$Id: refs.bib 1030 2009-05-22 08:04:06Z rvos $ % http://www.citeulike.org/user/rvosa/tag/nexml @article{citeulike:74916, abstract = {this article, we explain the role of ontologies in the architecture of the Semantic Web. We then briefly summarize key elements of XML and RDF, showing why using XML as a tool for semantic interoperability will be ineffective in the long run. We argue that a further representation and inference layer is needed on top of the Web's current layers, and to establish such a layer, we propose a general method for encoding ontology representation languages into RDF/RDF schema. We illustrate the...}, author = {Decker, Stefan and Melnik, Sergey and van Harmelen, Frank v. and Fensel, Dieter and Klein, Michel C. A. and Broekstra, Jeen and Erdmann, Michael and Horrocks, Ian }, citeulike-article-id = {74916}, journal = {IEEE Internet Computing}, keywords = {dbhack1, nexml, ontology, programming, xml}, number = {5}, pages = {63--74}, posted-at = {2008-02-01 00:36:47}, priority = {2}, title = {The Semantic Web: The Roles of XML and RDF}, url = {http://citeseer.ist.psu.edu/decker00semantic.html}, volume = {4}, year = {2000} } @misc{citeulike:2316899, abstract = {By now, XML has reached a wide acceptance as data exchange format in E-Business. An efficient collaboration between different participants in E-Business thus, is only possible, when business partners agree on a common syntax and have a common understanding of the basic concepts in the domain. XML covers the syntactic level, but lacks support for efficient sharing of conceptualizations. The Web Ontology Language (OWL [Bec04]) in turn supports the representation of domain knowledge using...}, author = {Bohring, Hannes and Auer, S\"{o}ren }, citeulike-article-id = {2316899}, keywords = {dbhack1, nexml, ontology, programming, xml}, posted-at = {2008-01-31 23:59:51}, priority = {2}, title = {Mapping XML to OWL Ontologies}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.59.8897} } @article{citeulike:2306364, author = {Klein, M. and Fensel, D. and van Harmelen, F. and Horrocks, I. }, citeulike-article-id = {2306364}, journal = {Proc. Workshop on Applications of Ontologies and Problem-Solving Methods}, keywords = {dbhack1, nexml, ontology, programming, xml}, posted-at = {2008-01-30 08:07:13}, priority = {2}, title = {The relation between ontologies and schema-languages: Translating OIL-specifications in XML-schema}, url = {http://www.cs.vu.nl/\~{}frankh/abstracts/ECAI00-WS2.html}, year = {2000} } @article{citeulike:1939993, abstract = {Summary: An XML document type definition (DTD) is provided for the description of taxonomic relationships between organisms. Two XSL stylesheets for the graphical presentation of simple taxonomic trees are also provided. Availability: The DTD and stylesheets along with sample files are available at http://www.albany.edu/\~{}gilmr/pubxml/. Contact: gilmr@cnsvax.albany.edu 10.1093/bioinformatics/16.4.406}, author = {Gilmour, R. }, citeulike-article-id = {1939993}, doi = {10.1093/bioinformatics/16.4.406}, journal = {Bioinformatics}, keywords = {dbhack1, nexml, software, taxonomy, xml}, month = {April}, number = {4}, pages = {406--407}, posted-at = {2007-11-19 22:09:35}, priority = {2}, title = {Taxonomic markup language: applying XML to systematic data}, url = {http://dx.doi.org/10.1093/bioinformatics/16.4.406}, volume = {16}, year = {2000} } @article{citeulike:2702801, abstract = {In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.}, address = {Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA. jleebensmack@plantbio.uga.edu}, author = {Leebens-Mack, J. and Vision, T. and Brenner, E. and Bowers, J. E. and Cannon, S. and Clement, M. J. and Cunningham, C. W. and dePamphilis, C. and deSalle, R. and Doyle, J. J. and Eisen, J. A. and Gu, X. and Harshman, J. and Jansen, R. K. and Kellogg, E. A. and Koonin, E. V. and Mishler, B. D. and Philippe, H. and Pires, J. C. and Qiu, Y. L. and Rhee, S. Y. and Sj\"{o}lander, K. and Soltis, D. E. and Soltis, P. S. and Stevenson, D. W. and Wall, K. and Warnow, T. and Zmasek, C. }, citeulike-article-id = {2702801}, doi = {10.1089/omi.2006.10.231}, issn = {1536-2310}, journal = {Omics : a journal of integrative biology}, keywords = {methods, nexml}, number = {2}, pages = {231--237}, posted-at = {2008-04-22 20:26:55}, priority = {0}, title = {Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).}, url = {http://dx.doi.org/10.1089/omi.2006.10.231}, volume = {10}, year = {2006} } @manual{citeulike:2791256, author = {Cannon, Ethalinda K. S. and Zmasek, Christian M. }, citeulike-article-id = {2791256}, institution = {Burnham Institute for Medical Research}, keywords = {classification, dbhack1, nexml, phyloinformatics, programming, software, taxonomy, xml}, posted-at = {2008-05-13 00:08:43}, priority = {2}, title = {Proposal for phyloXML level 1, version 0.3}, year = {2005} } @misc{citeulike:1237068, abstract = {Following a workshop on graph data formats held with the 8th Symposium on Graph Drawing (GD 2000), a task group was formed to propose a format for graphs and graph drawings that meets current and projected requirements. On behalf of this task group, we here present GraphML (Graph Markup Language), an XML format for graph structures, as an initial step towards this goal. Its main characteristic is a unique mechanism that allows to define extension modules for additional data, such as graph drawing information or data specific to a particular application. These modules can freely be combined or stripped without affecting the graph structure, so that information can be added (or omitted) in a well-defined way.}, author = {Brandes, U. and Eiglsperger, M. and Herman, I. and Himsolt, M. and Marshall, M. }, citeulike-article-id = {1237068}, keywords = {dbhack1, nexml, programming, software, xml}, posted-at = {2008-05-13 01:08:04}, priority = {2}, title = {GraphML progress report: Structural layer proposal}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.4.4374}, year = {2002} } @misc{citeulike:2346921, author = {Maddison, Wayne P. and Maddison, D. R. }, citeulike-article-id = {2346921}, keywords = {alignment, comparative, data-mining, dbhack1, evolution, nexml, phylogeny, phyloinformatics, programming, software}, posted-at = {2008-02-07 00:05:36}, priority = {2}, title = {Mesquite: a modular system for evolutionary analysis.}, url = {http://mesquiteproject.org}, year = {2001} } @article{citeulike:2306451, author = {Nixon, K. and Carpenter, J. and Borgardt, S. }, citeulike-article-id = {2306451}, journal = {Cladistics}, keywords = {data-mining, databases, dbhack1, nexml, phyloinformatics, software}, posted-at = {2008-01-30 08:07:20}, priority = {2}, title = {Beyond NEXUS: Universal cladistic data objects}, url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1096-0031.2001.tb00104.x}, year = {2001} } @article{citeulike:2011773, abstract = {NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc., private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.}, author = {Maddison, David R. and Swofford, David L. and Maddison, Wayne P. }, citeulike-article-id = {2011773}, doi = {doi:10.2307/2413497}, journal = {Systematic Biology}, keywords = {data-mining, dbhack1, nexml, phyloinformatics, software}, number = {4}, pages = {590--621}, posted-at = {2007-11-29 08:27:27}, priority = {2}, title = {NEXUS: An Extensible File Format for Systematic Information}, url = {http://dx.doi.org/doi:10.2307/2413497}, volume = {46}, year = {1997} } @article{citeulike:242, abstract = {Motivation: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML. Contact: Emmanuel.Barillot@infobiogen.fr}, address = {CRI Infobiogen, 523 place des terrasses de l'agora, 91000 Evry, France.}, author = {Achard, F. and Vaysseix, G. and Barillot, E. }, citeulike-article-id = {242}, doi = {10.1093/bioinformatics/17.2.115}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {data-mining, dbhack1, nexml, phyloinformatics, programming, software, xml}, month = {February}, number = {2}, pages = {115--125}, posted-at = {2008-05-13 00:39:04}, priority = {2}, title = {XML, bioinformatics and data integration.}, url = {http://dx.doi.org/10.1093/bioinformatics/17.2.115}, volume = {17}, year = {2001} } @article{citeulike:2791687, abstract = {A molecular phylogenetic tree is a tree-structured graph that represents the evolutionary process of genes, which is constructed from sequence data (such as DNA sequences) obtained from several organisms. Although molecular phylogenetic trees are fundamental data structures in evolutionary analysis, the database prepared so that to store the moleculer phylogenetic tree announced systematically and it can look it up didn't exist. In this research we develop a system which stores molecular phylogenetic tree data by a form based on XML. By adopting XML, we can handle not only the data themselves of molecular phylogenetic trees but also the additonal information related to the molecular phylogenetic trees such as their bibliographic information. It becomes possible to do with flexibly addition of the information about the new relations and functions which are obtained by the development of molecular evolution analysis. In this paper, we introduce the way to express the molecular phylogenetic tree data by using XML and explain about the way of reffering to the database.}, author = {Tomohisa, Masuyama and Risa, Kishinami and Takanobu, Yoshikawa and Hideo, Matsuda and Akihiro, Hashimoto }, citeulike-article-id = {2791687}, journal = {IPSJ SIG Notes}, keywords = {data-mining, databases, dbhack1, nexml, programming, software, xml}, number = {61}, pages = {31--36}, posted-at = {2008-05-13 00:49:40}, priority = {2}, title = {Representation and Retrieval Method for Molecular Phylogenetic Tree Data Based on XML}, url = {http://sciencelinks.jp/j-east/article/200005/000020000500A0172654.php}, volume = {99}, year = {1999} } @techreport{citeulike:2580222, author = {Bray, T. and Paoli, J. and Sperberg-Mcqueen, C. M. and Maler, E. }, citeulike-article-id = {2580222}, editor = {Yergeau, F. }, institution = {W3C}, keywords = {dbhack1, nexml, xml}, month = {August}, posted-at = {2008-05-14 04:59:15}, priority = {2}, title = {Extensible Markup Language (XML) 1.0 (Fourth Edition)}, url = {http://www.w3.org/TR/xml/}, year = {2006} } @article{citeulike:1937046, abstract = {XML is a new language designed to solve one of the biggest problems of the World Wide Web: its main language, HTML, is not extensible. In this article, the authors discuss the current successes and limitations of the World Wide Web, briefly explain the basics of XML and present the benefits of using XML as a data-exchange language. Finally, they discuss real-life applications that have been developed using XML, with a focus on biology.}, author = {Barillot, Emmanuel and Achard, Frederic }, citeulike-article-id = {1937046}, doi = {10.1016/S0167-7799(00)01465-7}, journal = {Trends in Biotechnology}, keywords = {data-mining, databases, dbhack1, nexml, phyloinformatics, programming, software, xml}, month = {August}, number = {8}, pages = {331--333}, posted-at = {2008-05-13 01:23:44}, priority = {2}, title = {XML: a lingua franca for science?}, url = {http://dx.doi.org/10.1016/S0167-7799(00)01465-7}, volume = {18}, year = {2000} } @article{citeulike:1888819, abstract = {Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ webcite under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.}, author = {Drummond, Alexei J. and Rambaut, Andrew }, citeulike-article-id = {1888819}, doi = {10.1186/1471-2148-7-214}, issn = {1471-2148}, journal = {BMC Evolutionary Biology}, keywords = {algorithms, bayesian, markov-chains, methods, nexml, phylogeny, phyloinformatics, software, xml}, month = {November}, pages = {214+}, posted-at = {2009-05-22 07:02:10}, priority = {2}, title = {BEAST: Bayesian evolutionary analysis by sampling trees}, url = {http://dx.doi.org/10.1186/1471-2148-7-214}, volume = {7}, year = {2007} } @inproceedings{citeulike:4594831, abstract = {Phylogenetic data involves operational taxonomic units, graph representations of their evolutionary relationships and comparative data from which the relationships are inferred. To represent phylogenetic data, different types of entities - lists, trees, matrices and their intersections, need to be modeled. These representations are not just sequential or recursive record sets, but rather more complex data models. The "nexus" flat file format implements such a model using blocks of "taxa", characters and trees. The relationships between entities - operational taxonomic units, character state sequences and nodes in trees within different blocks are defined by labels and implicit orderings of the entities. By virtue of its conciseness and readability, the nexus format has been widely adopted as the standard for many applications, both offline and online. Unfortunately, the format lacks some formal mechanisms to ensure its continuing robustness in the face of advances in the field of phylogenetics. Principally, it lacks a formal versioning scheme by which new features can be adopted or bugs can be deprecated. It lacks a formal grammar or schema by which its syntax can be validated and it lacks a formal definition of its semantics by which subtle differences in interpretation can be exposed (such as implicit or explicit rootedness of trees, uncertainty versus polymorphism). This has led to mutually incompatible dialects of the standard that hamper the interoperability necessary for more complex analyses and work flows. Two examples of this problem are the TreeBase project where data submissions need to be curated by hand and are not accessible at a level of granularity that promotes data re-use, and the CIPRES portal where around 20\% of submitted data sets contain unrecoverable errors. The success of the standard also has led the phylogenetics community to lag behind in the adoption and standardization around new technologies (e.g. standard markup languages, ontologies, web services) compared to related fields (for example genetics, where data standards are more strict, and where ontologies are becoming highly useful resources). To address these issues, the Evolutionary Informatics Working Group at the National Evolutionary Synthesis Center has undertaken several projects aimed at improving interoperability at the level of data syntax (NeXML), data semantics (CDAO) and data exchange (PhyloWS).. The aim of NeXML is to develop a next generation data standard for phylogenetics; a standard that is based conceptually on the nexus format but with strictly defined syntax and semantics and implemented in XML. Using the W3C stacks for XML (schema, namespaces, etc.) and ontologies (OWL, SAWSDL), members of the working group have developed a semantically annotated schema that models OTUs, character state matrices of various types, trees and networks. The schema is versioned and designed for extensibility. Application and web service support is growing, and a developer meeting to implement NeXML support on a variety of online data resources is planned for December 2008.}, author = {Vos, Rutger }, booktitle = {Proceedings of TDWG (2008), Fremantle, Australia.}, citeulike-article-id = {4594831}, editor = {Weitzman, A. L. and Belbin, L. }, keywords = {nexml}, location = {Fremantle, Australia.}, organization = {TDWG}, posted-at = {2009-05-22 08:57:46}, priority = {2}, title = {Data standards in phylogenetics: the NeXML project}, url = {http://www.tdwg.org/proceedings/article/view/439}, year = {2008} } @book{citeulike:2346708, address = {Sunderland, Massachussets}, author = {Felsenstein, Joseph }, citeulike-article-id = {2346708}, keywords = {methods, nexml, phylogeny, xml}, posted-at = {2008-02-07 00:05:17}, priority = {2}, publisher = {Sinauer Associates, Inc.}, title = {Inferring phylogenies}, url = {http://www.sinauer.com/detail.php?id=1775}, year = {2003} }