Specimen Data Management

The central purpose of Symbiota is to create an integrated biodiversity web resource that is specifically built upon a foundation of specimen and observation datasets. Typically, this is accomplished by individual collections periodically publishing a data snapshot from a central database managed within the home institution. Therefore, robust specimen management has not been a central goal for Symbiota portal development. However, it has become apparent that many collections do not have the technical resources and personnel needed to properly manage and publish an in-house database. For this reason, Symbiota has been developing basic online support for managing specimen data. This has allowed several collections to move away from the snapshot model to maintaining a live dataset directly within the portal.

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Establish “snapshot” or “Live Dataset”?
Before a collection manager decides to use a Symbiota portal as their central data management tool or just to feature a snapshot data, they should weigh the pros and cons and decide on a data management strategy that best fulfills their needs.

Pros:

  • Edits and new records are immediately available online
  • No need for infrastructure to periodically publish data to a Symbiota portal
  • No need for software purchase, installation, or updates
  • Platform independent management tool collection can be managed on a PC, Mac, etc.
  • Remote and multi-terminal management is built into the system
  • Exchange data can be easily imported from other participating institutions
  • Portal can offer data cleaning and georeferencing support
  • Crowdsourced data error detection and cleaning is available
  • Collection is not responsible for backups, server maintenance, etc.

Cons:

  • System is not specifically designed as an all-inclusive specimen management tool
  • Limited report and invoice options
  • Customized specimen labels are not yet supported by system; however, custom labels are possible using the MailMerge function in MS Word
  • Collection is reliant on portal to properly maintain regular backups. However, each institution has the ability to periodically download their dataset, thus establishing an additional off-site backup layer

If a Symbiota portal is used to feature a snapshot of a collection managed within the home institution, methods are needed to periodically refresh the data snapshot. Symbiota has several tools and protocols to facilitate this (see Data Interoperability). As long as a Primary Key can be maintained for each specimen record and the data can be rendered as a compatible export file, refreshing specimen data is typically a straightforward task. If determination history and image data are to be included in data transfers, portal updates are slightly more involved. Furthermore, if record edits are made within a portal (e.g. approved user corrects coordinates), the source institutions may need to develop their own methods to integrate the edits back into their central database. A benefit to managing specimen data directly within a portal is that it reduces the complexity of the data interoperability by removing the need to support bidirectional transfer protocols.

As noted above, the Symbiota data entry interface has the ability to import records previously entered by another institution. This feature is particularly useful for reducing the retyping of specimen records obtained by exchange. For example, if one enters the collector name and number into the data entry form and then clicks the Dupes button, a list of possible matching duplicate records will be displayed that have previously been entered by another member of the consortium.  Therefore, one only needs to select the best match from the list, enter their unique catalog number (accession), and click Save.

The duplicate import feature has the additional potential for reducing the need to key-in incoming specimens obtained by researchers and local collectors. Active collectors have the ability to enter newly acquired collection information into an observation project and print their specimen labels online directly from the portal (see Specimen Label Printing). When a collection receives the specimens from the collector, they will then be able to use the duplicate import feature to transfer the data into their own collection once it is properly accessioned. The significance of this workflow is that a specimen record is only entered once by the original collector without the need to reinterpret and key-in the specimen label at each of the receiving institutions. Furthermore, if the collector uploads an image of the live specimen obtained at time of collection, this image can remain associated with the physical specimens. For collectors to make use of the data entry and label printing functions, they should contact their regional collections for sponsorship.

Typically, Symbiota portals will only have a single, default label format available. In situations where the user requires a custom label design, they have the option of printing labels using MailMerge, or managing their specimen data within a desktop application for import into the portal at a later date. Several desktop applications have been developed using Microsoft Access or FileMaker database platforms. An additional option is to use the Specify EZDB specimen management application, which includes an imbedded database. The Specify 6 software project offers a set of tools for robust, full-service management of specimen data. Since they offer data import/export options that are compliant to commonly used data exchange standards, transferring data between a Specify database and Symbiota Data Portal is rather straightforward.

Sample of local Management Tool:

Specify EZDB: http://specifysoftware.org/download/
-Program listed around 2/3 down the page