ABI 2011 proposal

In July 2011, we submitted a proposal to the NSF ABI panel entitled "Collaborative Research: ABI Development: Towards a comprehensive, community-owned and sustainable repository of reusable phylogenetic knowledge. The PIs are Hilmar Lapp, William Piel, Michael Donoghue, Mark Westneat and Matt Bietz (senior personnel Karen Cranston).

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Project Summary

Despite the central role of evolutionary history in explaining and predicting biology, the results of most published phylogenetic studies are never archived in a form that allows effective discovery, sharing, and reuse of the phylogenetic knowledge that they codify. Consequently, it is difficult for the community to effectively curate, synthesize, enrich, and disseminate the current cumulative state of published phylogenetic knowledge, and to access this body of knowledge to address questions such as where the major gaps in knowledge are, and how best to fill them. To solve this problem, we aim to build new features into TreeBASE and the Tree of Life Web project (ToLWeb), two existing community informatics resources with the remit to address these challenges. Our central goal is to achieve a combined web resource that attracts the community participation necessary to sustain permanent archiving in reusable form, promotes rich annotation and web delivery of phylogenetic trees, and engenders collaborative curation and synthesis of our phylogenetic knowledge as it accumulates. Our development goals are designed to remove major barriers to user content creation, content flow, discovery, and reuse, and to add novel social features geared toward engaging users, rewarding participation, and incentivizing contribution. Specifically, we propose the following deliverables: 1) a usability-driven submission interface to TreeBASE focused on low-barrier to deposition and features assisting authors with submission issues; 2) efficient interfaces for browsing, finding, and accessing content in TreeBASE and ToLWeb; 3) tools that enable users to navigate bi-directionally between research trees in TreeBASE and their corresponding clade(s) in ToLWeb via links annotated with content quality indicators; 4) tools that assist ToLWeb clade editors by automating the process of merging newly available research trees into ToLWeb; 5) social computing capabilities chosen for, and continuously evaluated for, their effectiveness in increasing user participation; 6) nurture the community of authors, users, and external developers through dedicated community coordinator and helpdesk staff and hands-on engagement activities.

Intellectual Merit: Engaging a diverse group of people to adopt, utilize, and contribute to community resources is a major challenge. Data sharing and collaborative knowledge curation are social activities, and there is a growing body of social science research on factors influencing how people engage with informatics resources on collaborative scientific activities. We will translate the findings from this research to inform the social capabilities and user experience we develop, and our evaluations of the effectiveness of these features and user behavior will advance the understanding of the socio-technical aspect of cyberinfrastructure development. In addition, we align a collaborative research activity on synthesizing a mega-phylogeny from smaller research trees with our development plan to validate interface design, test functionality, and to provide scientifically validated tree-grafting methods. Simultaneously, this will populate ToLWeb with current, high-coverage phylogenies for fishes and flowering plants, and TreeBASE with the underlying research trees, all in fully reusable form.

Broader Impacts: This project involves diverse scientific communities, including a stakeholder meeting that will reach out to communities not previously involved in TreeBASE or ToLWeb, training workshops for content contributors as well as users, hands-on codefests to engage 3rd party developers, and recruiting existing networks of expert biologists through mega-tree synthesis activities. This project will result in a major step toward a synthetic Tree of Life that is comprehensive, up-to-date, and linked to the underlying published data, in a way that allows assessing and reusing our cumulative phylogenetic knowledge for a wide range of research applications. The data access APIs will also enable an ecosystem of 3rd party tools for aggregating and visualizing the data from both ToLWeb and TreeBASE in innovative ways. Social network capabilities will further ToLWeb’s ability to capture the attention of the public and K-16 students.

Project Description

You can download the pdf of the project description.