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Towards an Integrated Database for Fish Evolution

A NESCent Working Group

Model systems provide a way to untangle complex problems. Often concepts worked out in organisms such as fruit flies or frogs can be applied to other systems, including humans. Zebrafish have become a primary model for studying developmental genetics and evolutionary developmental biology, or "EvoDevo". Ichthyologists (fish biologists) have also studied zebrafish, among other cypriniforms (generally small, tropical fish like minnows, barbs, carps and goldfish), to understand their evolutionary relationships. Groups that work on the same organism, but from different viewpoints can learn a lot from each other and potentially advance their science dramatically by combining their information. However, developmental biologists and fish evolutionists have not historically interacted to a great extent, and generally have not "spoken the same language", making collaboration and interaction challenging.

This working group brings together members of the zebrafish research community (including those involved with the Zebrafish Information Network - ZFIN) and the Cypriniform research community (including those involved with the Cypriniform Tree of Life, or CToL, project) with the goal of linking information from both fields. The group proposes to join databases to combine the genetic information from developmental biology with the morphological data from evolutionary biology. One of the key challenges for this group is finding a common language, since every field has its own jargon and the same term can mean different things in different fields. One way of accomplishing this is by using ontologies, which are hierarchical constrained vocabularies. Another challenge will be determining how best to use the available data. What kinds of information would be most useful? How should one kind of information be linked to another? The group will tackle the logistics of developing such a database, from basic data entry curation through programming, beginning with a prototype.

The Fish Database Workgroup had their first meeting at NESCent November 4-7, 2005. The focus of our second meeting from April 9 to 11 was on tying homology relationships into anatomy, taxonomy, and phylogeny ontologies. We began technical discussions of developing taxonomy ontologies and how to reference anatomy using such ontologies. We talked through the coding of multiple systematic characters using two ontologies (Anatomy and PATO).

Participants are:

Paula Mabee, University of South Dakota

Monte Westerfield, University of Oregon

Miles Coburn, John Carroll University

Melissa Haendel, University of Oregon

Erik Hilton, Field Museum of Natural History

John Lundberg, Academy of Natural Sciences

Carol Lushbough, University of South Dakota

Rick Mayden, St. Louis University

Nelson Rios, Tulane University

Gloria Arratia, University of Kansas