Databasing Tools
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
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
Bug Fix Log
Botany Taxon Tree (Specify 6)
MicroSoft Access method
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.
The combined efforts of the A. C. Moore Herbarium (USCH) and the Clemson University Herbarium (CLEMS) have created a
Taxon Tree with more than 94,000 plant names including lichens, algae and various taxa from around the world.
Nomenclatural sources include ITIS, USDA Plants
Database, Tropicos, IPNI and
others. The MS Access file contains two tables and two append queries which are designed to append the data to the
corresponding tables in a Specify 6 database that contains no prior taxon tree info.
In order to append these data, you must first establish an ODBC connection to your MySQL Specify 6 database. To
create the ODBC connection, you will need the MySQL ODBC
connector. Once you have established the ODBC connection, you can connect to your MySQL database with MS Access by
selecting File>Open... and choosing "ODBC Databases()" from the Files of type: dropdown menu. Another window will open
prompting you to select a data source. Select your Specify 6 database and click OK. You will then be prompted to import
linked tables. You only need to highlight and import the taxon and taxontreedefitem tables.
Once you have imported these linked tables you will need to import the tables and queries from the downloaded
Specify6BotanyTaxonTree.mdb file. To import the Botany Taxon Tree tables and queries into your Specify 6-linked MS Access
file, in Access 2007 select the External Data tab and choose the Access button, navigate to the file
Specify6BotanyTaxonTree.mdb and follow the prompts (in earlier versions of Access, this option can be found under
File>Get external data...>import...). Import the two tables (Specify6TaxonTree and Specify6TaxonTreeDefItem) and the two
queries (APPEND1_RunFirst(TaxonTreeDefItem) and APPEND2_RunSecond(Taxon)). The final step involves running the two
queries in the order indicated by their names.
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.
You may download the Specify 6 Botany Taxon Tree here:
Bug Fix Log
Specify6BotanyTaxonTree.mdb 37MB
Fix for versions downloaded prior to April 21, 2010. See Bug Fix Log for details.
NOTE: You only need this file if you downloaded the Specify 6 Botany Taxon Tree prior to April 21, 2010.
UPDATE-to_make_preffered_taxon_work.mdb 184KB
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
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