Junior Bioinformatics major at Loyola University
REU Mentor: Dr. Scott Lidgard (Curator, Geology)
Symposium Presentation Title: Bryozoan Biodiversity on the Web
Symposium Presentation Abstract: The goal of this project is to put taxonomic, bibliographic, photographic, geographic data on the web. It should be easy for experts to contribute to or edit the data. It should also be easy to download the data or perform queries to reveal new information. There already exist a number of personal websites with overlapping data in custom formats. They offer advantages like freedom to post anything in any format. However, there are disadvantages. For example, the existence and maintenance of the sites depends on each individual author. Also, it’s not possible to perform a revealing query on the data from all such sites. So, the community would benefit from an effort to aggregate all available data into a central database. There are a many databases that handle aggregation of taxonomic information. For the Bryozoan research community, we prefer a database that not only allows, but promotes activity by community members. After evaluating several options like MediaWiki or Encyclopedia of Life (EOL), we decided to use Scratchpads. It is the most immediately available solution that has the right balance of freedom, ownership, and customization.
During the past three months, I wrote scripts in Perl and PHP to handle names, synonyms, and authors for 2,653 taxa of rank genus and higher and 20,044 species and subspecies. There are several sources of data, so I checked, compared, and combined them into a format suitable for import into Scratchpads. This is the first step in the move to a central database for the Bryozoan research community. There are problems with the import, but once it is complete, it will serve as a foundation for the community to contribute their content.
Original Project Description: This project is part of the development of an accessible, open-source research database. It deals with a remarkable group of colonial animals – the Bryozoa. They are unlike most animals in that many asexually budded modules, or zooids, comprise the body of a single genetic individual, the colony. Much of their taxonomy is based on the fact that these modules can be different morphologically (polymorphic), even though they are identical genetically. The evolution of complexity is richly portrayed in their fossil record, as zooid polymorphism has evolved repeatedly. They dwell on hard substrates and living ones in all the world's oceans and freshwater streams and lakes. Their colonies are essential habitats for fishes and countless numbers of invertebrates, thus playing key roles in benthic ecosystems and in our comprehension of marine biodiversity. However, their zooids are small, their taxonomy is complex, and they are grossly understudied.
The overarching goal, in which this project is a crucial stage, is to provide an interactive workspace for the worldwide community of bryozoan systematists and researchers. As the resource develops further, we will serve a broader audience of ecologists, evolutionary and conservation biologists. To this end, Field Museum is now becoming the second installation of Scratchpads (http://scratchpads.eu/about), a social networking application that enables communities of researchers worldwide to manage, share and publish taxonomic data online. Our initial progress includes a Linnaean taxonomy for all living and fossil bryozoans that contains over 40,000 species binomials (valid and synonym). We have completed a preliminary genus listing, but have yet to validate the species binomials. We believe this task is best suited to contributions from the entire research community. The project grew out of The Bryozoa Home Page (www.bryozoa.net), over 4,000 hyperlinked html pages of taxonomy, morphology, images, and references. However, the Home Page does not facilitate cooperative, interactive editing. This project is about overcoming the obstacles to interactive research community development of a fully relational information resource. Our goal this summer is to prepare and load the entire species listing and higher taxonomy into Scratchpads, making the information available for online contributions and editing by bryozoan systematists. We will also be concentrating our efforts on implementing the existing Scratchpad modules for bibliography, images, distribution records, a glossary and more.
Research methods and techniques: REU participants with bioinformatics/programming experience are particularly encouraged to apply, but all applicants will be considered. Participants in this project will receive an introduction to bryozoan morphology and systematics. They will also receive instruction and hands-on experience in biodiversity database design practices, and strategies for accommodating systematic and biogeographic analyses of species morphology, bio-molecular data, and geographic occurrences. They will actively participate in designing, implementation, and testing phases of the project. Scratchpads utilizes the Drupal content management system. Drupal modules are written in PHP, as are some of our tools for data cleaning and validation. Depending upon levels of expertise, participants will have the opportunity to co-develop Drupal modules and validation tools in PHP for the broader cyber-taxonomy community.