TAPIR FIMS

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TAPIR, or TDWG Access Protocol for Information Retrieval, is a standard protocol for sharing specimen data. The TAPIR FIMS connection reads in tissue data from a TAPIR server.

Integrating museum collection management systems (CMS) or field information management systems (FIMS) to a laboratory information system (LIMS) reliably can be difficult. Often, data needs to be exported and then re-imported into each system. The TAPIR protocol is an attempt to standardise the way in which collection databases communicate, and to remove the dificulties associated with collaborative collection managment.


Setting up a TAPIR provider with LIMS extension

These instructions assume the use of the TapirLink software (written in PHP), a collections management database with tissue records, stored in a TapriLink-compatible relational database, and the free version of Geneious (biomatters software), with the Biocode plugin installed.


  • Step 1: Setup TAPIR
There are several TAPIR software installation tools (http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirSoftware). This tutorial assumes you are using the Tapirlink software available (http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink).
TapirLink requires a webserver running PHP, with an appropriate module to connect to your FIMS database. We recommend Apache, although this is not required. Download the TapirLink installation archive, and follow the installation instructions included.


  • Step 2: Incorporate the LIMS extension into the TAPIR provider
While setting up your TAPIR provider (or afterwords), be sure to include the LIMS extension as an additional schema (available at: http://biocode.berkeley.edu/schema/lims_extension.xml). You will be asked to map your local database fields to the LIMS extension fields.


  • Step 3: Point the Geneious LIMS system to your TAPIR provider link.
Richt-click on the biocode icon in the service tree on the left hand side of the main Geneious window, and click "login". Choose "TAPIR" from the field database dropdown at the top of the connection dialog, and enter the address of your TAPIR server. Choose a LIMS database (see Remote LIMS and Local LIMS), and click OK.