$Id: refs.bib 606 2008-09-05 18:34:55Z rvos $

@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 = {ontology, programming, xml},
	number = {5},
	pages = {63--74},
	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 = {ontology, programming, xml},
	priority = {2},
	title = {Mapping XML to OWL Ontologies},
	url = {http://citeseer.ist.psu.edu/733967.html}
}

@article{Klein:2000p159,
	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 = {ontology, programming, xml},
	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 = {software, taxonomy, xml},
	month = {April},
	number = {4},
	pages = {406--407},
	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},
	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{Cannon2005,
	author = {Cannon, Ethalinda  K. S.  and Zmasek, C. M. },
	citeulike-article-id = {2346611},
	institution = {Burnham Institute for Medical Research},
	keywords = {classification, phyloinformatics, programming, software, taxonomy, xml},
	number = {August 9},
	posted-at = {2008-02-07 00:05:12},
	priority = {2},
	title = {Proposal for pyloXML level 1, version 0.2},
	volume = {2005},
	year = {2005}
}

@manual{citeulike:2791256,
	author = {Cannon, Ethalinda  K. S.  and Zmasek, Christian  M. },
	citeulike-article-id = {2791256},
	institution = {Burnham Institute for Medical Research},
	keywords = {classification, 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 = {programming, software, xml},
	posted-at = {2008-05-13 01:08:04},
	priority = {2},
	title = {GraphML progress report: Structural layer proposal},
	url = {http://citeseer.ist.psu.edu/670039.html},
	year = {2002}
}

@misc{Maddison2001,
	author = {Maddison, Wayne  P.  and Maddison, D. R. },
	citeulike-article-id = {2346921},
	keywords = {alignment, comparative, data-mining, evolution, 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{Nixon:2001p165,
	author = {Nixon, K.  and Carpenter, J.  and Borgardt, S. },
	citeulike-article-id = {2306451},
	journal = {Cladistics},
	keywords = {databases, data-mining, phyloinformatics, software},
	local-url = {file://localhost/Users/rvosa/Documents/Papers/2001/Nixon/Cladistics\%202001\%20Nixon.pdf},
	month = {Jan},
	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, 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://www.jstor.org/stable/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, 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 = {databases, data-mining, 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 = {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 = {databases, data-mining, 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}
}