http://www.bibsonomy.org/burst/user/thauBibSonomy BuRST Feed for /user/thau2008-07-21T01:35:48+02:00Gene Families: The Taxonomy of Protein Paralogs and Chimeras -- Henikoff et al. 278 (5338): 609 -- Sciencehttp://www.bibsonomy.org/bibtex/24d3280f18de976aa8ae377a18ac78b91/thauthau2008-07-02T20:31:42+02:00taxonomy gene <span style="color:#555555;">Steven <a href="http://www.bibsonomy.org/author/Henikoff">Henikoff</a> and Elizabeth A. <a href="http://www.bibsonomy.org/author/Greene">Greene</a> and Shmuel <a href="http://www.bibsonomy.org/author/Pietrokovski">Pietrokovski</a> and Peer <a href="http://www.bibsonomy.org/author/Bork">Bork</a> and Teresa K. <a href="http://www.bibsonomy.org/author/Attwood">Attwood</a> and Leroy <a href="http://www.bibsonomy.org/author/Hood">Hood</a> </span><em>Science</em><em>278(5338):609-614</em>(<em>1997</em>)Wed Jul 02 20:31:42 CEST 2008Science5338609-614Gene Families: The Taxonomy of Protein Paralogs and Chimeras2781997taxonomy gene ScienceDirect - Structure : CATH – a hierarchic classification of protein domain structureshttp://www.bibsonomy.org/bibtex/271af30586f2357b0fbe3438733868e3b/thauthau2008-07-02T20:12:38+02:00structure protein evolution fold families classification <span style="color:#555555;">CA <a href="http://www.bibsonomy.org/author/Orengo">Orengo</a> and AD <a href="http://www.bibsonomy.org/author/Michie">Michie</a> and S <a href="http://www.bibsonomy.org/author/Jones">Jones</a> and DT <a href="http://www.bibsonomy.org/author/Jones">Jones</a> and MB <a href="http://www.bibsonomy.org/author/Swindells">Swindells</a> and JM <a href="http://www.bibsonomy.org/author/Thornton">Thornton</a> </span><em>Structure</em><em>5(8):1093--1108</em><em>#aug#1997. </em>Wed Jul 02 20:12:38 CEST 2008Structure#aug#81093--1108CATH - a hierarchic classification of protein domain structures51997structure protein evolution fold families classification Background: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function can also be assigned. The ever increasing number of known protein structures is too large to classify all proteins manually, therefore, automatic methods are needed for fast evaluation of protein structures. Results: We present a semi-automatic procedure for deriving a novel hierarchical classification of protein domain structures (CATH). The four main levels of our classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). Class is the simplest level, and it essentially describes the secondary structure composition of each domain. In contrast, architecture summarises the shape revealed by the orientations of the secondary structure units, such as barrels and sandwiches. At the topology level, sequential connectivity is considered, such that members of the same architecture might have quite different topologies. When structures belonging to the same T-level have suitably high similarities combined with similar functions, the proteins are assumed to be evolutionarily related and put into the same homologous superfamily. Conclusions: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space. We find that nearly a third of the homologous superfamilies (H-levels) belong to ten major T-levels, which we call superfolds, and furthermore that nearly two-thirds of these H-levels cluster into nine simple architectures. A database of well-characterised protein structure families, such as CATH, will facilitate the assignment of structure-function/ evolution relationships to both known and newly determined protein structures.Phylogenetic Classification and the Universal Tree -- Doolittle 284 (5423): 2124 -- Sciencehttp://www.bibsonomy.org/bibtex/293b285a2cd09a8167302527d34817656/thauthau2008-07-02T20:07:55+02:00phylogeny taxonomy <span style="color:#555555;">W. <a href="http://www.bibsonomy.org/author/Ford Doolittle">Ford Doolittle</a> </span><em>Science</em><em>284(5423):2124-2128</em>(<em>1999</em>)Wed Jul 02 20:07:55 CEST 2008Science54232124-2128Phylogenetic Classification and the Universal Tree2841999phylogeny taxonomy dblphttp://www.bibsonomy.org/bibtex/22b5a1b9b4e53390817c71e7452820999/thauthau2008-05-26T21:49:04+02:00taxonomy merging <span style="color:#555555;">Dieter <a href="http://www.bibsonomy.org/author/Fensel">Fensel</a> and Ying <a href="http://www.bibsonomy.org/author/Ding">Ding</a> and Borys <a href="http://www.bibsonomy.org/author/Omelayenko">Omelayenko</a> and Ellen <a href="http://www.bibsonomy.org/author/Schulten">Schulten</a> and Guy <a href="http://www.bibsonomy.org/author/Botquin">Botquin</a> and Mike <a href="http://www.bibsonomy.org/author/Brown">Brown</a> and Alan <a href="http://www.bibsonomy.org/author/Flett">Flett</a> </span><em>IEEE Intelligent Systems</em><em>16(4):54-59</em>(<em>2001</em>)Mon May 26 21:49:04 CEST 2008IEEE Intelligent Systems454-59Product Data Integration in B2B E-Commerce.162001taxonomy merging http://www.bibsonomy.org/bibtex/2aaded26793f7e57acb651d7e78dc2f7a/thauthau2008-05-26T19:58:45+02:00alignment ontologies <span style="color:#555555;">M. <a href="http://www.bibsonomy.org/author/Klein">Klein</a> </span><em>Workshop on Ontologies and Information Sharing, IJCAI'01, </em><em>Seattle, USA, </em>(<em>2001</em>)Mon May 26 19:58:45 CEST 2008Seattle, USAWorkshop on Ontologies and Information Sharing, IJCAI'01Combining and relating ontologies: an analysis of problems and solutions2001alignment ontologies http://www.bibsonomy.org/bibtex/254851c7da60d5f105c1db903557dd51f/thauthau2008-05-26T19:56:38+02:00supertree <span style="color:#555555;">Olaf R.P. <a href="http://www.bibsonomy.org/author/Bininda-Emonds">Bininda-Emonds</a> </span><em>Trends in Ecology and Evolution</em><em>19(6):315-322</em><em>June2004. </em>Mon May 26 19:56:38 CEST 2008Trends in Ecology and EvolutionJune6315-322The Evolution of Supertrees192004supertree dblphttp://www.bibsonomy.org/bibtex/2df86c32d35f58ce9117593e912c1f161/thauthau2008-05-26T19:56:18+02:00reduction transitive <span style="color:#555555;">Alfred V. <a href="http://www.bibsonomy.org/author/Aho">Aho</a> and M. R. <a href="http://www.bibsonomy.org/author/Garey">Garey</a> and Jeffrey D. <a href="http://www.bibsonomy.org/author/Ullman">Ullman</a> </span><em>SIAM J. Comput.</em><em>1(2):131-137</em>(<em>1972</em>)Mon May 26 19:56:18 CEST 2008SIAM J. Comput.2131-137The Transitive Reduction of a Directed Graph.11972reduction transitive KDubiq Blueprinthttp://www.bibsonomy.org/bibtex/23b4ce6fd7fa6dbf1c39fd261fa39fcd6/thauthau2008-05-26T19:55:36+02:00taxonomy folksonomy <span style="color:#555555;">Paul <a href="http://www.bibsonomy.org/author/Heymann">Heymann</a> and Hector <a href="http://www.bibsonomy.org/author/Garcia-Molina">Garcia-Molina</a> </span><em>2006--10. </em><em>Computer Science Department, Stanford University, </em><em>April2006. </em>Mon May 26 19:55:36 CEST 2008April2006--10{C}ollaborative {C}reation of {C}ommunal {H}ierarchical {T}axonomies in {S}ocial {T}agging {S}ystems2006taxonomy folksonomy Collaborative tagging systems---systems where many casual users annotate objects with free-form strings (tags) of their choosing---have recently emerged as a powerful way to label and organize large collections of data. During our recent investigation into these types of systems, we discovered a simple but remarkably effective algorithm for converting a large corpus of tags annotating objects in a tagging system into a navigable hierarchical taxonomy of tags. We first discuss the algorithm and then present a preliminary model to explain why it is so effective in these types of systems.http://www.bibsonomy.org/bibtex/20819e5d4aa230687114821fc116bdba7/thauthau2008-05-07T22:32:31+02:00supertrees <span style="color:#555555;">O.R.P. <a href="http://www.bibsonomy.org/author/Bininda-Emonds">Bininda-Emonds</a> (eds.). </span><em>Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, </em><em>Kluwer Academic, </em><em>Dordrecht, </em>(<em>2004</em>)Wed May 07 22:32:31 CEST 2008DordrechtPhylogenetic Supertrees: Combining Information to Reveal the Tree of LifeSome desiderata for liberal supertrees2004supertrees http://www.bibsonomy.org/bibtex/2cd1d0744b29fc1f0f441e2fc843ca5a8/thauthau2008-05-07T22:00:33+02:00supertrees <span style="color:#555555;">Mariana <a href="http://www.bibsonomy.org/author/Constantinescu">Constantinescu</a> and David <a href="http://www.bibsonomy.org/author/Sankoff">Sankoff</a> </span><em>Journal of Classification</em>(<em>1995</em>)Wed May 07 22:00:33 CEST 2008Journal of Classification101-112An Efficient Algorithm for Supertrees121995supertrees Given k rooted binary trees A t,A2,..,Ak, with labeled leaves, we generate C, a unique system of lineage constraints on common ancestors. We then present an algorithm for constructing the set of rooted binary trees B, compatible with all of A I,A2,..,Ak. The running time to obtain one such supertree isdblphttp://www.bibsonomy.org/bibtex/2b275b61bbe7c739269beeaf2dfb15b10/thauthau2008-04-11T20:50:28+02:00data integration translation <span style="color:#555555;">Serge <a href="http://www.bibsonomy.org/author/Abiteboul">Abiteboul</a> and Sophie <a href="http://www.bibsonomy.org/author/Cluet">Cluet</a> and Tova <a href="http://www.bibsonomy.org/author/Milo">Milo</a> and Pini <a href="http://www.bibsonomy.org/author/Mogilevsky">Mogilevsky</a> and J&#233;r&#244;me <a href="http://www.bibsonomy.org/author/Siméon">Sim&#233;on</a> and Sagit <a href="http://www.bibsonomy.org/author/Zohar">Zohar</a> </span><em>IEEE Data Eng. Bull.</em><em>22(1):3-8</em>(<em>1999</em>)Fri Apr 11 20:50:28 CEST 2008IEEE Data Eng. Bull.13-8Tools for Data Translation and Integration.221999data integration translation dblphttp://www.bibsonomy.org/bibtex/21c78a29e6b9203f6c32b65d01c46ff07/thauthau2008-04-11T19:54:51+02:00merging ontology <span style="color:#555555;">Deborah L. <a href="http://www.bibsonomy.org/author/McGuinness">McGuinness</a> and Richard <a href="http://www.bibsonomy.org/author/Fikes">Fikes</a> and James <a href="http://www.bibsonomy.org/author/Rice">Rice</a> and Steve <a href="http://www.bibsonomy.org/author/Wilder">Wilder</a> </span><em>AAAI/IAAI, </em><em>page1123-1124. </em><em>AAAI Press / The MIT Press, </em>(<em>2000</em>)Fri Apr 11 19:54:51 CEST 2008AAAI/IAAIconf/aaai/20001123-1124The Chimaera Ontology Environment.2000merging ontology dblphttp://www.bibsonomy.org/bibtex/2c3bb0dd11c439795cb32880906326c8e/thauthau2008-04-10T22:29:11+02:00transformation data <span style="color:#555555;">Philip A. <a href="http://www.bibsonomy.org/author/Bernstein">Bernstein</a> and Thomas <a href="http://www.bibsonomy.org/author/Bergstraesser">Bergstraesser</a> </span><em>IEEE Data Eng. Bull.</em><em>22(1):9-14</em>(<em>1999</em>)Thu Apr 10 22:29:11 CEST 2008IEEE Data Eng. Bull.19-14Meta-Data Support for Data Transformations Using Microsoft Repository.221999transformation data dblphttp://www.bibsonomy.org/bibtex/29f9da7c7f6174bb4c11ee35c527da7ac/thauthau2008-04-10T22:13:16+02:00integration workflow <span style="color:#555555;">Shawn <a href="http://www.bibsonomy.org/author/Bowers">Bowers</a> and Kai <a href="http://www.bibsonomy.org/author/Lin">Lin</a> and Bertram <a href="http://www.bibsonomy.org/author/Ludäscher">Lud&#228;scher</a> </span><em>SSDBM, </em><em>page349-352. </em><em>IEEE Computer Society, </em>(<em>2004</em>)Thu Apr 10 22:13:16 CEST 2008SSDBMconf/ssdbm/2004349-352On Integrating Scientific Resources through Semantic Registration.2004integration workflow Bioinformatics Workflow Systemshttp://www.bibsonomy.org/bibtex/2b4b153d0b976b2dd64a345b926df7fe8/thauthau2008-04-10T22:08:03+02:00data transformation ontology <span style="color:#555555;">Shawn <a href="http://www.bibsonomy.org/author/Bowers">Bowers</a> and Bertram <a href="http://www.bibsonomy.org/author/Lud\&#034;ascher">Lud&#228;scher</a> </span><em>page1--16. </em>(<em>2004</em>)Thu Apr 10 22:08:03 CEST 2008Data Integration in the Life Sciences1--16An Ontology-Driven Framework for Data Transformation in Scientific Workflows2004data transformation ontology http://www.bibsonomy.org/bibtex/25e568a81ccc0cf5c202850e653d90b8b/thauthau2008-04-10T21:46:10+02:00merging ontology <span style="color:#555555;">D. L. <a href="http://www.bibsonomy.org/author/McGuinness">McGuinness</a> and R. <a href="http://www.bibsonomy.org/author/Fikes">Fikes</a> and J. <a href="http://www.bibsonomy.org/author/Rice">Rice</a> and S. <a href="http://www.bibsonomy.org/author/Wilder">Wilder</a> </span><em>Proc. of the Seventh International Conference on Principles of Knowledge, </em><em>Breckenridgeand Coloradoand United States, </em><em>April2000. </em>Thu Apr 10 21:46:10 CEST 2008Breckenridgeand Coloradoand United StatesProc. of the Seventh International Conference on Principles of KnowledgeApril{An Environment for Merging and Testing Large Ontologies}2000merging ontology dblphttp://www.bibsonomy.org/bibtex/22f6cf2684f65beb75294a8cb1ee3f423/thauthau2008-04-10T21:43:50+02:00composition ontology service <span style="color:#555555;">Andrew B. <a href="http://www.bibsonomy.org/author/Williams">Williams</a> and Anand <a href="http://www.bibsonomy.org/author/Padmanabhan">Padmanabhan</a> and M. <a href="http://www.bibsonomy.org/author/Brian Blake">Brian Blake</a> </span><em>AAMAS, </em><em>page647-654. </em><em>ACM, </em>(<em>2003</em>)Thu Apr 10 21:43:50 CEST 2008AAMASconf/atal/2003647-654Local consensus ontologies for B2B-oriented service composition.2003composition ontology service dblphttp://www.bibsonomy.org/bibtex/2a57a759197d6d5f3f00f023e8c531bba/thauthau2008-04-10T21:40:35+02:00integration xml <span style="color:#555555;">Borys <a href="http://www.bibsonomy.org/author/Omelayenko">Omelayenko</a> and Dieter <a href="http://www.bibsonomy.org/author/Fensel">Fensel</a> </span><em>DS-9, </em><em>volume239ofIFIP Conference Proceedings, </em><em>page221-235. </em><em>Kluwer, </em>(<em>2001</em>)Thu Apr 10 21:40:35 CEST 2008DS-9conf/ds/2001221-235IFIP Conference ProceedingsAn Analysis of Integration Problems of XML-Based Catalogs for B2B Electronic Commerce.2392001integration xml Ontology evolution and schema evolutionhttp://www.bibsonomy.org/bibtex/208ee0381e240c3ee414e0eefc7fe1a83/thauthau2008-04-10T21:22:26+02:00evolution ontology <span style="color:#555555;">Natalya F. <a href="http://www.bibsonomy.org/author/Noy">Noy</a> and Michel <a href="http://www.bibsonomy.org/author/Klein">Klein</a> </span><em>Knowledge and Information Systems</em><em>6(4):428--440</em><em>#jul#2004. </em>Thu Apr 10 21:22:26 CEST 2008Knowledge and Information Systems#jul#4428--440Ontology Evolution: Not the Same as Schema Evolution62004evolution ontology As ontology development becomes a more ubiquitous and collaborative process, ontology versioning and evolution becomes an important area of ontology research. The many similarities between database-schema evolution and ontology evolution will allow us to build on the extensive research in schema evolution. However, there are also important differences between database schemas and ontologies. The differences stem from different usage paradigms, the presence of explicit semantics and different knowledge models. A lot of problems that existed only in theory in database research come to the forefront as practical problems in ontology evolution. These differences have important implications for the development of ontology-evolution frameworks: The traditional distinction between versioning and evolution is not applicable to ontologies. There are several dimensions along which compatibility between versions must be considered. The set of change operations for ontologies is different. We must develop automatic techniques for finding similarities and differences between versions. ER -dblphttp://www.bibsonomy.org/bibtex/24905ee8a94fef2279dde0792d6850e30/thauthau2008-04-10T21:18:49+02:00ontology merging <span style="color:#555555;">Konstantinos <a href="http://www.bibsonomy.org/author/Kotis">Kotis</a> and George A. <a href="http://www.bibsonomy.org/author/Vouros">Vouros</a> </span><em>ESWS, </em><em>volume3053ofLecture Notes in Computer Science, </em><em>page137-151. </em><em>Springer, </em>(<em>2004</em>)Thu Apr 10 21:18:49 CEST 2008ESWSconf/esws/2004137-151Lecture Notes in Computer ScienceThe HCONE Approach to Ontology Merging.30532004ontology merging