Team Members

Matthew Collins

Abstract

The iDigBio project is a 10 year National Science Foundation funded project to digitize the natural history museum collections in the United States. The hub of the project is hosted at the Florida Museum of Natural History at the University of Florida.

There are currently over 45 million specimen records in the central database. Many of these records include genetic sequence information in their comments and metadata. This project aims to create an automated interface for generating phylogentic trees from genetic sequence data linked from specimen records in iDigBio.

Action Plan

Genetic sequences for building trees will be sourced from GenBank sequences. Limited work has been done to link specimen and sequence information in iDigBio so that will be a significant part of the data collection effort.

Appropriate phylogentic tree building tools will be used to align the sequences and build trees. One candidate software package is MEGA which is freely available and scriptable. Processing will be paralellized to the extent possible in the packages and run on the most appropriate server hardware available from EC2 or similar resources.

A web service will be constructed that accepts searches for specimen records in the same format as the iDigBio API and returns constructed trees in a format suitable for viewing in existing phylogentic tree viewing software used by biologists.

Constructed trees will be compared to published trees from www.treebase.org or phylomedb.org, online repositories for published trees, both visually and numerically using geodesic distance. An explanation of differences due to differing input data and computation methods will be made.

Workload Distribution

All work will be performed by Matthew Collins.

References

GitHub, ‘idigbio-api-hackathon/idigbio_sequences’, 2015. [Online]. Available: https://github.com/idigbio-api-hackathon/idigbio_sequences. [Accessed: 11- Oct- 2015].

B. Hall, ‘Building Phylogenetic Trees from Molecular Data with MEGA’, Molecular Biology and Evolution, vol. 30, no. 5, pp. 1229-1235, 2013.

G. Jolley-Rogers, T. Varghese, P. Harvey, N. dos Remedios and J. Miller, ‘PhyloJIVE: Integrating biodiversity data with the Tree of Life’, Bioinformatics, vol. 30, no. 9, pp. 1308-1309, 2014.

A. Matsunaga, A. Thompson, R. Figueiredo, C. Germain-Aubrey, M. Collins, R. Beaman, B. MacFadden, G. Riccardi, P. Soltis, L. Page and J. Fortes, ‘A Computational- and Storage-Cloud for Integration of Biodiversity Collections’, 2013 IEEE 9th International Conference on e-Science, 2013.