Building checklists from scratch is hard work. For convenience, J-Bird can import checklists from a few formats: comma-separated values (CSV), Excel spreadsheets, tables in web pages, dBase .dbf files, and relational databases. Many suitable checklists are available on the internet. Checklists are imported individually. (J-Bird is not capable of importing many checklists all at once.)
When you build a checklist manually, you perform many tasks. You find a suitable checklist, look down the columns for species names, ascertain whether the names are common or scientific, find the species names in the checklist template and tick them. Sometimes names on your checklist don't match those in the master list, and you locate suitable alternatives. All of these same tasks must be performed when you import checklists. You will perform some of them. You will instruct J-Bird what to do for some of them. And, J-Bird will make suggestions for others.
The process of importing checklists has been organized into several steps. First, you will identify the source of data (e.g., file, web page) to J-Bird. J-Bird will read the data and show them to you. If the data are in an Excel spreadsheet, you'll be asked to select a spread sheet from the file, or if they are in a web page table, you'll be asked to select a table. Next, J-Bird will show you the data in table form, and you will tell it which columns in the table contain species names. You'll also have an opportunity to edit the list before it is imported. Then, J-Bird will begin importing. If it encounters species that are not in the master list of species, it will try present you with some possibilities. If you are importing scientific names, J-Bird will list all species in the genus to cover the possibility that the specific epithet has changed. Next it presents species with similar specific epithets on the chance that the species has been moved to a different genus and the specific epithet remains unchanged or has a new suffix. If you are importing common names, it will present you with a list of common names that begin with the same letters as the species to be imported. Finally, when the import is complete, you'll see a summary of the action that includes box scores and a list of species that could not be imported.
J-Bird takes the following steps to identify imported species. It stops at the first successful step.
Initially, J-Bird contains no synonym. You can build a list of synonyms to minimize the task of identifying species that are not on the master species list. When you identify a species, you can save the name as a synonym of the species that you select from the master list. You also have the option of saving the genus name as a synonym of a genus in the master species list, if you are importing scientific names. If you save a species name as a synonym, the importer should identify that name in all future imports. If you save a genus name as a synonym, the importer should identify any species in the genus for which the specific epithet is identical to an entry in the master list. For example, some lists use the genus Chen for some geese. If species in that genus appear in the master list as members of the genus Anser, they will be correctly identified if Chen exists as a synonym of Anser and if the specific epithets match. Note that genus synonyms will not work for individual species that have been moved from one genus to another because J-Bird forbids genera that are synonyms from also being in the master list.
Bird names appear in many different forms. J-Bird accommodates some common forms.
| Scientific name | Common name |
|---|---|
| Molothrus ater | Brown-headed Cowbird |
| Molothrus rufoaxillaris | Screaming Cowbird |
| Genus | Species | Common name |
|---|---|---|
| Molothrus | ater | Brown-headed Cowbird |
| Molothrus | aeneus | Bronzed Cowbird |
| Scientific name | Common name |
|---|---|
| Molothrus ater | Brown-headed Cowbird |
| M. badius | Bay-winged Cowbird |
| Genus | Species | Common name |
|---|---|---|
| Euphagus | carolinus | Rusty Blackbird |
| cyanocephalus | Brewer's Blackbird | |
| Molothrus | ater | Brown-headed Cowbird |
| bonariensis | Shiny Cowbird |
| Scientific name | Common name |
|---|---|
| Molothrus ater | Cowbird, Brown-headed |
| Scaphidura oryzivora | Cowbird, Giant |
J-Bird attempts to convert cases of imported species names to match names in the database.
Species lists can be imported into existing J-Bird checklists. You can import a list at the time that a checklist is created or afterward. When you create a checklist, you may elect to import species into it by selecting the "Import" radio button on the dialog into which you enter information about the checklist. After the dialog is dismissed, a wizard will appear and guide you through the process of importing species.
Species can be added to any existing checklist on the tree of checklists that appears when you select the task "browse/edit checklists". Select the checklist into which you want to import species, right-click on it (control-click on Mac OS X), and select "import species list - ...". A wizard will appear. The wizard will ignore any species to be imported that is already on the checklist.
Use the first panel of the wizard to identify the source of the data.
For CSV files and for Excel spreadsheets, the source will probably be
a file on your computer. You can enter the name directly into the text
box or by pushing the "Browse files ..." button. If you decide to type
the name into the box, the file is assumed to be in your home directory.
Web pages that contain tables from which species names will be extracted may be files on your computer, or they may be pages on the world-wide web if your computer is connected to the internet. You can type the URL of the web page into the text box, or you can browse the web by pushing the "Browse WWW ..." button. Go to the page that contains the table and dismiss the browser. Not all web pages on the internet will work because of the simplicity of Java's web page rendering engine. Links in web pages that run Javascript code will not work. (Java and Javascript are very different despite the similarity of their names.) To avoid this issue, use your favorite web browser to visit the page that contains the table; save a local copy of the page; and use the "Browse files ..." button to locate the saved page.
What happens next depends on the data source.
If you are importing from an Excel spreadsheet, the next panel to appear
will show the first sheet of the file and tabs for switching between
sheets. Use the tabs to select the correct sheet,
and click forward.
In the example shown, two sheets are available, and the user has selected sheet MARC 2003.
The next step is Identifying column types and modifying data.
To select a table, click on cells in opposite corners of the table. For
example, you might click on the upper right cell and then the lower left
cell. When you click on the first cell, it will turn green, and when you click
on the cell in the opposite corner, it, too, will turn green. All cells
between the two selected cells will turn green.
You can select a subset of a table rather than the whole table. Click on opposite corners of the section of the table that you want.
In the example shown, the table is a little cryptic because it has no border. It contains three columns. The middle column contains nothing on the visible portion of the table. Elsewhere, the middle column contains single-letter codes. To select the table, the user clicked on the entry "Fulvous Whistling-Duck", and scrolled to the bottom of the table and clicked on the last scientific name. The selected table entries turned green.
You must indicate which columns contain names of species to be imported.
Columns are identified by the column headings. Initially, all columns are
labeled "ignored". To identify columns, click on the
column header, and select from the pop-up menu that
appears.
Choose how to handle entries in the table that are absent from J-Bird's master list. Attempts can be made to find entries in the master list based on similarities in species names. Similar names are presented for approval. Alternatively, you can elect to skip all entries in the table that are not found in the master list. A list of unknown species will be presented after the table is processed.
In the example shown, the user has identified the first column as a column of common names but has not yet identified the third column as a column of scientific names. The user has chosen to handle entries that are absent from the master list by screening similar names.
Data in the table can be edited. You can change the value of any cell by clicking in it. A cursor will appear. Make the change, and press return or click in another cell. Rows and columns can be deleted. Right-click in a cell (ctrl-Click on Mac OS X) and select from the pop-up menu that appears. Note that there is no undo feature. If you blow it, you blow it, although you can press the Back button, reconfigure and try again. Changes that you make to the table are not transmitted back to the data source.
As J-Bird imports a list of species names, it displays its progress. A status column is added to the displayed table of names, and it is updated as the import progresses. If J-Bird encounters species names that it cannot resolve, it will present suggestions if it can discern reasonable possibilities otherwise, unresolved names are marked as "unknown" in the status column.
When names that are being imported do not match names in the master species
list or synonyms, the wizard displays a list of alternatives for your
selection if it can. If both scientific names and common names are being
imported it tries congeners, species with similar specific epithets and
species with similar common names in that order. If the species is
identifiable in the set of choices, select the choice and accept it. You
can save the name as a synonym by ticking the appropriate check box before
accepting your selection. If no species is acceptable, indicate that.
Species that cannot be identified will be labeled "unknown" in the status
column of the display, and they will be available to view in the summary
table as well as in the J-Bird log.
If you tire of screening mismatches between species in the table and those in the master list, you can skip all remaining mismatches by clicking on the button "Skip all uknown species".
You can cancel the import by dismissing the window that requests identities of unknown species.
In the example shown, congeners of the unknown American Three-toed Woodpecker (Picoides dorsalis) are presented for selection. The user has selected the Three-toed Woodpecker (P. tridactylus) from the master species list and chosen to save the American Three-toed Woodpecker as a synonym of the Three-toed Woodpecker. It would not make sense to try to save the genus Picoides as a synonym of itself, and if the box were checked, the wizard would ignore it.
You can cancel the import of a checklist while it is in progress by dismissing the import dialog, by pressing the "Back" button or by dismissing the dialog that is used to identify species that are not in the master species list.
Suppose that you use a list of world birds as the master species list and that you would like to import the AOU Checklist of North American birds as your checklist for North America.
Be warned that this is a big job because the AOU list is up to date and many names in it are likely to differ from those in the master species list.
Avibase is a very nice source of checklists. Note that checklists from Avibase are for personal use only. If you publicly post or otherwise publish a checklist that is derived from Avibase, you should include a citation of the Avibase web site.
To import a checklist from Avibase, you will use your favorite web browser to display the checklist and then save it as an HTML file on your computer. Then, you'll import the checklist from the file that you saved. This is necessary because Avibase web pages use Javascript to generate checklists and Java (and hence J-Bird) cannot handle Javascript.
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Last updated 18 March 2007