Yasumasa Shigemoto

Publications of Yasumasa Shigemoto

• The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

  Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano [......] Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

  Journal of biomedical semantics. 08/2011; 2:4.

  ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperabilityABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

  Authors: Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts [......] Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi

  Journal of biomedical semantics. 01/2010; 1(1):8.

  Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands forWeb services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

• The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation.

  Authors: Anthony J Brookes, Heikki Lehvaslaiho, Juha Muilu, Yasumasa Shigemoto, Takashige Oroguchi, Takeshi Tomiki, Atsuhiro Mukaiyama, Akihiko Konagaya, Toshio Kojima, Ituro Inoue [......] Gudmundur A Thorisson, Debasis Dash, Haseena Rajeevan, Matthew W Darlison, Mark Woon, David Fredman, Albert V Smith, Martin Senger, Kimitoshi Naito, Hideaki Sugawara

  Human mutation. 07/2009; 30(6):968-77.

  Torrents of genotype-phenotype data are being generated, all of which must be captured, processed, integrated, and exploited. To do this optimally requires the use of standard and interoperableTorrents of genotype-phenotype data are being generated, all of which must be captured, processed, integrated, and exploited. To do this optimally requires the use of standard and interoperable "object models," providing a description of how to partition the total spectrum of information being dealt with into elemental "objects" (such as "alleles," "genotypes," "phenotype values," "methods") with precisely stated logical interrelationships (such as "A objects are made up from one or more B objects"). We herein propose the Phenotype and Genotype Experiment Object Model (PaGE-OM; www.pageom.org), which has been tested and implemented in conjunction with several major databases, and approved as a standard by the Object Management Group (OMG). PaGE-OM is open-source, ready for use by the wider community, and can be further developed as needs arise. It will help to improve information management, assist data integration, and simplify the task of informatics resource design and construction for genotype and phenotype data projects.

• Web API for biology with a workflow navigation system.

  Authors: Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara

  Nucleic acids research. 06/2009;

  DNA Data Bank of Japan (DDBJ) provides Web-based systems for biological analysis, called Web APIs for biology (WABI). So far, we have developed over 20 SOAP services and several workflows thatDNA Data Bank of Japan (DDBJ) provides Web-based systems for biological analysis, called Web APIs for biology (WABI). So far, we have developed over 20 SOAP services and several workflows that consist of a series of method invocations. In this article, we present newly developed services of WABI, that is, REST-based Web services, additional workflows and a workflow navigation system. Each Web service and workflow can be used as a complete service or a building block for programmers to construct more complex information processing systems. The workflow navigation system aims to help non-programming biologists perform analysis tasks by providing next applicable services on Web browsers according to the output of a previously selected service. With this function, users can apply multiple services consecutively only by following links without any programming or manual copy-and-paste operations on Web browsers. The listed services are determined automatically by the system referring to the dictionaries of service categories, the input/output types of services and HTML tags. WABI and the workflow navigation system are freely accessible at http://www.xml.nig.ac.jp/index.html and http://cyclamen.ddbj.nig.ac.jp/, respectively.

• Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes.

  Authors: Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara

  Nucleic acids research. 02/2007; 35(Database issue):D339-42.

  Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence DatabaseGenome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at http://gib-v.genes.nig.ac.jp/.

• The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information.

  Authors: Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto, Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A Antonio, Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi Gojobori, Takuji Sasaki

  Nucleic acids research. 02/2006; 34(Database issue):D741-4.

  With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of riceWith the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.

• Genome Informatics 14: 669--670 (2003) 669 Enhancement of the SOAP Server in DDBJ Web

  Authors: Yasumasa Shigemoto, Masahito Yamaguchi, Satoru Miyazaki, Hideaki Sugawara

  07/2004;

  Introduction Thanks to the Internet and HyperText Transfer Protocol (HTTP) [5], we can browse a number of biological databases and results from analytical tools that are distributed in the Web. TheIntroduction Thanks to the Internet and HyperText Transfer Protocol (HTTP) [5], we can browse a number of biological databases and results from analytical tools that are distributed in the Web. The results are also become available in eXtensible Markup Language (XML) [7] documents at many sites in the Internet. In addition, web services [4] start prevailing in bioinformatics domain [3] following the trend in business domain. DNA Data Bank of Japan (DDBJ) reported the implementation of the XML technology in 2002 [1] and web services in 2003 [2]. In the meantime, we recognized the need to process a long job and a large data file to cope with the tsunami of biological data. However, the SOAP server that we set up using tools in the public domain could not satisfy the requirements. Therefore, we have enhanced the SOAP server in DDBJ by use of three kinds of technologies. 2 Method and Results 2.1 The Enhancement to Process a Long Job The execution time a job can be very long, e.g. from

• Genome Informatics 14: 671--672 (2003) 671 A Prototype of PubMed Central Japan

  Authors: Hideaki Sugawara, Takashi Gojobori, Takeshi Konno, Yasumasa Shigemoto, Masahito Yamaguchi

  07/2004;

  Introduction "PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to PMC is free and unrestricted." [3]. It covers 78 journalsIntroduction "PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to PMC is free and unrestricted." [3]. It covers 78 journals and also 57 journals of BioMed Central [1]. It provides not only bibliographic information and abstracts but also full texts including figures and tables. Thus PMC is a rich and valuable information resource for research and development in biology and medicine. 2 Method and Results Figure 1: A sample list of articles hit by keyword (s). The National Center for Biotechnology Information [2] provided us with files of 190 sample articles to set up PubMed Central Japan. They consist of XML files, Document Type Definition files, entity files, image files and PDF files. The total file size is 200Mbytes. We developed a search engine by JAVA and implemented into a conventional Pentium machine. A list of articles hit by keyword(s) is displayed as shown in Fig. 1. From the list, the user can cho

• Splicing profile based protein categorization between human and mouse genomes by use of the DDBJ Web services.

  Authors: Ake Västermark, Yasumasa Shigemoto, Takashi Abe, Hideaki Sugawara

  Genome informatics. International Conference on Genome Informatics. 02/2004; 15(2):13-20.

  In one scenario of gene evolution, exon shuffling plays a fundamental role in increasing gene diversity. This paper is an appraisal of the biological relevance of categorising proteins by theirIn one scenario of gene evolution, exon shuffling plays a fundamental role in increasing gene diversity. This paper is an appraisal of the biological relevance of categorising proteins by their splicing profiles (exon-intron structures). The central question is whether protein function is more correlated with splicing profiles than sequence similarity, or not. To approach this question, a splicing profile similarity (SPS) index, which measures relative exon length discrepancy, was devised. Arbitrary human proteins were compared, in terms of SPS and amino acid sequence similarity, to their 1) mouse orthologues and 2) human paralogues, which epitomise functional equivalence and non-equivalence, respectively, to methodically elucidate the global relationship between a) biological function, b) splicing profile similarity, and c) sequence similarity. Protein function is more correlated with splicing profile similarity than sequence similarity as demonstrated by the fact that human-mouse orthologues (HMOs) display significantly higher splicing profile similarity than do human-human paralogues (HHPs), despite the mutual sequence similarity between these two categories. This finding indicates that splicing profile-based protein categorisation is biologically meaningful.