The A. C. Moore Herbarium (USCH) is proud to offer a few tools that have proved useful to our staff and those of other herbaria in the establishment of a herbarium collections database using Specify collections management software! Cooperation with staff from the South Carolina Department of Natural Resources Heritage Trust Program, the University of South Carolina's A. C. Moore Herbarium (USCH), the Clemson University Herbarium (CLEMS), and the University of North Carolina Wilmington's David J. Sieren Herbarium (WNC) and Center for Marine Science has played a vital role in the development of these tools. While we cannot offer unlimited support for their use, your feedback and suggestions will be used to improve the quality of this content.

SPECIFY 6

Database Files for NEW Specify 6 Users

Botany Taxon Tree (Specify 6)

MySQL method

This Botany Taxon Tree contains 100,071 taxonomic records developed in large part through the combined efforts of the University of South Carolina's A. C. Moore Herbarium (USCH) and the Clemson University Herbarium (CLEMS). Non-algal nomenclatural sources include ITIS, USDA Plants Database, Tropicos, IPNI and others. A significant update (October 26, 2011) to algal nomenclature has been incorporated based on current taxonomic research at the University of North Carolina Wilmington's Center for Marine Science. Many thanks are owed to the developers of the PHYKOS database (Dr. Line Le Gall - Muséum National d'Histoire Naturelle, Brian Wysor - Roger Williams University, Dr. D. Wilson Freshwater - University of North Carolina Wilmington) for sharing the current upper-level taxonomic hierarchy and nomenclature for algae. Species-level nomenclature relies heavily on Algaebase.

Contributors

Herrick Brown	University of South Carolina - A. C. Moore Herbarium (USCH)
Dixie Damrel	Clemson University Herbarium (CLEMS)
Dr. D. Wilson Freshwater	University of North Carolina Wilmington's David J. Sieren Herbarium (WNC) and Center for Marine Science
Dr. Line Le Gall	Muséum National d'Histoire Naturelle
Jessica Luker	University of North Carolina Wilmington's David J. Sieren Herbarium (WNC) and Center for Marine Science
John Nelson	University of South Carolina - A. C. Moore Herbarium (USCH)
D. Alex Vance	University of North Carolina Wilmington's David J. Sieren Herbarium (WNC) and Center for Marine Science
Brenda L. Wichmann	University of Georgia Herbarium (GA) (formerly with WNC)
Dr. Brian Wysor	Roger Williams University

As the size of this file is apparently too large to import via PHPMyAdmin, it is recommended that interested parties use the command shell to complete the importation. To do this, locate your MySQL bin directory which contains the commands necessary to execute the import. For example, "C:\MySQL\MySQL Server 5.1\bin". In the bin folder verify that there is an executable file named 'mysql.exe'. Once this has been verified and located, open the command shell. To do this, in Windows select "Run..." from the Start menu. At the "Open:" prompt type 'cmd' (no quotes) and hit enter or click OK. This will open 'the little black box'. You will probably need to change your directory to the one you located earlier. To do this type 'cd "C:\MySQL\MySQL Server 5.1\bin"' (without single quotes, double quotes are only required around the file path if there are spaces in it) then hit enter. Your directory should change to what you just typed. Next, you will invoke the mysql command. To do this type 'mysql -u USER -pPASSWORD DATABASENAME < "c:\file path to file\FILENAME.sql"' (without single quotes) and then hit enter. Note, space between -u and USER (likely your 'root' username), but no space between -p and PASSWORD (likely the 'root' user password). The DATABASENAME should be the name of your Specify 6 database. Double quotes are only required around the file path to the .sql file if there spaces in it. Repeat this process for both files below (the order in which these file are imported does not matter).

HINT: If you plan to run both imports in succession, you can save yourself a lot of typing. Once the first command has executed and your "C:\DIRECTORY>" prompt returns to the screen, hit the up arrow once and the last command you typed will reappear. Assuming you downloaded both import files to the same directory, you can then use the back arrow to position the cursor over the file name and edit to the next import file name and hit enter.

IMPORTANT!!! Execution of this command will delete any pre-existing TaxonTreeDefItem or Taxon table and the data contained therein. This process has only been tested on versions Specify 6.3.03 through 6.3.07 and the associated database schema.

File downloads have been temporarily disabled due to a pending update. Please contact the developer for more information.

To save, right click then choose 'Save Link As...'
Specify 6.3.03 Taxon Tree Item Definitions for MySQL import 6KB

To save, right click then choose 'Save Link As...'
Specify 6.3.07 Taxon Tree for MySQL import 35MB

CAUTION!!!

Recently, it was discovered that the Taxon Tree offered here is prone to issues when performing Taxon Tree Updates within SPecify6. Due to erroneous ParentID linkages, sub-generic taxa (or polynomials) were recombined incorrectly in the FullName field. These erroneous combinations were reflected in the Taxon picklist when entering Collection Object Determinations. Please use the updated MySQL method above to import the Taxon Tree.

File downloads have been disabled due to apparent issues with taxon tree structure. Please consider the MySQL method above or contact the developer for more information.

Agent (Specify 6)

Many active collectors in the Southeast have distributed duplicate specimens to regional herbaria. Therefore, it may be useful to strive for some standardized representation of individual collector names. The combined efforts of the A. C. Moore Herbarium (USCH) and the Clemson University Herbarium (CLEMS) have generated an exhaustive list of collectors' names that may imported into a Specify 6 database via the Specify WorkBench. Pertinent fields should map automatically, but the file will require splitting as the import only allows 2,000 records at a time (be sure to retain column headers in each split file prior to import). Specify also offers and automated file splitter for this purpose.

You may download the Agent table here:
USCH_Agent_20110217(Sp6Formatted).xls 0.8MB

NOTE: This import has only been tested on a blank Specify 6 database. Importing this file into an established database with existing collectors' names or agents may generate duplicates and other errors.

SPECIFY 5.2.3

Specify 5.2.3 Installation Recordings

As part of the Carolina's SPECIFY 'How to' Workshop (offered March 11 and 12, 2009 and hosted by the A. C. Moore Herbarium with support from SERNEC), we developed several recordings of the initial installation of Specify 5.2.3. These recordings contain screen caps of the installation process and follow the Specify 5.2.3 Installation Manual.

Introduction - Minimum System Requirements
Installation - Part 1 0f 2
Installation - Part 2 of 2

Database Files for NEW Specify 5.2.3 Users

TaxonName (Specify 5.2.3)

The combined efforts of the A. C. Moore Herbarium (USCH) and the Clemson University Herbarium (CLEMS) have created a Taxon Tree with more than 90,000 plant names including lichens, algae and various taxa from around the world. Nomenclatural sources include ITIS, USDA Plants Database, Tropicos, IPNI and others. The Taxon Tree is an excel file that matches the Specify 5.2.3 format and may be copied and pasted into the dbo.TaxonName in a blank Specify database. Note there is a tab for accepted and not accepted names. Accepted names must be pasted into the TaxonName table first and in the order they are sorted (due to constraints placed on records in Specify, we recommend that you do NOT change the sort sequence, otherwise errors might arise). When copying records, do NOT include the column headers.

You may download the Specify 5 Botany Taxon Tree here:
Bug Fix Log
USCH_TaxonName_20090326.xls 44MB

Agent (Specify 5.2.3)

Many active collectors in the Southeast have distributed duplicate specimens to regional herbaria. Therefore, it may be useful to strive for some standardized representation of individual collector names. The combined efforts of the A. C. Moore Herbarium (USCH) and the Clemson University Herbarium (CLEMS) have generated an exhaustive list of collectors' names that may be pasted into the dbo.Agent in a blank Specify database.

You may download the Agent table here:
USCH_Agent_20090401.xls 0.8MB

Geography (Specify 5.2.3)

USCH and CLEMS are offering their combined geography data which includes many extralimital place names in addition to the core geography that ships with Specify 5.2.3. To add this dataset to the dbo.Geography in a blank Specify database requires the deletion of some records first. Open the dbo.Geography in a blank Specify database. You will notice that the table is prepopulated with geography values that are part of the installation. By selecting the upper left corner of the dbo.Geography you can select all of the existing records. Once selected, hitting 'delete' will delete all of the geography values (don't worry, you will replace them with the paste operation). Once your dbo.Geography is empty, you can paste the USCH and CLEMS geography into the dbo.Geography.

You may download the Geography table here:
USCH_Geography_20090401.xls 2MB