31 research outputs found
Ozymandias: a biodiversity knowledge graph
No full textEnormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com
Modified mincut supertrees
No full textA polynomial time supertree algorithm could play a key role in a divide-and-conquer strategy for assembling the tree of life. To date only a single such method capable of accommodate conflicting input trees has been proposed, the MinCutSupertree algorithm of Semple and Steel. This paper describes this algorithm and its implementation, then illustrates some weaknesses of the method. A modification to the algorithm that avoids some of these problems is proposed. The paper concludes by discussing some practical problems in supertree construction
BioNames: linking taxonomy, texts, and trees
No full textBioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic “dashboard” where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question “what is this taxon?” BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, images from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org
DNA barcoding and taxonomy: dark taxa and dark texts
No full textBoth classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline (‘dark texts’). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These ‘dark taxa’ hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global ‘digital dashboard’ to assess the extent to which biodiversity data are available online.
This article is part of the themed issue ‘From DNA barcodes to biomes’
Taxonomy, Supertrees, and the Tree of Life
No full textSome of the main practical impediments to the application of supertrees in large-scale phylogenetic analysis are inconsistent use of taxonomic names, trees incorporating taxa of different ranks, and poor taxonomic overlap between different phylogenetic studies. This chapter considers these problems and suggests some solutions. The notion of a “classification graph” is introduced to test for consistency between higher-level classifications. One strategy for coping with poor taxonomic overlap is to use a constraint tree that specifies some taxonomic groups that must appear in the supertree
An interactive DNA barcode browser
No full textThis paper describes an interactive web application to display DNA barcode data. It supports both query by sequence and query by geographic area. By using n-gram indexing of DNA sequences, and alignment-free phylogeny construction, the user can interactively explore DNA barcode data in real time
Introduction to Comparing Large Sequence Sets
No full textComparisons of whole genomes can yield important insights into the evolution of genome structure, such as the role of inversions in bacterial evolution and the identification of large-scale duplications in the human genome. This unit briefly compares two tools for aligning whole genome sequences: MUMmer and PipMaker. These tools differ in both the underlying algorithms used, and in the interface they present to the user
Introduction to Inferring Evolutionary Relationships
No full textThis unit provides a general introduction to phylogeny. It defines common terms and discusses the issue of rooting trees, in addition to comparing gene and species trees. Methods for inferring phylogenies, such as distance methods, parsimony methods, and maximum likelihood are also presented. The unit concludes with discussion of how to assess tree confidence
Visualizing Phylogenetic Trees Using TreeView
No full textTreeView provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE-PUZZLE, and ClustalX. While some phylogenetic programs (such as the Macintosh version of PAUP*) have excellent tree printing facilities, many programs do not have the ability to generate publication quality trees. TreeView addresses this need. The program can read and write a range of tree file formats, display trees in a variety of styles, print trees, and save the tree as a graphic file. Protocols in this unit cover both displaying and printing a tree. Support protocols describe how to download and install TreeView, and how to display bootstrap values in trees generated by ClustalX and PAUP*
