A Synonymized Checklist of the Vascular Flora of the United States, Puerto Rico, and the Virgin Islands
Full Text Index - July, 1998

OVERVIEW:  Synonymized nomenclatural treatments express the best available 'fit', in the view of the author, between biodiversity and phylogeny in that hierarchial placment of taxa represents patterns of relative affinity and difference.  Floristic information for a given geographic region is often available as hardcopy floras and manuals that present data on that region's flora within the context and framework of a synonymized array of taxon names that are organized within a nested hierarchy.  While species-specific information, such as distribution, is an important data element of a floristic treatment, the nomenclatural treatment is of fundamental significance in that it provides both a superstructure for placement of species-specific data and an expression of current knowledge regarding patterns of biological relationships.  Systematic research is focused on defining patterns of biological or phylogenetic relationship and, as a result, our picture of affinities and differences is constantly changing.  Traditional publication of floristic treatments as hardcopy documents does not accomodate this change, i.e., these documents are obsolete on the date of issue.  This problem can be resolved via expression of floristic data within a digital context which allows relatively easy 'versioning' or updating.  Thus, a primary rationale for development of this website is the capability for immediate update and change.  Hardcopy publication of floristic data is also 'fixed' with regard to content whereas the potential for data expansion of digital data is unlimited.  Thus, work with this site has also centered on development of systems that allow incorporation of relevant species-specific data that might be openly available on the network.  Digital expression of floristic data also opens a new suite of computational options relative to traditional publication of floras and manuals.  Exploration of these is another focus of site development via collaboration between the Biota of North America Program and the Texas A&M Bioinformatics Working Group.

PROCEDURES:  Production of this site involves - in essence - conversion of two BONAP data files (nomenclature and geographic distribution) to binary data tables that can be processed by local (Win95) database programs.  Two separate programs act on these tables to produce two large ASCII files.  Actions include HTML formatting and insertion of various reference links to either outside or local sources of ancillary data for each species.  The two large ASCII files generated by these programs are transferred to a specific UNIX server directory the Center for the Study of Digital Libraries and indexed using Managing Gigabytes (MG).   Indexing is accomplished automatically when new ASCII files are generated via a 'big button' web page.  The indices place each species as a basic MG 'document'.  Once indexing is accomplished, the indices are available for query from any network node.  The frame-based user interface of this site functions - in essence - to send pre-formatted URL queries to either the mapping or nomenclature index.  With the exception of the 'String Query' option, all involve programmed (Win95) interaction with the two base data tables to generate suites of alphabetical and taxon-based query pages that allow the user to 'mouse click' through the data.  However, the indices can be queried from 'outside' the user interface using an appropriately formatted URL.  The nomenclature index is available for query via the URL:

http://www.csdl.tamu.edu/FLORA/cgi/ruled_html_query?colldir=kartesz%2Fmgdata&collname=bonap98&query=whatever

with 'whatever' replaced by the desired query string.

The diversity mapping index can be queried using the URL 'root':

http://www.csdl.tamu.edu/FLORA/cgi/b98_map?

with, after the ?, addition of the following (Replace items in [] by the taxon name (so "genus=Bouteloua"):

all=yes (to map everything - all taxa)
group=[group_letter] where [group_letter] is P(Pteriodphytes)),G(Gymnosperms),M(Monocots), or D(Dicots)
subclass=[subclass_name]
order=[order_name]
family=[family_name]
genus=[genus_name]
genus=[genus_name]&species=[species_name]
genus=[genus_name]&species=[species_name]&tri=[tri_name]
genus=[genus_name]&species=[species_name]&tri=[tri_name]&quad=[quad_name]

For the species, tri, and quad views, by default you get the distribution map for that level. If you add "&show_infras=yes" to the URL, you get the diversity map for the next lower level down, that is, adding show_infras=yes to a species-level URL shows you the diversity of the tri-level items and adding it to a tri-level URL shows you the diversity of the quads.