http://precedings.nature.com/users/b16ff4bc0fc20d123b346d86f531bda2/ Documents posted by Roderic Page Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3173/version/1 Although the Web has transformed science publishing, scientific papers themselves are still essentially “black boxes”, with much of their content intended for human readers only. Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical coordinates, publishers could greatly increase the scientific value of their digital content. At the same time this will provide novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic citation.As a proof of concept, my entry in the Elsevier Grand Challenge extracted extended metadata from a set of articles from the journal Molecular Phylogeny and Evolution and used it to populate a entity-attribute-value database. A simple web interface to this database enables an enhanced display of the content of an article, including a map of localities mentioned either explicitly or implicitly (through links to geotagged data), taxonomic coverage, and both data and citation links. Metadata extraction was limited to information listed in tables in the articles (such as GenBank sequences and specimen codes), the body of the article wasn’t used. This restriction was deliberate, in order to demonstrate that making extended metadata available doesn’t require a journal’s publisher to make the full-text freely available (although this is desirable for other reasons). http://precedings.nature.com/documents/3173/version/1 Fri, 24 Apr 2009 17:31:02 UTC Enhanced display of scientific articles using extended metadata hdl:10101/npre.2009.3173.1 2009-04-24 Roderic D. M. Page Nature Precedings 2009-04-24T17:31:02Z Manuscript Ecology Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3079/version/1 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, HTTP URIs, and LSIDs). bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. bioGUID is available at http://bioguid.info/. Source code is available from Google Code. http://precedings.nature.com/documents/3079/version/1 Fri, 17 Apr 2009 21:01:04 UTC bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics hdl:10101/npre.2009.3079.1 2009-04-17 Roderic Page Nature Precedings 2009-04-17T21:01:04Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1029.1 Aligning RNA sequences can be a challenging task. Automatic sequence alignment programs typically align sequences only with respect to primary sequence, and as a result may yield spurious alignments. Incorporating information on RNA secondary structure can improve the alignment, but this must usually be done by hand. One approach to aligning RNA sequences uses “conserved motifs”, however relying on these motifs may lead to gross errors of alignment if, in fact, those motifs are not conserved. http://dx.doi.org/10.1038/npre.2007.1029.1 Tue, 18 Sep 2007 10:48:38 UTC On The Dangers Of Aligning RNA Sequences Using “Conserved” Motifs doi:10.1038/npre.2007.1029.1 2009-03-04 Roderic Page Nature Precedings 2007-09-18T10:48:38Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.1030.1 TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling’s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality criterion than TreeMap 1, addressing Dowling’s second concern. http://dx.doi.org/10.1038/npre.2007.1030.1 Tue, 18 Sep 2007 10:49:19 UTC Treemap Versus BPA (Again): A Response to Dowling doi:10.1038/npre.2007.1030.1 2009-03-04 Roderic Page Nature Precedings 2007-09-18T10:49:19Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.1028.1 This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals. http://dx.doi.org/10.1038/npre.2007.1028.1 Tue, 18 Sep 2007 11:42:40 UTC Towards a Taxonomically Intelligent Phylogenetic Database doi:10.1038/npre.2007.1028.1 2009-03-04 Roderic Page Nature Precedings 2007-09-18T11:42:40Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2008.2579.1 This paper describes my entry in the Elsevier Grand Challenge “Knowledge Enhancement in the Life Sciences” contest. The entry takes a collection of fulltext issues of Molecular Phylogenetics and Evolution as the starting point, then extracts citation links to both papers and data, such as Genbank sequences and specimens, together with geotagged localities, and builds a “web” of objects linked by typed relationships. Each object (such as a publication, a sequence, a specimen, a taxon name, etc.) is treated equally, so that you can take a publication and see what taxa it refers to, or take the taxon and find all the publications that refer to the taxon. Although the database has been seeded with some articles from Molecular Phylogenetics and Evolution, much of the data comes from GenBank, PubMed, and specimen databases. These are accessed through bioGUID, a tool I constructed to resolve globally unique identifiers and return associated metadata. http://dx.doi.org/10.1038/npre.2008.2579.1 Fri, 28 Nov 2008 16:52:15 UTC Visualising a scientific article doi:10.1038/npre.2008.2579.1 2008-11-28 Roderic Page Nature Precedings 2008-11-28T16:52:15Z Manuscript Ecology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2217.1 The fact that all living organisms are related by common descent is one of the central principles of modern biology. Since the early 1990’s the amount of data available to evolutionary biologists has exploded, and Elsevier’s journal Molecular Phylogenetics and Evolution, has become the largest single publisher of evolutionary trees (phylogenies). These trees and their supporting data potentially form a tremendous resource for biologists, with applications in genomics, evolutionary biology, biodiversity, and public health. However, most published trees are not available in any public database, but instead languish as images, “locked up” in the pages of journals. A long term solution to this problem is to invert the relationship between journal and database, such that the database is the primary repository, and the journal article becomes effectively a “report” on that data, albeit a report that is citable, and thus has the same status as a scientific article. This vision is some way off being achieved. However, publishers could greatly enhance the scientific value of their digital content by expanding article metadata to include taxonomic names, shared digital identifiers, geographical coordinates, and data structures such as evolutionary trees. This metadata doesn’t require making the full text available, but could substantially improve the findability of that text. http://dx.doi.org/10.1038/npre.2008.2217.1 Fri, 22 Aug 2008 15:07:45 UTC Towards realising Darwin’s dream: setting the trees free doi:10.1038/npre.2008.2217.1 2008-08-22 Roderic Page Nature Precedings 2008-08-22T15:07:45Z Manuscript Ecology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1760/version/1 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 DOIs and LSIDs), and the implementation of services that link those identifiers. http://precedings.nature.com/documents/1760/version/1 Thu, 03 Apr 2008 20:10:36 UTC Biodiversity informatics: the challenge of linking data and the role of shared identifiers hdl:10101/npre.2008.1760.1 2008-04-03 Roderic Page Nature Precedings 2008-04-03T20:10:36Z Manuscript Ecology Bioinformatics http://creativecommons.org/licenses/by/3.0/