Botanical Cyberinfrastructure: Issues, Challenges, Opportunities, and Initiatives
Cellinese, Nico , Beaman, Reed S. , Green, Ashley M. , Smith, Stephen A. , Donoghue, Michael J. .
TOLKIN - Tree OF Life Knowledge and Information Network: managing a forest of Ents.
TOLKIN, formerly known as the Botany Browser, is an information management and analytical web application actively being developed by the Yale Peabody Museum to provide informatics support for phylodiversity and biodiversity research such as that funded by the NSF Assembling the Tree of Life (AToL) and Planetary Biodiversity Inventory (PBI) programs. TOLKIN actively supports the Angiosperm and the Liverwort AtoLs; funding for the Euphobia PBI and Gymnosperm AToL are pending. As a web-based application, collaborators in different locations and environments can access shared data on voucher specimens, taxonomy, bibliography, morphology, DNA samples and sequences. Automated out-links are currently available to relevant external data resources e.g, IPNI, GenBank, TreeBASE, and BioGeomancer. A developing analytical component of TOLKIN includes workbench functionality for analysis of sequence data by automating the assemblage of Fasta files, alignments, and output of Nexus files, in addition to sequence BLASTing capability. Our current funding supports work to integrate tools for phylogeographical analyses, including estimation of phylogeographic diversity (PD Explorer), and phylogenetic tree navigation. A major goal of our bioinformatics research is integration with other funded and proposed informatics projects. Numerous initiatives (e.g., MorphBank, CIPRes, SEEK, TreeBASE, GBIF, GenBank, IPNI, and BioGeomancer) are developing tools useful for ToL and biodiversity research, and there has been growing interest in coordinating informatics research across the AToL and PBI communities. For example, we are actively collaborating with the MorphBank project for long-term management of morphological images used in phylogenetic analysis. We are planning future development through a web services framework that can be accessed through online workbench applications. A web services framework provides the best opportunity to integrate new ATOL resources with existing tools that are being developed in various ATOLs, as well as MorphBank, CIPRes, BioCorder, and other bioinformatics tool development projects that are using or will be using web services.
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1 - Yale University, Peabody Museum of Natural History, Botany Division, Po Box 208118, New Haven, Connecticut, 06520-8118, USA
2 - Yale University, Peabody Museum of Natural History, Biodiversity Informatics, Po Box 208118, New Haven, Connecticut, 06520-8118, USA
3 - Yale University, Department Ecology & Evolutionary Biology, Po Box 208105, New Haven, Connecticut, 06520-8105, USA
Tree of Life.
Presentation Type: Symposium or Colloquium Presentation
Location: 206/Performing Arts Center
Date: Monday, July 31st, 2006
Time: 1:30 PM