Texas A&M Bioinformatics Working Group

Program description pages are generated by programs that produce experimental WWW products of the Texas A&M Bioinformatics Working Group. These provide an archival reference, a reminder of how things were done, a tracker of various files involved, and general information.
GATEMAK1.IPF, generates a base HTML file - FPGFAMZZ.HTM - that carries alphabetical links to a series of 25 HTML pages [FPG?FAM.HTM] that are also created as the program 'walks' through the data table FULLFAM1.ITB. This table carries a listing of 1,682 vascular plant family names in alphabetical order and a numerical field that tracks the number of links established for each family when the program VASCWWWO.IPF is run. VASCWWWO creates a text file [VASCWWWO.TXT] that, when indexed, is the source for queries by family name to produce the URL listings in this version of the flowering plant gateway. As it moves through FULLFAM1, the program consults data tables carrying all family names used in the Cronquist (CRONQ3.ITB), Thorne (THORBASE.ITB), Takhtajan (TAKFAM.ITB), and Angiosperm Phylogeny Group (APG.ITB) flowering plant classification systems. As of July 1999, it also consults a data table (FERNGYM.ITB) that carries a classification of non flowering vascular plant families. Each of these source tables are indexed by family name and each family name present in FULLFAM1.ITB is used as a query string to all data tables using the 'pluck' function of Kman. If a family record is present in a given source table (#found=true), Gatemak1.ipf inserts appropriate links, depending on data present or absent in text or numerical fields of the record. This 'walk' occurs within a 'while loop' that also checks the first character of family names as it proceeds through FULLFAM1.ITB and forms a new HTML page with each change and, at completion, output of this page.

GATEMAK1.IPF is being built with Kman database programming code and Kman database files created by Hugh Wilson. The primary reference table, FULLFAM1.ITB, contains family names present in several on-line data sources (USDA-GRIN, KEW, BONAP) that were added to a local file that initially carried 736 names. The Thorne and Takhtajan databases are being developed from files provided by James Reveal at the Norton-Brown Herbarium. The URLs utilized to search the indexed file function via CGI programming and 'full text' indexing performed by Erich Schneider, during his tenure with the Texas A&M Center for the Study of Digital Libraries.

Last run of GATEMAK1.IPF: 05/10/2000

Total names checked from FULLFFAM1.ITB: 1679

Total names used from CRONQ3.ITB: 728
  Cronquist accepted names: 389
  Cronquist synonyms: 339

Names used from THORBASE.ITB: 451

Total names used from TAKFAM.ITB: 1399
  Takhtajan accepted names: 592
  Takhtajan synonyms: 807

Total names used from APG.ITB: 757
  Angiosperm Phylogeny Group accepted names: 476
  Angiosperm Phylogeny Group synonyms: 281

Total names used from FERNGYM.ITB (non flowering vasc plants): 63

FULLFAM1 names not present in any reference table: 131

Families with internet info: 859
  Total links referenced: 7563

Families with a VPIG page: 290

Start run: 10:06:31
End run: 10:09:18

This page produced by gatemak1.ipf on: 05/10/2000