Electronic Tagging Data Repository

Background

John Sibert

Pelagic Fisheries Research Program

A presentation at 2003 meeting of the Standing Committee on Tuna and Billfish explored differences in vertical distribution and behavior of bigeye tuna in different parts of the Pacific Ocean. The author stated that the work was made more difficult because of problems encountered in accessing relevant archival tagging data. Subsequently several scientists from around the Pacific sent a request to the Pelagic Fisheries Research Program to use the auspices of the PFRP to host an electronic tagging data exchange facility.

This simple request evolved into a more complex project than originally envisaged. A talk by Bill Michener of Long Term Ecological Research Network (LTER) at the 2003 PFRP Principal Investigators workshop convinced me that a simple password protected web page would not be of long-term value. It is equally important to document the data being shared.

We have adapted the data sharing and documentation tools created by Knowledge Network for Biocomplexity (KNB). The KNB “focuses on research into informatics and biocomplexity, through the development of software products and by providing education, outreach and training”. It is sponsored and developed by the National Science Foundation Knowledge and Distributed Intelligence Program, National Center for Ecological Analysis and Synthesis, Texas Tech University, Long Term Ecological Research Network, and the San Diego Supercomputer Center. The KNB toolbox includes: (1) Ecological Metadata Language (EML) a XML-based metadata standard, (2) Metacat, a web server for managing EML data bases, controlling access, searching, and uploading and downloading, and (3) Morpho, a java program for assembling EML data bases, and importing and exporting data.

We have implemented a secure metacat server on a dedicated computer at the Joint Institute of Marine and Atmospheric Research at the University of Hawaii. By adopting the KNB tools, we avoid the having to reinvent several wheels. Another advantage of the KNB tools is that we could, if necessary, transfer files to the KNB website where our material would, in principle, be archived permanently. The KNB system is widely used, and thousands of data sets publicly available on their website.

Simple data documents can be created using Morpho interactively. More complex data, such as raw data downloaded from archival tags, are less conveniently processed by Morpho. We have created “templates” and scripts that can be used to import such data into EML format. Once the data have been imported into EML, you can use Morpho to complete the metadata and upload data documents to this site.

EML provides complete control of access to data documents. Access can be restricted to specified users of the repository, or data can be specified as being freely accessible by anyone.

Morpho is a useful tool for using this repository. We have provided an specialized version of Morpho that has been modified for use with this repository.