Difference between revisions of "USING DINOFLAJ3"

Latest revision as of 12:45, 6 January 2017

Users should be familiar with the basics of Linnean classification and the organization of the Dinoflagellate Index (Williams et al., 2017; See Introduction) 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 those that 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:

• 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;
• Select from a hierarchical "Table" of the suprageneric classification
• Browse a list of Family or other suprageneric ranks
• Browse an alphabetical list of Genera
• Browse an alphabetical list of Species, or subspecific taxa (ordered by the epithet)
• Browse an alphabetical list of bibliographic References
• Browse an alphabetical list of Glossary entries
• 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:

• A list of only the taxa in the "Main Index" (exclusive of Appendices)
• A list of Appendix A and Appendix B entries
• A list of calcareous fossil dinoflagellates
• A list of siliceous fossil dinoflagellates
• A list of taxa for which new entries have been added for this version (mostly taxa published since 2004) ("New Taxa")
• A list of taxa for which the entires have been changed for this version because of new taxonomic changes or observations (e.g., new combinations or synonymies) or to correct errors ("Changed Taxa")
• A list of entries with drawings ("Taxa with images")
• A special "What links here" page that lists other pages that link to the current one.

Some conventions exist for the titles of the entry pages:

• 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.
• 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 (See Introduction for a full explanation). In DINOFLAJ3, 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.
• Bibliographic citations are in the conventional Index form. 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 computationally more 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. Therefore, 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.

A technical note about linking and bookmarks

There are some issues to be aware of when establishing bookmarks or when linking to DINOFLAJ3 pages from other web sites. Normally a taxon or reference can be cited via a predictable and stable URL, but there are some subtle issues:

1. Homonyms. Already discussed above. Homonym pages are made unique by adding the author citation at the end of their name. While this should be a relatively stable URL in most instances, sometimes the interpretation of the year of publication by an author may change between DINOFLAJ versions (e.g., 1837a to 1838c), thus changing the title of the page and URL for the homonym. The changes are generally due to a further research and a better understanding of when an article was effectively published. Thus, this issue is especially pertinent with regard to early publications.
2. A similar issue exists for links to Appendix entries, which have "Appendix A" or "Appendix B" appended to the end of the taxon names. This can create issues if the taxon happens to change status from one edition of DINOFLAJ to another (e.g., moving from the Main Index into an Appendix or vice-versa). The URL will change, and thus a previously-established link may break.
3. Orthographic changes between versions are relatively rare. Approximately 6 taxa had changes in their orthography between DINOFLAJ2 and DINOFLAJ3, and thus the URLs for those pages have correspondingly changed.
4. References can change their year of effective publication or sometimes even the correct spelling of their authorship may change (e.g., transliteration from other languages). This again can result in a changed page title and URL. This is especially an issue for recent changes to the interpretation of publication year for 19th-century publications by Ehrenberg.

All four cases are uncommon, but unfortunately they mean that stable URLs cannot be absolutely guaranteed between different versions of DINOFLAJ for all taxa or references. Currently no URL forwarding mechanism has been implemented for changes of these types.