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Publications BioCreative Workshop | ORIEL Partner Publications
The following papers resulted from the ORIEL-funded BioCreative Workshop (Critical Assessment for Information Extraction in Biology), which was co-organized by partner CSIC-CNB and took place from 28 - 31 March 2004 in Granada, Spain. For more information, please visit the BioCreative website and click here if you are interested in downloading the BioCreative resources.
EMBO (European Molecular Biology Organization) Fingerprinting the Literature (Interview), The Scientist, Vol. 17, No. 23, December 01, 2003. Les Grivell, Mining the bibliome. EMBO Reports, 3 (2002) 200-203 CNR-ITB and CNR-IBC (Consiglio Nazionale delle Ricerche) Milanesi L. and Rogozin I.B. ESTMAP: A System for Expressed Sequence Tags, Mapping on Genomic Sequences. IEEE Transaction on Nanobioscience, Vol. 2 NO. 2, 75-78, June 2003. CSIC-CNB (Consejo Superior de Investigaciones Científicas) Molecular biology nomenclature thwarts information-extraction progress. By Christian Blaschke and Alfonso Valencia, IEEE Intelligent Systems May/June 2002. Information extraction in Molecular Biology. By Christian Blaschke, Lynette Hirschman and Alfonso Valencia, to appear in Briefings in Bioinformatics, Vol. 3, No. 2, 2002. EUR (Erasmus University) Jelier
R, Jenster G, Dorssers LC, van der Eijk CC, van Mulligen EM, Mons
B, Kors JA. Co-occurrence based meta-analysis of scientific texts:
retrieving biological relationships between genes. Bioinformatics.
2005;21:2049-58. Schuemie
MJ, Kors JA, Mons B. Word sense disambiguation in the biomedical domain:
an overview. J Comput Biol 2005 (accepted for publication). Schijvenaars
RJA, Mons B, Weeber M, Schuemie MJ, Van Mulligen EM, Wain HM, Kors
JA. Thesaurus-based disambiguation of gene symbols. BMC Bioinformatics
2005 (accepted for publication). Weeber
M, Schijvenaars RJA, van Mulligen EM, Mons B, Jelier R, van der Eijk
CC, Kors JA. Ambiguity of human gene symbols in LocusLink and MEDLINE:
creating an inventory and a disambiguation test collection. In: Proceedings
of AMIA Annual Symposium. 2003, 704-8.
Van der Eijk CC, van Mulligen EM, Kors JA, Mons B, van den Berg J.
Constructing an associative concept space for literature-based discovery.
JASIST 2004;55: 436-44. Schuemie
MJ, Weeber M, Schijvenaars BJA, van Mulligen EM, van der Eijk CC,
Jelier R, Mons B, Kors JA. Distribution of information in biomedical
abstracts and full-text publications. Bioinformatics 2004 [in press]. ICGEB (International Centre for Genetic Engineering and Biotechnology) Vlahovicek K, Kajan L, Agoston V, Pongor S. (2005) The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. Nucleic Acids Res.; 33 Database Issue: D223-5. Vlahovicek
K, Pintar A, Parthasarathi L, Carugo O, Pongor S. (2005) CX, DPX and
PRIDE: WWW servers for the analysis and comparison of protein 3D structures,
Nucleic Acids Res.; 33 Web-Server Issue, (in press). Carugo,
O. and Pongor, S. (2002) Protein Fold Similarity Estimated by a Probabilistic
Approach Based on C(alpha)-C(alpha) Distance Comparison, J Mol Biol.,
315(4), 887-898. Pintar, A., Carugo, O. and Pongor, S. (2002) DPX: for the analysis of the protein core, Bioinformatics 19(2), 313-314. PDF Vlahovicek, K., Kaján and Pongor, S. (2003) DNA analysis servers: plot.it., bend.it, model.it and IS, Nucleic Acids Res., 31(13), 3686-7. PDF IGH (Institut de Génétique Humaine) IMGT-Choreography
for Immunogenetics and Immunoinformatics. Marie-Paule Lefranc,
Oliver Clement, Quentin Kass, Elodie Duprat, Partick Chastellan, Isabelle
Coelho, Kora Combres, Chantal Genestoux, Véronique Giudicelli,
Denys Chaume and Gérard Lefranc. IMGT-Choreography:
processing of complex immunogenetics knowledge. Denys Chaume, Véronique
Giudicelli, Kora Combres, Chantal Genestoux and Merie-Paule Lefranc. IMGT-ONTOLOGY
and IMGT-ML for Immunogenetics and Immunoinformatics. D. Chaume, V.
Giudicelli, K. Combres and M.-P. Lefranc. ECCB'2003 Satellite Event:
Sequence Databases and Ontologies, Paris Sep. 26, 2003
Ingenta plc ORIEL Web Services: a REST-ful Lightweight Services Integration Protocol Based. Presentation by David Durand, Ingenta plc, at the University of Bologna, Italy, 20 May 2005.
INRIA (Institut National de Recherche en Informatique et Automatique) A. Morgat, F. Rechenmann. Modélisation des Données Biologiques. In " Médecine/Sciences ", Numéro 3, Volume 18, 2002, Pages 366-374. (In French) F. Rechenmann. Genostar : A Bioinformatics Platform for Exploratory Genomics. In " Ercim News ", October, 2002. F. Boyer, A. Viari. Ab Initio Reconstruction of Metabolic Pathways. In " Bioinformatics ", Suppl. 2, Volume 19, 2003, Pages 26-34. P.
Durand, C. Médigue, A. Morgat, Y. Vandenbrouck, A. Viari, F.
Rechenmann. Integration of Data And Methods for Genome Analysis. In
" Current Opinion In Drug Discovery and Development ", Number
3, Volume 6, 2003, Pages 346-352. LIRMM (Laboratoire d'Informatique, de Robotique et de Microéelectronique de Montpellier) Jean
Sallantin, Jacques Divol, Patrice Duroux "Conceptual Framework
for Interactive Ontology Building" Second IEEE International
Conference on Cognitive Informatics Jean Sallantin, Jacques Divol, Patrice Duroux, Germana M. da Nobrega and Edilson Ferneda "Descartes, a Methodical Elimination of Paradoxes for (De)-Ontology Building"; III CMSRA, Third International Workshop on Computational Models of Scientific Reasoning and Applications, Argentine National Library, Buenos Aires, September 14-15, 2003. Sallantin J., Da Nobrega G., Divol J., Duroux P. Apprentissage et Rationalité :vers une construction interactive de théories scientifiques. In COGNITIQUE éditeurs P. Aniorte et S. Gouarderes.- ISBN 285 428 612 X - CEPADUES Editions - Toulouse 2003 pp 15-31. Sallantin
J., Da Nobrega G., Divol J., Duroux P. Agent rationnel :Architecture
d'une machine assistant une construction interactive de théories
In COGNITIQUE éditeurs P. Aniorte et S. Gouarderes.- ISBN 285
428 612 X -CEPADUES Editions - Toulouse 2003 pp33 48. Sallantin J., Divol J. , Duroux P. , Szczeciniarz J.J. Construction de modalités par des agents rationnels in la modalité dans tous ses états Editeurs André Rousseaux et Christian Delcourt Liège Revue belge de philologie et d'histoire pp567-583 (à paraître 2004) UOXF-AT (University of Oxford) Rodriguez, A., Guil, N., Shotton, D. M. and Trelles, O. (2005). Analysis and description of the semantic content of cell biological videos. Multimedia Tools and Applications 25: 1-22. Sparks,
S., Catton, C. and Shotton, D. M. (2004) Publishing and finding images
in the BioImage Database, an image database for biologists. Cell Biology:
A Laboratory Handbook 3rd Edition (J. Celis, ed.) Volume 3. Elsevier
(in press). David Shotton, Simon Sparks & Chris Catton (University of Oxford): Poster on the BioImage Database presented at the ELMI meeting/ EMBO Advanced Light Microscopy Workshop in Gothenberg, May 2004. David Shotton (University of Oxford): Using ontologies to provide semantic richness in biological image databases (Abstract of paper to be presented at the Seventh Annual Bio-ontologies Meeting in Glasgow, 30 July 2004). Machtynger, J. and Shotton, D. M. (2002). VANQUIS, a system for the interactive semantic content analysis and spatiotemporal query by content of videos. J. Microscopy 205: 43-52. Shotton, D. M., Rodriguez, A., Guil, N. and Trelles, O. (2002). A metadata classification schema for semantic content analysis of videos. J. Microscopy 205: 3342. Shotton, D. M., Rodriguez, A., Guil, N. and Trelles, O. (2000). Object tracking and event recognition in biological microscopy videos. Proc. 15th International Conference on Pattern Recognition: ICPR 2000, Barcelona, Spain. (3-8 September 2000) ) 4: 226-229. Boudier, T. and Shotton, D. M. (2000). VIDOS, a system for video editing and format conversion over the Internet. Computer Networks 34: 931-944. Shotton, D. M. (2000). From image to knowledge: the state of the art in image bioinformatics. Microscopy and Analysis, 80: 23-25. |
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