones

16.1 \ Advantages of the App over the Web version

The main advantage of the AbaTax mobile application is that, once installed, you can use it without the need for an internet connection. The App is a reduced version of the web version, and its main objective is properly the use of polykeys for identification, which is why several functionalities are not available, such as the generation of taxonomic descriptions or the display of images.

Figure 16.1\ Representative screens of the AbaTax mobile application. a) Start´s menu screen showing that two keys has been installed: FAMEX (key to families of flowerings plants of Mexico) and GENCOMEX (key to genera of Asteraceae of Mexico); b) List of elegible character states of the FAMEX key; c) List of possible identities of the specimen given the list of selected character states.

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16.2 \ How to install the App

There are two versions of the App, one for mobile devices with Android and another with iOS operating system. You must install the appropriate version for your mobile device by entering the corresponding store: Google Play or App Store, and search using the word "AbaTax"; Once located, follow the common steps to install an App. The information in the App can be divided into two large groups: on the one hand the program and on the other the identification keys. When installing the App, only the program is installed, and during the installation you will be asked if you want to install the FAMEX polykey.

16.3 \ How to install polykeys

To copy policlaves to your mobile device from the web, you need an internet connection, but once installed, you can check them directly without the need for a connection. Not all the keys on the web are available for download in the App. To install a key, follow these steps:

1) 1) Having already installed the App on your mobile device, enter your username and password from the App. 2) 2) Select the “Add password” icon (Fig. 16.1 a) 3) 3) In the dialog box, search by some keyword (e.g. key full name, authors, description, taxonomic group, etc.), once located, select it and the installation process will begin. 4) 4) When the key finishes installing, a new box will be added to the main window to access it.

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17 \ Tools linked to AbaTax

17.1 \ SimilMatrix

SimilMatrix is an Abaco tool to build similarity matrices from presence absence matrices, available at www.similmatrix.abaco2.org

Since the matrices of the polykeys are presence–absence matrices, it is possible to calculate similarity matrices. AbaTax has built in several similarity indices to generate these matrices. All you have to do is select the similarity index you want to apply under the “SimilMatrix” option, and the similarity matrix will be generated (Figure 16.1).

Figure 17.1 \ Generation of a similarity matrix with the Jaccard index using the FAMEX presence-absence matrix.

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18 \ Interactive lists: other uses of AID

The Dynamic Identification Environment interface can be seen as a tool that relates two lists: objects and their attributes. Thus, it can be used to summarize the characteristics of one of several objects. For example, we have built two “polyclaves” on historical figures from genetics (Figure 17.1) and from biochemistry (“Characters from Genetics” and “Characters from Biochemistry”).

The biogeography celebrities tool was built as part of a learning exercise for biology students. Each student found out the data of some character that was incorporated into the matrix.

Figure 18.1 \ Use of AbaTax as a viewer for interactive object-attribute lists. The "Biogeography Characters" polykey allows to know the attributes of each character interactively.

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References

Murguía-Romero, M. 1992. Métodos en la identificación biológica automatizada. Master thesis. Facultad de Ciencias. Universidad Nacional Autónoma de México. México, Distrito Federal. http://132.248.9.195/pmig2017/0187269/Index.html

Murguía-Romero, M. & Villaseñor, J. L. 1998. GENCOMEX: a computerized key for identify the genera of Asteraceae of Mexico. En P. R. Scott, P. Bridge, P. Jeffries & D. Morse (Eds.), Information Technology, Plant Pathology and Biodiversity (pp. 305-314). Wallingford, United Kingdom: CAB International.

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Glossary

Advanced view.- AbaTax AID display and operation mode in which it is possible to select taxa as well as character states. AID.- see "Dynamic identification environment" Basic view.- AbaTax AID display and operation mode in which it is not possible to select taxa, but only character states. Character state.- Each of the possible variations of a character. Character.- Set or type of structure or attribute of a group of organisms used to define it as a taxon. Checkbox / Checkboxes.- Selection box, element of the user interface that can be selected independently from other elements. Collaborator.- AbaTax user who is invited by another to jointly build and edit a polykey with AbaTax tools. Dynamic identification environment.- AbaTax interface that implements the theoretical model for the taxonomic determination "Dynamic Identification Model". It is made up of two lists: the left containing the list of character states and the right containing the taxa. Dynamic identification model.- Theoretical proposal on the taxonomic identification process and on which the AbaTax tool is based and built (MID for its initials in Spanish). IBdata.- Web system for consulting specimens of biological collections available at www.ibdata.abaco2.org Identification hypothesis.- In the AbaTax AID, taxon or group of these that the user indicates by selecting them, by means of a checkbox, indicating them as possible identities of the specimen under identification. Interactive list.- In AbaTax AID, it is a way of naming the possible use other than taxonomic identification, such as, for example, the interactive list of "Biogeography celebrities" available as a public key in AbaTax. MID.- see "Dynamic Identification Model".

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Polykey.- Tool for taxonomic identification of a polythetic nature. Polytetic.- A means of identification that does not necessarily discriminate by diagnostic characters, but by the combination of a set of character states. SimilMatrix.- AbaTax tool for the construction of similarity matrices available at www.similmatrix.abaco2.org Statement.- In the AbaTax AID, and in general, in the Dynamic Identification Model, a way to represent both names: that of the character and that of a character state. Taxon.- Group of organisms that are organized by authorities (taxonomist) in that group of organisms under the same name. Taxonomic description.- Set of sentences in natural language that describe a taxon by means of the characteristics that the taxonomists have defined that are present in the set of analyzed specimens. Taxonomic identification.- Process by which a specimen (organism) is assigned a name of a taxon, for example, the name of a species.

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