Biota Supplement 2

The Biota Manual is your primary source of information about how to use Biota (Biota: The Biodiversity Database Manager © 1996 by Robert K. Colwell, published by Sinauer Associates). The Manual was written for Version 1.0, released in December, 1996.
The Supplement to the Biota Manual (© 1997 by Robert K. Colwell) documents changes and features added to Biota up to the release of Version 1.2, in June, 1997. The Supplement provides information of particular importance to Windows users.
This document, Supplement 2 to the Biota Manual (© 1998 by Robert K. Colwell) explains additional changes and added to Biota between Version 1.2 and Version 1.3.
The ReadMe file, which you will find on one of the Biota diskettes, provides a complete version history, and may include updates or corrections to this document.
The Biota Website, at http://viceroy.eeb.uconn.edu/biota, is the place to go for post-release updates to this documentation, suggestions, warnings, workarounds for problems, and news of further program updates.

Note on page numbers: Throughout this document, references to pages in the Biota Manual will be of the form "Manual pp. 215-218" and references to the (original) Supplement will be of the form "Supplement pp. S23-S24."

How to Use Supplement 2

Supplement 2 to the Biota Manual is organized in precisely the same way as the Manual itself. Sections of the next chapter, "New and Modified Features in Biota Version 1.2," follow the chapter organization of the Manual (and Supplement). Each section is specifically referenced to the corresponding part of the Manual and/or Supplement. Some sections add new information to the analogous section or chapter of the Manual or Supplement, but others actually replace a section in the Manual or Supplement.

Register Your Copy of Biota for Upgrades and Support

Once you become a registered owner of Biota, you can download maintenance upgrades free of charge through the Biota Website (http://viceroy.eeb.uconn.edu/biota) using your last name (surname) and registration number.

Registration also entitles you to discounts on any major upgrades to Biota (from Sinauer Associates, www.sinauer.com) in the future as well as free e-mail support (Manual p. 535).

New and Modified Features in Biota Version 1.3

Entering Data (Manual Chapter 6)

Overriding Wildcard Input for Linking Fields

This section supplements Manual pp. 44-48 and p. 96.

Normally, when you make an entry in a linking field (any double-bordered entry area) in Biota, you will want to take advantage of wildcard entry. You type in the first letter or letters of the desired entry, and Biota completes the entry based on values for records in parent table. If no existing value matches your entry, Biota offers to create a new record in the parent table, on the fly. If more than one value matches your entry, Biota presents a pick list of the matches.

For example, suppose you are entering a new Species record for the species Musanga recta, and you have an existing record in the Genus table for the genus Musanga, you can type "musa " in the Genus field of the Species input screen and Biota will automatically fill in Musanga (or display it in a choice window along with any other existing Genus names that begin with the letters "musa ").

In Version 1.3, you can force Biota to create a new parent record, even if one or more matches already exists. Why would you want to do this? Continuing with the previous example, suppose you need to create a Species record for Musa nana. If you enter "musa " in the Genus field of the Species input screen, Biota will complete the entry as Musanga. Previously, the only way to create a new genus record for Musa (assuming a Genus record for Musanga was already present) would be through the Input Genus command. It could not be done on the fly.

In Version 1.3 and later, you can override the wildcard lookup of parent records in any double-bordered linking field very simply.

1. Type in the value for which you want to create a new parent record (Musa in the example).

2. Depress the option key (Macintosh) or the alt key (Windows) while pressing the tab key to enter the new value. Biota will offer to create the new parent record.

3. Create the new parent record in the normal way (Manual pp. 44-48).

Special Data Types (Manual Chapter 8)

Automatic Support for International Date Format

This section revises Manual p. 111 and Supplement p. S19.

In earlier versions, Biota required the settings in your operating system (Windows or Mac OS) to be set to U.S. date format (Month/Day/Year). In Biota 1.3, this restriction has been completely eliminated. (This change first appeared in Version 1.2.3.)

You may now set your operating system (Windows or Mac OS) to either International date format (Day/Month/Year) or U.S. format (Month/Day/Year). All dates in the Biota interface are automatically displayed to match the operating system setting, including dates on input screens, output (record listing) screens, and dates in printed reports.
In the Sort and Search Editors, all dates match the system setting. When using the Search Editor for a date field, be sure to enter the date using the same format as the system setting.
On labels, all dates are in International format, regardless of the system setting. (Unchanged from earlier versions.)
In the Import and Export Editors, if you select a data field, Biota now offers a choice of International, U.S., or ANSI (YYYYMMDD) date formats, regardless of the system setting.
In all other Export tools, dates match the system setting.
Existing Biota Data Files are completely compatible with these changes.
All Biota Data Files are completely date-cross-compatible, regardless of the current system setting, the system setting under which they were created, the Biota version under which they were created, or the platform (Windows or Mac OS) on which they were created.
Users of the U.S. date format will see no changes in the interface they are used to, with the exception of the options for dates in the Import and Export Editors.

Operating System Number Formats

This section references Supplement p. S19.

As in earlier versions, Biota 1.3 requires the number format setting in your operating system (Windows or Mac OS) to be set to use the period as the decimal separator character, not the comma.

Working with Records in Output and Input Screens (Manual Chapter 9)

Longer Fields in the Species and Locality Tables

This section supplements Chapter 10 and Appendix A of the Manual. (See also "Longer Fields in Auxiliary Fields Tables," in this document.)

Field length has been increased (beginning in Version 1.2.4) to 80 characters for several fields in the Species and Locality Tables.

The Locality Name field in the Locality table.
The Species Author, Subspecies Author, Variety Author, and Common Name fields in the Species table.

To allow very long values for these fields to be displayed, a "zoom" button (a small, square button with an icon showing crossed, double-headed arrows) appears next to each field in the input screen for the appropriate files.

When you click the zoom button, the full text for the field appears in a small window.

Input--Table by Table (Manual Chapter 10)

Locality Input: Duplicate Locality Name Warning

This section supplements Manual pp. 160-161.

In the Locality table, a warning now appears if you enter a value for Locality Name that is already in the database. Biota offers to display the matching record or records if you wish.

This feature works just like the warning for duplicate Species Name (specific epithet) in the Species input screen, described in the Manual on pp. 166-167. The duplicate Locality Name feature is always enabled, however, unlike the duplicate Species Name feature (see p. S31 in the Supplement).

Locality Names need not be unique (since Locality Code is the key field in the Locality table), but this feature helps prevent accidental creation of two or more records for the same locality. You may indeed want to create more than one record with the Locality Name "San Ramon" or "Springfield" for identically-named places in different countries, provinces, or states, but creating more than one Locality record for the same San Ramon defeats the purpose of a relational database.

Locality Input: Feet to Meters Conversion Button

This section supplements Manual p. 161.

In the Locality input screen, Biota Version 1.3 offers a "Convert ft to m" button next to the Elevation field, to simplify metric conversion of elevations (or depths) that were originally recorded in feet.

Once you click the button and the conversion is made, Biota records the metric value only, along with the unit abbreviation "m" to make clear that the conversion was made, as shown below.

If the original entry includes the character "m" (e.g., "m" or "meters" or "metres"), Biota posts a warning.

If the original entry includes any other alphabetic characters (e.g. "f" or "ft"), these are replaced with "m" in the converted value when you use the Convert button. If you do not use the button, any alphabetic characters that you have entered are recorded in the Locality record.
On specimen labels, if the Elevation value has no units, Biota assumes the value is in meters and appends "m" as the unit abbreviation (Manual, p. 161). If the value already includes "m" it is printed as you entered it.
Elevations may be recorded in feet if you prefer. If you append "f," "ft," "feet," or any alphabetic string that includes the letter "f" to a numeric entry in the Elevation field, and you do not use the Convert button, Biota will print specimen labels with the value and units just as you entered them (Manual, p. 161).

Finding and Updating Records (Manual Chapter 11)

Using the Search Editor to Find Records Based on Notes

This section supplements Manual pp. 192-200 as well as Chapter 15.

You can now use the Search Editor to find records in the Locality, Collection, Specimen, Species, or Loans table based on Notes linked to these records. You can search in the Note Date, Note By (note author), or Note Text fields.

1. From the Find menu, choose By Using Search Editor. A table selection window appears.

2. Click and hold the popup list to select the Notes table you want to search. In the illustration below, the Species Notes table is being selected.

The appropriate search options in the window become activated.

3. Choose a search option in the window (above).

Either: Search all records in the selected Notes table.
Or: Search only those Notes linked to records in the active Record Set for the parent table.

If there are no records in the active Record Set for the parent table (the Species table, in this example), the lower button will not be activated. If there are no records in the parent table, Biota informs you with a message; in this case, neither button is activated and the search is canceled.

4. Click the Search button in the options window to launch the Search Editor. The Search Editor window appears, displaying the fields of the Notes table (Species Notes, in this example. Set up a query based values in the Note Date, Note By, and/or Note Text fields.

Note: If you are not familiar with the Search Editor, please consult the Manual, pp. 192-200.

5. Click the OK button to launch the search. Biota will find and display all the parent table records (Species records, in this example) for which the criteria you set are true in the linked Species Notes records.

Notes: You can also include criteria from the parent table or any table linked to it, with the same restrictions as for any other query. See pp. 197-200 in the Manual.

For any complex and time-consuming search, it is a good idea to create a Record Set Pointer File to record the result for future reference or use. These files are very small and very efficient. See Manual pp. 16-19.

Printing Labels (Manual Chapter 13)

Print Preview (Macintosh Only)

This section supplements Manual pp. 243-245.

With certain printers under Macintosh (Mac OS) System 8 and later, you must now take an extra step to reach the "Preview on screen" checkbox in the system Print window that allows you to display Biota labels or reports before printing.

1. From the popup menu that initially reads "General" in the print screen, select BiotaApp. (If you are using Biota4D, you need to choose "4D Server" or "4th Dimension" instead.)

The "Preview on screen" checkbox appears.

2. Check the "Preview on screen" checkbox, then the Print button.

New Options for Herbarium Specimen Labels

This section supplements Manual pp. 255-258 and Supplement pp. S44-S48.

Note: If an option you want to know about is not described in this section, please consult the Manual (pp. 255-258) or the Supplement (pp. S44-S48). All features described in those documents are still valid.

In Biota Version 1.3, several new options have been added to the Herbarium Labels tool, which you access by choosing Herbarium Labels from the Labels menu.

In the More Options screen&emdash; which you display by clicking the More Options button in the initial Options screen&emdash;you can now control the font size for all text in the body of the label by selecting a size from the popup menu shown below. (Font size for the Project Name area is controlled separately; see Supplement p. S48).

Other new options appear in the Even More Data Options panel (illustrated below), which you display by clicking the Even More Options button in the lower left corner of the More Options screen, shown above.

Collector's Number Placement Options
Print Collector's Number in its own field. If you choose this option, the Collector's Number appears on the label in its own field, just below the Collection Date, as illustrated on p. S48 in the Supplement.
Append Collector's Number to Collector's Name. If you choose this option, the Collector's Number appears (preceded by a comma) after the Collector's name in the Collector or Collector Group field on the label.

Note: Two other options affect the Collector's Number. In the Data Option panel of the initial Options screen, you can indicate which field you have used to store Collector's Numbers (see Supplement pp. S45-S46). In the Field Label Options panel of the More Options screen, you can choose a phrase to precede the Collector's Number (see Supplement pp. S47-S48). Several new phrase options have been added in Version 1.3

Layout Options
- Print labels 4 to a page (7.6 x 12.5 cm, landscape). This option offers maximum space for long locality names and field descriptions.
- Print labels 6 to a page (8.1 x 9.6 cm, portrait). This option less space for long locality names and field descriptions.
Note: You can also increase the amount of text that will fit on herbarium labels by reducing the Font Size in the More Options screen (see above).
Border Options
- Print labels with border lines. If you choose this option, Biota prints a simple, fine line border around each label.
- Print labels with tick marks, but no border lines. If you choose this option, Biota prints place very fine tick marks outside the area of the labels as a guide for cutting the labels apart after printing.
Checkbox Options
- Preview labels before printing. If you check this option, Biota displays the labels on the screen so you can check them before printing. (You can also do this by checking the "Preview on screen" checkbox in the system Print window; see Manual pp. 243-245 and this document, "Print Preview (Macintosh Only)"). If the preview is acceptable, you can proceed directly to printing by clicking the Print button at the bottom of the preview screen.
- Save label text to disk file instead of printing. If you check this option, Biota creates a disk file (which you name and place) containing exactly the same information that would otherwise be printed on labels. You are then free to edit or format the information any way you wish.
- Save Herbarium Label settings between sessions. You can save all Herbarium Label settings between Biota sessions by checking this box. (Settings are recorded invisibly in the Data File, so you will not lose them if you use the Data File with another copy or version of Biota.) Otherwise, settings are saved only until you quit Biota, and the default settings will be applied next time you launch Biota.

User-Defined Auxiliary Fields (Manual Chapter 15)

Longer Fields in Auxiliary Fields Tables

This section supplements Chapter 15 and Appendix A of the Manual.

Field length has been increased (beginning in Version 1.2.4) to 80 characters for all Field Value fields in the Auxiliary Fields system (in the Specimen Field Value, Species Field Value, Collection Field Value, and Locality Field Value tables).

To display very long Auxiliary Field Values, take these steps.

1. Display the parent records (e.g., Species records) in the output (listing) screen for the parent table.

2. Click the Aux Fields button at the bottom of the output screen and select the Transposed format option. (See Manual pp. 302-304.)

3. Double-click the row for the desired Auxiliary Field. The Values for Auxiliary Field screen appears (Manual, p. 304).

4. Click any record to display it in full in a window like the one below.

Auxiliary Field Link Maintenance

This section supplements Manual pp. 281-282.

Under normal operations, Biota correctly maintains links between parent records in the Specimen, Species, Collection, and Locality tables and records in the tables that contain information on Auxiliary Fields (the Field Value and Field Name tables&emdash;see Chapter 15 of the Biota Manual). In addition, the number of (non-blank) Auxiliary Field Values for each parent record is normally maintained correctly in the Auxiliary Fields field of each parent record.

Power failures, system crashes, and partially imported data, however, can produce anomalies. A record in a Field Value table may become orphaned (either the Record Code field or the Field Name field contains a nonexistent parent record value), a blank entry for Field Value may appear, or the Auxiliary Fields field of a parent record (a Specimen, Species, Collection, or Locality record) may indicate the wrong number of Auxiliary Field Values. This utility corrects all these problems, without in any way affecting legitimate records. Whereas none of these problems is very serious, it is recommended that you run this utility from time to time if you work with Auxiliary Fields, especially if you suspect problems.

1. From the Special menu, choose Maintenance Utilities. A setup window appears with (at present) a single checkbox option.

2. Check the checkbox and click the Launch button. Biota checks for problems and informs you of the results with a series of messages such as this one.

Note: If you have defined any Auxiliary Fields in your Data File, the first time you open it with Version 1.3 Biota presents a message screen suggesting you run this utility. The message appears only once for each such Data File.

Images (Manual Chapter 18)

Image Zoom Windows

This section supplements Manual pp. 355-357.

To accommodate large format, high-resolution images, Version 1.3 offers zoom windows for viewing single images at full size. (The window is 768 by 576 pixels, corresponding to the PAL video format.)

To display an image in a zoom window, click the small zoom button in the lower right corner of the standard Image Input window (shown with the cursor, below). (See the Manual, pp. 355-357 for information on the Image Input window.)

Biota displays the image in a separate, "floating" window, with the window title showing the species name and Image Name.

To close a zoom image window, click anywhere in the window or use the close box. Because each image zoom window is opened as a separate Biota process, you can open as many as you like simultaneously and close them individually when no longer needed.

The Synonymy System (Manual Chapter 20)

Displaying Specimen Records for Junior Synonyms

This section supplements Manual Chapter 20 and pp. 125-126.

In Biota Version 1.3.0, when you display the Species record for a senior synonym (a Valid Species record with one or more junior synonyms in the Data File), you can use the Specimens button to display not only all Specimen records linked to Species record for the senior synonym, but (as an option) all Specimen records linked to the Species records for its junior synonyms as well.

1. In the Preferences screen (Special menu), enable the "Show full Synonymy status" checkbox (see p. 385 in the Manual).

2. Display the Species record for a senior synonym and click the Specimens button. An option screen appears. The options are self-explanatory.

Finding Valid Species in the Species Record Set

This section supplements Manual pp. 380-381 and 558.

In Biota Version 1.3.0, an option has been added to the Find Valid Species tool (Find menu) to limit the search to the active Species Record Set.

Exporting Data (Manual Chapter 24)

Exporting Text with Special Characters (Windows Only)

This section supplements Manual Chapter 24.

In Biota Version 1.3 (beginning with 1.2.3), all "high-ASCII" characters (characters with accents and other diacritical marks) are handled correctly by all export (and import) tools in Biota versions for Windows 95 and NT, correcting an earlier problem with high ASCII import/export in Windows. (This was never a problem on the Macintosh platform.) The Windows files Input.4fi and Output.4fi, installed automatically when you install Biota, must be present in the same folder (directory) as the Biota application files for these characters to be imported and exported correctly.

Exporting Localities-by-Species Incidence or Abundance Tables

This section supplements Manual pp. 469-472.

This new tool in the Export menu is identical to the Export Collections-by-Species tool (see the Biota manual, pp. 469-472), but creates abundance or incidence matrices for Species in Localities instead of Species in Collections. You can base the exported table on either the Species, Specimen, Collection, or Locality Record Set. The setup screen is illustrated in the next section.

Progress indicators and abort options have been added to both tools to help with large matrices, which may take several minutes to export.

Special Export Formats for Collections-by-Species and Localities-by-Species Tables

This section supplements Manual pp. 469-472.

Biota now offers two special Format Options for exporting incidence and abundance tables based on selections of records (see the previous section and Manual pp. 469-472 for background information). The Localities-by-Species option screen is illustrated below; the Collections-by-Species screen is analogous.

Export in EstimateS format. If you check this option, the exported text files can be directly read by EstimateS, a freeware application (© Robert K. Colwell, author of Biota) for the statistical estimation of species richness and shared species from specimen-based sampling data. You can learn more about EstimateS and download a free copy of the software and User's Guide from http://viceroy.eeb.ucconn.edu/estimates.
Export in Cornell Condensed Format. If you check this option, the text file is exported in Cornell Condensed Format&emdash;the required input format for FORTRAN statistical programs such as CANOCO and DECORANA, widely used for ordination. (Click the Cornell Help button below the checkbox for details.)

When this option is checked and you click the OK button, Biota presents a second screen requesting a data set title (optional) offering options for creating the species and sample abbreviations required for the Cornell format. (The options for Collections-by-Species tables are analogous.) Click the Help button in the option screen for details.

Importing Data (Manual Chapter 26)

Importing Text with Special Characters (Windows Only)

This section supplements Manual Chapter 26.

In Biota Version 1.3 (beginning with 1.2.3), all "high-ASCII" characters (characters with accents and other diacritical marks) are handled correctly by the Import Editor in Biota versions for Windows 95 and NT, correcting an earlier problem with high ASCII import/export in Windows. (This was never a problem on the Macintosh platform.) The Windows files Input.4fi and Output.4fi, installed automatically when you install Biota, must be present in the same folder (directory) as the Biota application files for these characters to be imported and exported correctly.

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The Biota Website is maintained by Robert K. Colwell, colwell@uconnvm.uconn.edu. This page updated February 23, 1997.