Trees To Data

Convert PDFs of Evolutionary Trees into Data

Background

There is a large body of scientific literature that contains taxonomies in the form of tree structures. The paleontologists need the images of the trees contained in the PDFs converted into nested data.

Solutions

• Machine vision, character recognition, turn a tree into a data structure
• Create a crowdsourcing system to allow people to easily transcribe nested tree structures into the formats below

Resources

• Ross Mounce's explanation of tree figures, phylogeny with lots of examples
• (everything non-PLOS ONE)
• (PLOS ONE only)
• Github repo of PLOS images 1
• Github repo of PLOS images 2
• Github repo of PLOS images 3
• Github repo of PLOS images 4
• Explanation of parenthetical tree notation
• FigTree - reads parenthetical notation of trees and visualizes it in image form
• Sample .tre file 1 - output format nested data
• Sample .tre file 2 - output format nested data
• Onezoom Tree of Life Explorer and its software - Site using tree data