MorphoBank: phylophenomics in the “cloud”

Abstract

A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single-user, filebased desktop software wholly unsuitable for real-time, team-based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with ''cloud'' computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at-large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self-assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X-Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

“…Some journals have more specific requirements, e.g., the “Journals” page at TreeBASE website (see Table 1) lists 35 journals that recommend or require submission of trees to TreeBASE [11]. Researchers wishing to archive phylogenies or character data in conjunction with a peer-reviewed phylogeny report may use TreeBASE [11], Dryad [9], or MorphoBank [12]. Researchers also may choose to make their data available as supplementary data via a scientific publisher’s web site.…”

“…MorphoBank [12] is designed to support collaborative sharing and archiving of comparative morphological data, as opposed to trees, on the premise that much of the re-useable information in a comparative analysis of morphology is not in the published tree, but in the character matrix, and particularly in the specimen identifiers and photographic images linked to character-state encodings. MorphoBank also allows molecular characters, as these often are mixed together in phylogenetic analyses (e.g., study #563).…”

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

“…In the Mesquite-o-Tastic screencast (Table 1), a NEXUS file from a published scientific study [57] is downloaded from an online archive (MorphoBank [58]), and opened in Mesquite, which shows that the file contains a character matrix with 51 taxa, but not a phylogeny. When the user invokes a custom menu item (added for this project), Mesquite automatically formulates a query URI using the names in the character matrix, executes the query remotely (invoking the MapReduce pruner above) and incorporates the resulting tree in memory.…”

TreeSnatcher plus: capturing phylogenetic trees from images

“…Using already published trees in research projects would be trivial if all phylogeny related data were also published in open-access online repositories, e.g., TreeBASE [6], MorphoBank [7], or Dryad [8]. Leebens-Mack et al [9] propose a roadmap for the development of minimal reporting standards for phylogenetic analyses, MIAPA (Minimal Information about a Phylogenetic Analysis).…”