GCE-LTER Taxonomic Database: An automated database application for

displaying custom species lists on the web

Wade SheldonWade Sheldon

GCE Information ManagerGCE Information Manager

GCE WWW Site: http://gce-lter.marsci.uga.edu/lter/

Design Goals Create database structure to store taxonomic information Create database structure to store taxonomic information

for GCE-LTER (plants, animals, fungi)for GCE-LTER (plants, animals, fungi) Create web application to generate dynamic species listsCreate web application to generate dynamic species lists

Pre-defined lists (GCE researchers)Pre-defined lists (GCE researchers) User-customized lists (by taxa, habitat)User-customized lists (by taxa, habitat) Multiple formats (list, table, CSV file)Multiple formats (list, table, CSV file)

Automatically Include links to ancillary information Automatically Include links to ancillary information (habitats, voucher specimen, GCE data sets, site (habitats, voucher specimen, GCE data sets, site occurrences, photos, pubs)occurrences, photos, pubs)

Support LTER cross-site syntheses, educational programs, Support LTER cross-site syntheses, educational programs, add value to data setsadd value to data sets

Components Relational database (SQL Server)Relational database (SQL Server) Database front-end application for entering/editing Database front-end application for entering/editing

taxonomic info and managing web lists and page taxonomic info and managing web lists and page captions (Access Data Project)captions (Access Data Project)

Dynamic web pages to build queries, display Dynamic web pages to build queries, display results (ASP)results (ASP) List catalog page (with custom list selector form)List catalog page (with custom list selector form) Species list pageSpecies list page Taxonomic details page with links to ancillary infoTaxonomic details page with links to ancillary info Species table pageSpecies table page CSV file generator pageCSV file generator page

Web application server (IIS)Web application server (IIS)

WWW Species List Selection Page

http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp

WWW Species List Page

WWW Species Detail Page

WWW Species Table Page

Species Table Download (CSV File)

Kingdom,Phylum/Division,Class,Order,Family,Genus,Species,”Common Name”Animalia,Mollusca,Bivalvia,Eulamellibranchia,,Cyrenoida,floridana,”Florida or Dall’s Marsh Clam”Animalia,Mollusca,Bivalvia,Eulamellibranchia,,Polymesoda,caroliniana,”Carolina Marsh Clam”Animalia,Mollusca,Bivalvia,Eulamellibranchia,,Tagelus,plebius,”Stout Razor Clam” Animalia,Mollusca,Bivalvia,Filibranchia,,Amygdalum,papyrium,”Paper Mussel”Animalia,Mollusca,Bivalvia,Filibranchia,,Crassostrea,virginica,”Eastern or American Oyster”Animalia,Mollusca,Bivalvia,Filibranchia,,Geukensia,demissa,”Ribbed Mussel”Animalia,Mollusca,Bivalvia,Archaeogastropoda,,Neritina,usnea,”Olive Nerite”............

Data Entry, Web Management Application Task-based forms developed to ease data entry (MS Task-based forms developed to ease data entry (MS

Access ADPs connected to remote SQL Server)Access ADPs connected to remote SQL Server) Add/Update taxonomic listings, define links to ancillary Add/Update taxonomic listings, define links to ancillary

information (photos, files, vouchers)information (photos, files, vouchers) Define species lists, including taxa to include, sort orders, Define species lists, including taxa to include, sort orders,

web page labels and captions, responsible partiesweb page labels and captions, responsible parties Maintain lookup tables used by forms, web menusMaintain lookup tables used by forms, web menus Direct database access only provided to authorized GCE Direct database access only provided to authorized GCE

investigators, IM staffinvestigators, IM staff Database integrity protected using granular role-base Database integrity protected using granular role-base

security scheme, DRI constraints, list-based entry of security scheme, DRI constraints, list-based entry of primary/foreign keysprimary/foreign keys

Data Entry Forms – Main Task Menu

Data Entry Forms – Upper-level Taxa

Data Entry Forms – Lower-level Taxa

Data Entry Forms – Web List Management

Database Schema

(ERD on WWW)

http://gce-lter.marsci.uga.edu/lter/files/erds/gce_taxonomic_erd.pdf

Concluding Remarks Web-management tables in database allow designated Web-management tables in database allow designated

researchers to define/edit web lists in real time without researchers to define/edit web lists in real time without HTML editing (including labels, captions, menus)HTML editing (including labels, captions, menus)

Shared keys, junction tables used to link taxonomic Shared keys, junction tables used to link taxonomic records with other GCE databases (metadata, geography, records with other GCE databases (metadata, geography, personnel, publications), support automatic hyper-linkingpersonnel, publications), support automatic hyper-linking

Future development: starting to incorporate ITIS TSN Future development: starting to incorporate ITIS TSN identifiers to support complete taxonomic lookup, identifiers to support complete taxonomic lookup, systematics researchsystematics research

Caveat:Caveat: RDMS not always ideal for managing highly hierarchical RDMS not always ideal for managing highly hierarchical data like taxonomic listings, so compromises usually required; data like taxonomic listings, so compromises usually required; however, there are significant benefits like excellent development however, there are significant benefits like excellent development tool support and performance, technological stability, many web-tool support and performance, technological stability, many web-enabled features in latest versions (XML, web queries)enabled features in latest versions (XML, web queries)