Specify at the Biodiversity Centre

Saturday, 9 July 2011

This post replaces an obsolete static page of the Canadensys website, which was last updated on June 8, 2010. We have since moved to FileMaker Pro for our database needs, which – although not perfect or cheap – allows batch importing, editing and exporting: features missing from Specify at the time (see also my message to Specify) and absolutely necessary for our data cleaning procedures. The database we developed in FileMaker is also less complicated (and thus more easily understandable) and highly customizable. The files and guidelines presented below are published in the hope that they will be useful for other Specify users, but they are no longer updated and we offer no warranty they will work. Please use at your own risk.

Introduction

We are using Specify for the collections at the Université de Montréal Biodiversity Centre and we want to share our experience and guidelines on this page. The collections that will be using Specify are:

• Marie-Victorin Herbarium (MT)
• Ouellet-Robert entomological collection (QMOR)

List of Specify fields we use

The following document is a list of the Specify fields we use per collection. We decided to follow the intended use of the Specify fields as closely as possible, as it will be more understandable for future database managers and to avoid problems with software updates. The file was first introduced in this Canadensys forum post and is updated as we go.

Information about this document

Column 1 & 2: Specify table and field name, logically grouped by colour.

Column 3: Correlating field in the Specify WorkBench.

• White: The field is available in the WorkBench by default.
• Orange: The field is not available in the WorkBench.
• Yellow (added to xml): The field is added by us to the WorkBench by editing the xml files (see below). We hope to add all the fields we need eventually.

Column 4: Indication if the field is visible in the Specify user interface.

• Green (y): The field is visible by default. This may depend on the collection type: botany, insect.
• Green (xml): We added the field to the user interface by editing the xml files. We hope we can add all the fields we need eventually.
• Orange (n): The field is not (yet) visible in the user interface.

Column 5: Explanation and remarks regarding the field or why we choose that field.

Column 6: Field length in Specify. Useful to detect limitations.

Adding fields to the WorkBench

Not all fields of the Specify database are available in the Specify WorkBench (see this outdated list), but most can be added rather easily by editing two XML files. Below you can find the versions we created. To see what fields we have added, see column 3 of Specify fields used at the Université de Montréal Biodiversity Centre (see above).

• /Specify/config/specify_workbench_datamodel
• /Specify/config/specify_workbench_upload_def

How to install a Specify xml file

• Download the file. Select ‘File > Save page as’ if the xml file opens in your browser.
• Go to indicated folder of your Specify installation folder, for example: /Specify/config.
• Rename the current (default) file to ‘<filename>_default.xml’ so it is backed up.
• Move the downloaded (custom) file to the folder.
• Open Specify to check if everything works correctly.

Important: if you update Specify, it will overwrite the custom files with the default ones. Backup the custom files before you update!