USING DINOFLAJ3

Users should be familiar with the basics of Linnean classification and the organization of the Dinoflagellate Index (Fensome et al., 2017) and the dinoflagellate classification of Fensome et al., 1993b, to use DINOFLAJ3 effectively.

There are three main types of data in DINOFLAJ3:

1. taxonomic entries (e.g., genera, species, and suprageneric taxa such as families, orders, etc.)
2. bibliographic entries (i.e. references)
3. glossary entries (i.e. definitions of terms used in the suprageneric classification)

For all three types of data, there are multiple ways to search for and view a given entry: some of the methods are the same as the MediaWiki software implements (so experience with the Wikipedia will help you use DINOFLAJ3); some others are conventions peculiar to DINOFLAJ3.

The menu at the left side of the screen provides access to the home page (called "Main Page" – also accessible by clicking on the orange and green stylized dinoflagellate logo), and multiple search and browsing methods. You can:

1. Start at the top of the dinoflagellate classification "Tree" (i.e. Division Dinoflagellata) and work your way through the Linnean hierarchy down to any taxon;
2. Select from a hierarchical "Table" of the suprageneric classification
3. Browse a list of Family or other suprageneric ranks
4. Browse an alphabetical list of Genera
5. Browse an alphabetical list of Species, or subspecific taxa (ordered by the epithet)
6. Browse an alphabetical list of bibliographic References
7. Browse an alphabetical list of Glossary entries
8. Use the "Search" box at upper right after entering some text.

A number of additional listings are available under the "Other Groupings" heading, which can be expanded by clicking on it:

1. A list of only the taxa in the "Main Index" (exclusive of Appendices)
2. A list of Appendix A and Appendix B entries
3. A list of calcareous fossil dinoflagellates
4. A list of siliceous fossil dinoflagellates
5. A list of New taxa added since the 2004 edition of the Index
6. A list of Changed taxa that have been modified since the 2004 edition of the Index
7. A list of all taxa
8. A special "What links here" page that lists other pages that link to the current one.

Some conventions exist for the names of the entries:

1. Homonyms are distinguished by adding the author citation to names. For example, to view Meristaulax granulata would require typing in "Meristaulax granulata Brenner 1988" or "Meristaulax granulata Klement 1960", whichever was of interest. If you do not know the author names, try "Search" instead – titles of matching entries are shown first. Alternatively, browse to the relevant taxon using the other techniques.
2. In the Index, Appendix A contains species names combined with genera not (or no longer) assigned to the dinoflagellates; and Appendix B contains species names combined with modern genera. In DINOFLAJ2, names from these appendices are distinguished from names in the "main index" by the appended terms "Appendix A" or 'Appendix B" after the name. (Note: if the names are also homonyms, the "Appendix" term is added after the author.) Appendix entries can also be found by browsing the taxon lists or using Search.
3. Bibliographic citations are in the conventional form and punctuation. For example:
   • Singh, 1964
   • Fensome et al., 1993b
   • Lentin and Williams, 1993

Entry of accented characters is browser-dependent (check your browser documentation), but if it poses problems, it is always possible to access an entry through the alphabetical lists, or by doing a partial match using "Search".

Once an entry is displayed, various links within the entry allow further navigation. The list of "Categories" at the bottom indicates the categories to which this entry has been assigned. Some of these lists are extremely long, so you may wish to avoid accessing them for performance reasons (the server may take a while to provide them, and some browsers have difficulty displaying the long lists). A special Category, "Parent", will take you to the parent of a taxonomic entry. Some entries also have "children" (e.g., species assigned to a genus), which will be presented as a list towards the bottom of the entry. Clicking on the links will take you to the relevant entry.

In general, hypertext links are shaded blue (though this may change depending upon your browser configuration). A red link in a taxonomic entry means that the link does not point to an existing page, usually due to error on our part. If you find such links, please let us know.

A technical note about spaces and cut-and-paste

Throughout the Dinoflagellate Index document, sentences are delimited by a period and two spaces. This rather minor, if surprisingly controversial, typographic feature is important internally to the programs that parse the Index document into the form used in DINOFLAJ3.

Regardless of the reason for preserving it, this sentence convention poses a problem for display in HTML-based systems on the web because the convention in HTML web browsers is to collapse any "extra" spaces into a single space. It is part of the W3 HTML standard. Without special treatment, cut-and-pasted text from a web browser would therefore differ from the Index document or from the text that is internal to the DINOFLAJ3 system. It would always have a single space between sentences. Because we (RAF, GLW, and RAM) use the DINOFLAJ3 system and often cut-and-paste text from it during our work, it would be a constant source of irritation to have to correct the text to follow the existing convention and our preferences.

One simple way around this limitation is to introduce a "non-breaking space" (HTML  ) as the first of the two spaces after a period. On-screen this looks the same as a regular space but is not "collapsed" by the web browser, and the word-wrap at the end of the line occurs on the following ordinary space. While it is not an ideal solution and there are more fancy (cool but more computationally expensive) solutions, we find it works adequately. Users therefore have two choices upon cut-and-pasting information from DINOFLAJ3 into their favourite document processor:

1. replace non-breaking spaces with ordinary spaces to preserve two spaces between sentences
2. remove the non-breaking spaces to transform it into single spaces between sentences

This approach allows users (or typesetters) to convert the text to whichever sentence convention they prefer. If users have cut-and-pasted text from DINOFLAJ3 into word processing documents they have prepared to submit for publication, it is recommended that you do one of these two search-and-replace operations before finalizing the document.