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| Registros recuperados: 11 | |
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| Roderic Page. |
| 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... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2217/version/1 |
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| Roderic Page; Michael Charleston. |
| 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... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1030/version/1 |
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| Roderic Page. |
| 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... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1760/version/1 |
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| Roderic Page. |
| 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... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2579/version/1 |
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| Roderic Page. |
| In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4242/version/1 |
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| Roderic Page. |
| 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. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1028/version/1 |
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| Roderic Page. |
| The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article finding service is exposed as a standard OpenURL resolver on the... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4928/version/1 |
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| Roderic Page. |
| 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. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1029/version/1 |
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| Roderic Page. |
| 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/":http://bioguid.info/. Source code is... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3079/version/1 |
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| Roderic Page. |
| This talk describes a mapping between the NCBI taxonomy database and Wikipedia. These two databases were chosen because the NCBI taxonomy contains all the taxa for which sequences are publicly available, and for many taxa Wikipedia is the first site returned in a Google search on that taxon's scientific name. The NCBI web pages for nearly 53,000 NCBI taxa now have a link to the corresponding page in Wikipedia. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4583/version/1 |
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| Roderic Page. |
| Taxonomy is in many ways still predigital. Most taxonomic databases are little more than digitized index cards linking names to often-cryptic bibliographic citations, oblivious to the growing volume of scientific literature that is now online. A growing fraction of taxonomic literature is becoming freely available, either through adoption of Open Access publishing models, or through digitizing efforts such as the Biodiversity Heritage Library. Yet much of the most basic information about biodiversity, namely taxonomic description, remains either behind a pay wall, or only available in paper form. This talk sketches the goal of an "Open Taxonomy." The first step towards this goal is digitally linking scientific names to the primary... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6560/version/1 |
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| Registros recuperados: 11 | |
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