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Applied Artificial Intelligence
An International Journal
Volume 15, 2001 - Issue 10
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Original Articles

Agent interaction for bioinformatics data management

K. Bryson
,
M. Luck
,
M. Joy
&
D. T. Jones
Pages 917-947 | Published online: 30 Nov 2010

  • Achard , F. , Vaysseix , G. and Barillot , E. 2001 . XML, bioinformatics and data integration . Bioinformatics , 17 : 115 – 125 .
  • Altschul , S. F. , Gish , W. , Miller , W. , Myers , E. W. and Lipman , D.J. 1990 . Basic local alignment search tool . Journal of Molecular Biology , 215 : 403 – 410 .
  • Altschul , S. F. , Madden , T. L. , Schaffer , A. A. , Zhang , J. , Zhang , Z. , Miller , W. and Lipman , D.J. 1997 . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs . Nucleic Acids Research , 25 : 3389 – 3402 .
  • Andrade , M. A. , Brown , N. P , Leroy , C. , Hoersch , S. , de Daruvar , A. , Reich , C. , Franchini , A. , Tamames , J. , Valencia , A. , Ouzounis , C. and Sander , C. 1999 . Automated genome sequence analysis and annotation . Bioinformatics , 15 : 391 – 412 . 1999
  • Apweiler , R. , Attwood , T. K. , Bairoch , A. , Bateman , A. , Bimey , E. , Biswas , M. , Bucher , P , Cerutti , L. , Corpet , F. , Craning , M. D. , Durbin , R. , Falquet , L. , Fleischmann , W. , Gouzy , J. , Hermjakob , H. , HuIo , N. , Jonassen , I. , Kahn , D. , Kanapin , A. , Karavidopoulou , Y. , Lopez , R. , Marx , B. , Mulder , N.J. , Oinn , T. M. , Pagni , M. and Servant , F. 2001 . The InterPro database, an integrated documentation resource for protein families, domains and functional sites . Nucleic Acids Research , 29 : 37 – 40 .
  • Bairoch , A. and Apweiler , R. 2000 . The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 . Nucleic Acids Research , 8 : 45 – 48 .
  • Baker , P. G. , Goble , C. A. , Bechhofer , S. , Paton , N. W , Stevens , R. and Brass , A. 1999 . An ontology for bioinformatics applications . Bioinformatics , 15 : 510 – 520 .
  • Barker , W.C. , Garavelliand , J. S. , McGarvey , P. B. , Marzec , C. R. , Orcutt , B. C. , Srinivasarao , G. Y. , Yeh , L.-S. L. , Ledley , R. S. , Mewes , H.-W. , Pfeiffer , F. , Tsugita , A. and Wu , C. The PIR-international protein sequence database. 1999 . Nucleic Acids Research , 27 (1) 39 – 43 .
  • Baxevanis , A. D. 2001 . The molecular biology database collection: an updated compilation of biological database resources . Nucleic Acids Research , 29 : 1 – 10 .
  • Bernstein , F. C. , Koetzle , T. F. , Williams , G. J. , Meyer , E. E. , Brice , M. D. , Rodgers , J. R. , Kennard , O. , Shimanouchi , T. and Tasumi , M. 1977 . The Protein Data Bank: a computer-based archival file for macromolecular structures . Journal of Molecular Biology , 112 : 535 – 542 .
  • Bryson , K. , Luck , M. , Joy , M. and Jones , D.T. 2000 . “ Applying agents to bioinformatics in GeneWeaver ” . In Cooperative Information Agents IV, volume 1860 of LNAI , volume 1860 , 60 – 71 . Berlin : Springer .
  • Collins , F. S. , Patrinos , A. , Jordan , E. , Chakravarti , A. , Gesteland , R. , Walters , L. and the members of the DOE and NIH planning groups . 1998 . New goals for the U.S. human genome project 1998-2003 . Science , 282 : 682 – 689 .
  • 2000 . The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology . Nature Genetics , 25 : 25 – 29 .
  • The Genome International Sequencing Consortium . 2001 . Initial sequencing and analysis of the human genome . Nature , 409 : 860 – 921 .
  • Parley , J. 1998 . Java Distributed Computing . OReilly ,
  • Foss , J. D. 1998 . “ Brokering the info-underworld ” . In Agent Technology: Foundations, Applications, and Markets , Edited by: Jennings , N. and Woodridge , M. 105 – 123 . Berlin : Springer .
  • Frishman , D. , Albermann , K. , Hani , J. , Heumann , K. , Metanomski , A. and Mewes , H.-W. 2001 . Functional and structural genomics using PEDANT . Bioinformatics , 17 : 44 – 57 .
  • Gaasterland , T. , Sczyrba , A. , Thomas , E. , Aytekin-Kurban , G. , Gordon , P. and Sensen , C. W. 2000 . MAGPIE/ EGRET annotation of the 2.9-mb drosophila melanogaster adh region . Genome Research , 10 : 502 – 510 .
  • Guttman , R. H. , Moukas , A. G. and Macs , P. 1998 . Agent-mediated electronic commerce A survey . Knowledge Engineering Review , 13 : 147 – 159 .
  • Huhns , M. N. and Singh , M.P. 1998 . “ Multiagent systems in information-rich environments ” . In Cooperative Information Agents II, volume 1435 of LNAI , volume 1435 , 79 – 93 . Berlin : Springer .
  • Jennings , N. R. and Wittig , T. 1992 . “ ARCHON: Theory and practice ” . In Distributed Artificial Intelligence: Theory and Praxis , 179 – 195 . Kluwer Academic Press .
  • Jones , D. T. 1999 . GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences . Journal of Molecular Biology , 287 : 797 – 815 .
  • Jones , D. T. 1999 . Protein secondary structure prediction based on position-specific scoring matrices . Journal of Molecular Biology , 292 : 195 – 202 .
  • Jones , D. T. , Taylor , W. R. and Thornton , J.M. 1992 . A new approach to protein fold recognition . Nature , 358 : 86 – 89 .
  • Jones , D. T. , Taylor , W. R. and Thornton , J.M. 1994 . A model recognition approach to the prediction of all-helical membrane protein structure and topology . Biochemistry , 33 : 3038 – 3049 .
  • Kitcher , P. 1996 . The Lives to Come. The Genetic Revolution and Human Possibilities , London : Penguin .
  • Kuokka , D. and Harada , L. Matchmaking for information agents . Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence (IJCAI95) . pp. 672 – 679 .
  • Kuokka , D. and Harada , L. On using KQML for matchmaking . Proceedings of the First International Conference on Multi-Agent Systems . Menlo Park, CA. pp. 239 – 245 . AAAI Press .
  • Luck , M. 1999 . From definition to deployment What next for agent-based systems? . Knowledge Engineering Review , 14 : 119 – 124 .
  • Luck , M. and d'lnverno , M. Engagement and cooperation in motivated agent modelling . Distributed Artificial Intelligence Architecture and Modelling: Proceedings of the First Australian Workshop on Distributed Artificial Intelligence, volume 1087 of LNAI . volume 1087 , pp. 70 – 84 . Berlin : Springer .
  • Luck , M. and d'lnverno , M. Motivated behaviour for goal adoption . Multi-Agent Systems: Theories, Languages and Applications-Proceedings of the Fourth Australian Workshop on Distributed Artificial Intelligence, volume 1544 of LNAI . Berlin. volume 1544 , pp. 58 – 73 . Springer .
  • Mayfield , J. , Labrou , Y. and Finin , T. Evaluation of KQML as an agent communication language . Intelligent Agents: Theories, Architectures, and Languages, volume 1037 of LNAI . volume 1037 , pp. 347 – 360 . Berlin : Springer .
  • Moller , S. , Leser , U. , Fleischmann , W. and Apweiler , R. 1999 . EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation . Bioinformatics , 15 : 219 – 227 .
  • Pearson , W. R. 1990 . Rapid and sensitive sequence comparison with FASTP and FASTA . Methods in Enzymology , 183 : 63 – 98 .
  • Pearson , W. R. 1996 . Effective protein sequence comparison . Methods in Enzymology , 266 : 227 – 258 .
  • Rost , B. and Sander , C. 1993 . Improved prediction of protein secondary structure by use of sequence profiles and neural networks . Proceedings of the National Academy of Sciences USA , 90 : 7558 – 7562 .
  • Thompson , J. D. , Higgins , D. G. and Gibson , T.J. 1994 . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice . Nucleic Acids Research , 22 : 4673 – 4680 .
  • Vossen , G. The CORBA specification for cooperation in heterogeneous information systems . Peter Kandzia and Matthias Klusch, editors, Proceedings of the First International Workshop on Cooperative Information Agents, volume 1202 of LNAI . volume 1202 , pp. 101 – 115 . Berlin : Springer .

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