collBook development

A desktop application, collBook was written in Python 3.7 (https://www.python.org/) using the Qt5 (The Qt Company, Espoo, Finland) framework for the graphical user interface. Qt Designer 5.12 was used to design the interface layouts. Multiple custom Python modules are present in collBook's source code. A list of those modules and a brief description of their function is provided in Table 1. Available for Linux, OS X, and Windows, collBook is designed to use at the same time as specimen identification for refining field notes into database‐ready files and specimen labels. Performing data refinements in collBook, as opposed to collNotes, permits web service–dependent features without cell service dependency.

The Python modules written for collBook, and a brief description of their functions

Designed to be feature rich, the user interface contains four prominent panes: a label preview, form view, site navigator, and table view (Fig. 1). The label preview (Fig. 1A) presents a dynamically generated label, which is updated as edits are made. The form view is the primary method of editing or adding new records (Fig. 1B). Many of the form view's fields (e.g., date, latitude, and longitude) impose DwC‐recommended formatting. The site navigator is used to select which records are to be edited, refined, or exported (Fig. 1C). All edits made to parent classes (i.e., those of a higher class) are automatically propagated to their associated children records (i.e., lower class records). For example, in Fig. 1C, selecting “Site 1” sets the scope of records to be acted upon as all those that were collected at that site. To avoid confusion caused by changing scopes, reminder text was placed in the status bar along the bottom of the interface informing the user of the current selection type (i.e., “All records,” “Site view,” or “Specimen view”). The table view presents spreadsheet‐style access to all selected records (Fig. 1D). Contrary to the rest of the interface, the table view imposes no formatting, validation, or inheritance, providing a method to override many of the functions discussed above. Data entered using the table view may not always be visible in the form view, yet will be reflected on the label preview and in the exported data. Features included in collBook are: reverse geocoding localities, taxonomic alignments, inferred associated taxa, and creation of customizable labels that can optionally include catalog number barcodes.

The collBook user interface, showing (A) the label preview, which presents an image of the label to be produced for a selected record; (B) the form view, where data pertinent to the selected class (e.g., “Site 1”) may be edited; (C) the site navigator, which is used to select record(s) for editing or refining; and (D) the table view, which provides an overview of the selected record(s) and allows unrestricted edits to the data.

In collBook, location data not recorded in collNotes (i.e., “state,” “county,” “municipality”) are inferred from the GPS coordinates and prepended to the user‐entered locality string, supplementing the minimal locality data recorded in collNotes. Inference from coordinates is performed using Google's reverse geocoding web service (Google, 2019). For example, the locality string: “50 m northeast of the Illinois Monument” would become: “US, Tennessee, Hamilton County, Chattanooga, Orchard Knob Reservation, near East 4th Street, 50 m North East of the Illinois Monument.” One flaw inherent to this feature is that the user‐entered locality and the generated preamble may contain redundant terms. While testing these programs, familiarity with this feature when using collNotes was found to reduce the occurrences of such redundant terms. Nevertheless, it must remain the user's responsibility to verify labels in collBook for accuracy and redundancy.

When refining records, the status of the taxonomy, and the associated authority, are verified. To accomodate user preference, several sources for these alignments were included. The most recent version of the Integrated Taxonomic Information System (ITIS; https://www.itis.gov/) is bundled with the program, whereas Catalog of Life (Roskov et al., 2013) and the Taxonomic Name Resolution Service (TNRS; Boyle et al., 2013) are made available through their web services. So as not to overload web services, a one‐second delay is imposed on web service requests, making alignments through ITIS much faster. Because ITIS was packaged with collBook, it is also used to inform autofill suggestions when entering scientific names. TNRS is capable of performing partial matches, correcting minor spelling discrepancies when verifying taxonomies. In those cases, TNRS returns a score of the match's accuracy; a minimum threshold for this score can be modified at the user's preference. Alignments from these sources are applied based on user‐defined policies that delegate how recommendations should be made, and whether they should ever be automatically applied. Although not discussed in detail here, collNotes and collBook are being evaluated for groups beyond Plantae. Fungi, for example, is currently supported with a locally bundled MycoBank (Robert et al., 2013; http://www.mycobank.org/) taxonomy, as well as Catalog of Life support.