In Silico Biology - Volume 4, issue 1

Authors: Takai-Igarashi, Takako | Takagi, Toshihisa | Wingender, Edgar

Article Type: Other

Citation: In Silico Biology, vol. 4, no. 1, pp. 1-3, 2004

Authors: Camon, Evelyn | Barrell, Daniel | Lee, Vivian | Dimmer, Emily | Apweiler, Rolf

Article Type: Short Communication

Citation: In Silico Biology, vol. 4, no. 1, pp. 5-6, 2004

Authors: Kasukawa, Takeya | Bono, Hidemasa | Hayashizaki, Yoshihide | Okazaki, Yasushi | Matsuda, Hideo

Article Type: Research Article

Abstract: Although the sequencing of the human genome and several model organisms is almost complete, the number of genes in the human is still in debate. cDNA (complementary DNA) is generated from mRNA that is transcribed from the genome and can be regarded as a gene itself; therefore, decoding cDNA sequences is important in characterizing genes. Recently, biologists have been able to describe more knowledge about genes in order to characterize them, and this information is generally …called 'annotation'. Furthermore, annotation is important in understanding the systems of organisms in various fields of research. We therefore constructed the MaXML (Mouse annotation XML) format with which mouse cDNA annotation data can be exchanged and shared between laboratories more efficiently. Defining strict data types for annotations is difficult, but we consider XML a feasible format for describing them. We have used the MaXML format to express mouse annotation data in FANTOM DB. We have also developed tools and systems utilizing these MaXML data, including a parser and a server to provide data on-the-fly. Show more

Keywords: functional annotation, transcriptome, computational annotation, mouse cDNA

Citation: In Silico Biology, vol. 4, no. 1, pp. 7-15, 2004

Authors: Lefranc, Marie-Paule | Giudicelli, Véronique | Ginestoux, Chantal | Bosc, Nathalie | Folch, Géraldine | Guiraudou, Delphine | Jabado-Michaloud, Joumana | Magris, Séverine | Scaviner, Dominique | Thouvenin, Valérie | Combres, Kora | Girod, David | Jeanjean, Stéphanie | Protat, Céline | Monod, Mehdi Yousfi | Duprat, Elodie | Kaas, Quentin | Pommié, Christelle | Chaume, Denys | Lefranc, Gérard

Article Type: Research Article

Abstract: IMGT, the international ImMunoGeneTics information system© (http://imgt.cines.fr), is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D …and 3D structures. IMGT consists of several sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB) and one three-dimensional structure database (IMGT/3Dstructure-DB), interactive tools for sequence analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery), and Web resources ("IMGT Marie-Paule page") comprising 8000 HTML pages. IMGT other accesses include SRS, FTP, search by BLAST, etc. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (scFv, phage displays, combinatorial libraries) and therapeutical approaches (grafts, immunotherapy). IMGT is freely available at http://imgt.cines.fr. Show more

Keywords: IMGT, ontology, database, information system, knowledge resource, immunoinformatics, immunogenetics, antibody, immunoglobulin, T cell receptor, immunoglobulin superfamily, leukemia, lymphoma, MHC, HLA, Collier de Perles, three-dimensional (3D) structure, primer, polymorphism

Citation: In Silico Biology, vol. 4, no. 1, pp. 17-29, 2004

Authors: Hishiki, Teruyoshi | Ogasawara, Osamu | Tsuruoka, Yoshimasa | Okubo, Kousaku

Article Type: Research Article

Abstract: As a first step toward the quantitative comparison of clinical features of diseases, we indexed the text descriptions in the Clinical Synopsis section of the Online Mendelian Inheritance in Man (OMIM) with concepts for the body parts, organs, and tissues contained in the Metathesaurus of the Unified Medical Language System (UMLS). We also indexed the text with the diseases and disorders having links to body parts specified in the thesaurus. The vocabulary size was approximately 177,540 …representations for 81,435 concepts, and 2,161 concepts were indexed to 3,779 OMIM entries. The indexed concepts included 134 concepts for the noun forms of anatomical concepts and 985 indexed concepts for diseases and disorders that were linked to 132 and 408 anatomical concepts, respectively. We report herein that the retrieval of OMIM entries for diseases affecting specific organs can be made more comprehensive through the anatomical concepts indexed to the Clinical Synopsis or linked to the indexed concepts, as compared to simply matching organ names to the Clinical Synopsis text. The recall and precision of identifying relevant body parts in the Clinical Synopsis were calculated as 78% and 92.5%, respectively, based on random sampling. The examination of the unidentified body parts due to lack of indexed diseases and disorders showed that although most of the concepts for diseases and disorders were contained in the Metathesaurus, their relations to body parts were not. The indexing result proved the effectiveness of the Metathesaurus as a resource for the identification of concepts indicating body parts, diseases, and disorders. Show more

Keywords: text mining, automated indexing, OMIM, UMLS

Citation: In Silico Biology, vol. 4, no. 1, pp. 31-54, 2004

Authors: Wingender, Edgar

Article Type: Research Article

Abstract: Building an ontology of a defined knowledge domain can help to model an appropriate database structure for the relevant contents. On the other hand, having a comprehensive overview of the knowledge of a certain domain as it may be provided by corresponding databases facilitates building an appropriate ontology, or ontologies with different granularities, which may then provide many additional benefits in handling the stored and in retrieving additional information from heterogenous sources. In this communication, the …first steps are reported how we may derive an ontology for the domain of "molecular regulation" from our databases TRANSFAC© (transcriptional regulation), TRANSPATH© (signal transduction) and CYTOMER© (cellular locations). Show more

Keywords: regulatory networks, signal transduction pathways, transcriptional regulation, databases, ontological modeling

Citation: In Silico Biology, vol. 4, no. 1, pp. 55-61, 2004

Authors: Fukuda, Ken Ichiro | Yamagata, Yuki | Takagi, Toshihisa

Article Type: Research Article

Abstract: An intelligent system for signal transduction pathways and other higher order functional knowledge is presented. Molecular mechanisms of biological processes are typically represented as diagrams ("pathways") that have a graph-analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and range from metal ion to protein to biological processes in general. In addition, the kinds of interactions that connect biological entities are …likewise diverse. Consequently, current knowledge about pathways is highly heterogeneous both in the sense of the types of constituents and the granularity of descriptions. To cope with this problem, the proposed system adopts a recursive and hierarchical representation model that enables the annotation and query of pathways or sub-pathways of arbitral granularity. By combining the use of this hierarchical structure and biological ontologies, literature-based information regarding biological mechanisms becomes accessible by computer. Show more

Keywords: pathway database, ontology, signal transduction, textual knowledge

Citation: In Silico Biology, vol. 4, no. 1, pp. 63-79, 2004

Authors: Takai-Igarashi, Takako | Mizoguchi, Riichiro

Article Type: Research Article

Abstract: Although databases for cell signaling pathways include numbers of reaction data of the pathways, the reaction data cannot be used yet to deduce biological functions from them. For the deduction, we need systematic and consistent interpretation of biological functions of reactions in cell signaling pathways in the context of "information transmission". To address this issue, we have developed a functional ontology for cell signaling pathways, Cell Signaling Network Ontology (CSN-Ontology), which provides …framework for the functional interpretation presenting some important concepts as information, selectivity, movability, and signaling rules including passage of time. Show more

Keywords: ontology, cell signaling pathway, biological function

Citation: In Silico Biology, vol. 4, no. 1, pp. 81-87, 2004

Authors: Rojas, Isabel | Ratsch, Esther | Saric, Jasmin | Wittig, Ulrike

Article Type: Research Article

Abstract: In this paper we aim at presenting the main flavours and uses that are given to the term ontology in the bio-domains. The paper does not intend to be a thorough review of the existing work in the area. It highlights the uses that are given to ontologies in the Scientific Databases and Visualisation Group at EML Research, in Heidelberg.

Keywords: formal ontology, databases, information extraction, biochemical information

Citation: In Silico Biology, vol. 4, no. 1, pp. 89-96, 2004