Biodiversity informatics: the challenge of linking data and the role of shared identifiers

Page, R. (2008) Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Briefings in Bioinformatics, 9(5), pp. 345-354. (doi:10.1093/bib/bbn022)

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Publisher's URL: http://dx.doi.org/10.1093/bib/bbn022

Abstract

Background: 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 identifiers (including, but not limited to, DOIs, A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Page, Professor Roderic
Authors: Page, R.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
Journal Name:Briefings in Bioinformatics
ISSN:1467-5463
ISSN (Online):1477-4054

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
391761A taxonomically intelligent phylogenetic databaseRoderic PageBiotechnology and Biological Sciences Research Council (BBSRC)BB/C004310/1Institute of Biodiversity Animal Health and Comparative Medicine