Metadata Enhanced PhyloXML (MEP)

Authors

  • Jim White
  • Ignazio Carbone

Description

In T-BAS, DNA sequences and associated specimen metadata are phylogenetically placed on curated multilocus reference trees and the placement results are saved as Metadata Enhanced PhyloXML (MEP) files. The MEP format allows placements and associated specimen attributes (e.g. host, locality, environmental traits) to be readily viewed, archived and importantly analyzed within a phylogenetic context. MEP files are structured to adhere to the minimum information about any (x) sequence (MIxS) family of standards defined by the Genomic Standards Consortium. A template is provided for users to fill in and submit when performing a phylogeny-based placement in T-BAS. Additional categories of metadata information can be added. MIxS headers and metadata are saved in MEP files as defined in the XML schemas below. The use of MEP files ensures interoperability and retrieval of relevant sequences and metadata for downstream applications. MEP is based on XML, a widely used markup language for representing and sharing information, and PhyloXML, an extension of XML with custom tags for describing evolutionary trees or networks.

The standard pre-defined XML schema for phyloXML is used as a starting point for validating MEP files. PhyloXML includes a phylogeny element that saves the tree information and associated alignments. MEP extends this by adding (1) a tag to each clade that is a leaf in the tree and saving the metadata for that leaf, (2) a gene tag that saves the locus name, the number of sequence characters, and the positions of the excluded unaligned character set (i.e. exset) for each alignment, and (3) an OTUs tag that saves the taxonomic assignments, associated query metadata and sequences for each OTU.

MEP uses two associated schema definitions:

Citation

Carbone, I., White, J. B., Miadlikowska, J., Arnold, A. E., Miller, M. A., Magain, N., U'Ren, J. M. and F. Lutzoni. 2019. T-BAS version 2.1: Tree-Based Alignment Selector toolkit for evolutionary placement of DNA sequences and viewing alignments and specimen metadata on curated and custom trees. Microbiology Resource Announcements 8:e00328-19. https://doi.org/10.1128/MRA.00328-19.

Please also cite the URL https://decifr.hpc.ncsu.edu/schemas/ when describing the MEP format in a manuscript.

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