TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email

Library Module.

<p>Citation information is stored, view, and linked to data across all modules.</p

The TOLKIN architecture is built upon open source platforms and software, including Linux, Ruby on Rails and support for libraries, formats, and services such as BioRuby, NeXML, and GenBank.

<p>The diagram shows the relationship between TOLKIN modules and core data classes within each.</p

In a typical phylogenetic analysis workflow, common practice has been to manage data inside spreadsheets and in collaborative teams, to share them via email, as represented by Alternative a).

<p>While easy and effective for small data sets, spreadsheets can get out of sync and provenance is not well maintained. TOLKIN provides an Alternative b) to provide collaboration through a web portal, bulk data import and export of common formats, metadata and versioning support.</p

Morphology Module.

<p>Characters are defined in the ‘Characters’ tab and can be scored directly in each cell of the matrix. Characters can be grouped together and assigned to informal groups (‘Character groups’). OTU groups from the taxonomy module and character groups can be imported into a matrix for viewing, scoring and general editing.</p