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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, Gymnosperm and Liverwort AToLs, as well as the Euphorbia PBI. 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 such as IPNI, Tropicos, GenBank, ING, TreeBASE, and BioGeomancer. Functionality of these concepts for botanical data was demonstrated by Nico Cellinese (2002) in a prototype tool, FileTaxon, developed with FileMaker Pro.

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, Morphobank, CIPRes, SEEK, TreeBASE, BioCorder, GBIF, GenBank, IPNI, UBio, Lifemapper, 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 at Florida State University for long-term management of morphological images used in phylogenetic analysis.

We are planning future development of TOLKIN 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.



Funded by the National Science Foundation
NSF-ATOL: Collaborative Research: Resolving the Trunk of the Angiosperm Tree & 12 of its Thorniest Branches (NSF-0431258)
NSF-ATOL: Collaborative Research: Assembling the Liverwort Tree of Life: A window into the Evolution and Diversification of Early Land Plants (NSF-0531730)
NSF-ITR: Building the Tree of Life: A National Resource for Phyloinformatics and Computational Phylogenetics (NSF-0331654)
NSF-PBI Euphorbia: Collaborative Reserach: EuphORBia - A global inventory of the spurgres (DEB-0614791)
NSF-ATOL: Collaborative Research: Gymnosperms on the Tree of Life: Resolving the phylogeny of seed plants (EF-0629686)