Biodiversity Informatics

Biodiversity Informatics: the emergence of a field

Authors: Indra Neil Sarkar

Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community

Currently primary scientific data, especially that dealing with biodiversity, is neither easily discoverable nor accessible. Amongst several impediments, one is a lack of professional recognition of scientific...

Authors: Vishwas S Chavan and Peter Ingwersen

Location, location, location: utilizing pipelines and services to more effectively georeference the world's biodiversity data

Increasing the quantity and quality of data is a key goal of biodiversity informatics, leading to increased fitness for use in scientific research and beyond. This goal is impeded by a legacy of geographic loc...

Authors: Andrew W Hill, Robert Guralnick, Paul Flemons, Reed Beaman, John Wieczorek, Ajay Ranipeta, Vishwas Chavan and David Remsen

Googling DNA sequences on the World Wide Web

New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available...

Authors: Mehrdad Hajibabaei and Gregory AC Singer

bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics

Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique...

Authors: Roderic DM Page

Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life

Natural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite s...

Authors: Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott and David Roberts

Learning to classify species with barcodes

According to many field experts, specimens classification based on morphological keys needs to be supported with automated techniques based on the analysis of DNA fragments. The most successful results in this...

Authors: Paola Bertolazzi, Giovanni Felici and Emanuel Weitschek

Rapid DNA barcoding analysis of large datasets using the composition vector method

Sequence alignment is the rate-limiting step in constructing profile trees for DNA barcoding purposes. We recently demonstrated the feasibility of using unaligned rRNA sequences as barcodes based on a composit...

Authors: Ka Hou Chu, Minli Xu and Chi Pang Li

Efficient alignment-free DNA barcode analytics

In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). T...

Authors: Pavel Kuksa and Vladimir Pavlovic

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to de...

Authors: Frederic Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, Raphael Leblois, Michel Veuille and Catherine Laredo