Atsuko Yamaguchi
Research interests
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InterestsGraph Algorithms
Publications
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The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
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 interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices ... [more] ABSTRACT: 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.
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Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering.
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, USA, 12-15 November, 2011; 01/2011
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Allie: a database and a search service of abbreviations and long forms.
Database : the journal of biological databases and curation. 01/2011; 2011:bar013.
Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader's expertise. Thus, we have developed Allie, a database and a search service of ... [more] Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader's expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly. Database URL: The Allie service is available at http://allie.dbcls.jp/.
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Natural Language Query Processing for Life Science Knowledge - Position Paper.
Active Media Technology, 6th International Conference, AMT 2010, Toronto, Canada, August 28-30, 2010. Proceedings; 01/2010
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The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.
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 for efficient systems without the need to transfer entire databases for every step of an analysis. However, vario... [more] 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 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.
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Visualization of Genetic Networks: Edge Crossing Minimization of a Graph Drawing with Vertex Pairs
03/2001;
Introduction Inference of genetic networksfrom expression profile data is still one of the challenging works in the field of themO11+b(O yinformzMTTM A good visualization tool would provide us a great insight into the interactionsamac the genes in the inferred networks. Here, we focus on the tim ser... [more] Introduction Inference of genetic networksfrom expression profile data is still one of the challenging works in the field of themO11+b(O yinformzMTTM A good visualization tool would provide us a great insight into the interactionsamac the genes in the inferred networks. Here, we focus on the tim series data of expression profiles, and discuss themeOT d to draw a two-layered graph representing the causality am[b the genes. Weassum that the causalityam(( the genes is given. For a two-layered graph, layers corresponds totim steps t and t +1, respectively. Each vertex in a layer corresponds to a gene. The causality between a pair of genes is expressed as an edgefrom a vertex in the layer for tim t to a vertex in the layer for tim t + 1. There is a restriction for drawing two-layered graphs for genetic networks that the sam gene should occupy the sam positions in the two layers. In drawing a visually understandable graph on
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An Approximation Algorithm for the Minimum Common Supertree Problem.
Nord. J. Comput. 01/1997; 4:303-316.
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寄生虫および遺伝学的手法による長崎周辺４海域産シログチの系群判別
The previous studies on life history of white croaker, Pennahia argentata, suggested that three stocks, comprising of Ariake Bay-Tachibana Bay, the Goto Sea and Omura Bay, may exist in the coastal areas of Nagasaki Prefecture, Japan. In this study, prevalence and abundance of a parasite species (Ces... [more] The previous studies on life history of white croaker, Pennahia argentata, suggested that three stocks, comprising of Ariake Bay-Tachibana Bay, the Goto Sea and Omura Bay, may exist in the coastal areas of Nagasaki Prefecture, Japan. In this study, prevalence and abundance of a parasite species (Cestoda) and mitochondrial DNA (mtDNA) variation were used to confirm the stock structure of P. argentata in these areas. Based on prevalence and abundance of Cestoda, study areas were grouped into three: Ariake Bay-Tachibana Bay, the Goto Sea and Omura Bay. Two regions of mtDNA (l6SrRNA and D-loop) were amplified by polymerase chain reaction (PCR.), and restriction fragment length polymorphism (RFLP) analyses were used for the genetic stock study. Of the ten restriction enzymes assayed for 16SrRNA, only three showed multiple restriction patterns with low variation. On the other hand, of the three restriction enzymes assayed for D-loop, all showed twothree multiple restriction patterns and nine haplotypes were determined. Haplotype diversity for each population varied from 0.484 to 0.698. The genetic distances divided four localities into two groups (Ariake Bay-Tachibana Bay and Omura Bay-the Goto Sea). It is needed to further examine the population of the Goto Sea whose sample size was small compared to other localities. The present results supported the previously estimated stock structure of p, argentata in the coastal areas of Nagasaki Prefecture estimated based on life history studies
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Characteristics of a self-assembled fibrillar gel prepared from red stingray collagen
A translucent collagen gel was formed from a transparent acidic solution of red stingray collagen by adjusting to physiological ionic strength and pH in phosphate buffer and then incubating at 25–37°C. During fibril formation from red stingray collagen, the turbidity increased when the NaCl concentr... [more] A translucent collagen gel was formed from a transparent acidic solution of red stingray collagen by adjusting to physiological ionic strength and pH in phosphate buffer and then incubating at 25–37°C. During fibril formation from red stingray collagen, the turbidity increased when the NaCl concentration was increased at constant pH and the rate of fibril formation was accelerated by higher pH or lower NaCl concentration. The T m of red stingray collagen fibrillar gel was estimated as 44.3 ± 3.5°C, which was higher than that of the collagen solution, 33.2°C. In addition, red stingray collagen gel maintained its shape without melting and was suitable for culture of mouse stromal cells at 37°C
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日本産アカエイ属魚類１種に対する新和名の提唱
The genus Dasyatis includes approximately 36 species around the world, and at least 8 species of which are distributed around Japan. In Ariake Bay, a total of 5 species of Dasyatis were identified based on our periodic studies to clarify the elasmobranch fauna since 2001. In addition, an undescribed... [more] The genus Dasyatis includes approximately 36 species around the world, and at least 8 species of which are distributed around Japan. In Ariake Bay, a total of 5 species of Dasyatis were identified based on our periodic studies to clarify the elasmobranch fauna since 2001. In addition, an undescribed species of Dasyatis was identified which is characterized by a unique combination of morphological characters. We also collected specimens of Dasyatis sp. from western coastal areas of Kyushu. In this paper, we propose a new Japanese name "Ariake-akaei" for Dasyatis sp. to avoid taxonomic confusion
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Biology of Herbivorous Fish in the Coastal Areas of Western Japan
Nagasaki University Major Research Project: Restoration of Marine Environment and Resources in East Asia Seaweed beds in Japanese coastal waters have significantly declined in recent years and feeding by herbivorous fish has been identified as one of the potential causes of this decline. In the west... [more] Nagasaki University Major Research Project: Restoration of Marine Environment and Resources in East Asia Seaweed beds in Japanese coastal waters have significantly declined in recent years and feeding by herbivorous fish has been identified as one of the potential causes of this decline. In the western coastal areas of Kyushu, seaweed consumption by fish species such as the mottled spinefoot (Siganus fuscescens), sea chubs (Kyphosus spp.), and the Japanese parrotfish (Calotomus japonicus) has become a matter of concern. Our research group has been investigating the biology of herbivorous fish in the coastal waters around western Kyushu and Okinawa. This paper presents some of the results of our work with a focus on the biology of herbivorous fish, including their distribution, age, growth, sexual maturity, sex change, feeding, behavioral ecology, and population structure. Investigation of the stomach contents of herbivorous fish revealed that Kyphosus bigibbus fed mainly on the seaweed sargassum throughout the year. In contrast, other fish supplemented their diet of seaweed with amphipods and other organisms. Experiments to determine food preference were performed on captive K. bigibbus, and their results supported the results of the stomach content analysis. Both experiments showed that the fish selectively fed on Sargassum fusiforme and Undaria pinnatifida. Herbivorous fish off the west coast of Kyushu were tracked using a biotelemetry technique, which indicated that the fish inhabited seaweed beds during the daytime. The activity of S. fuscescens and K. bigibbus markedly declined when the water temperature decreased to approximately 20°C and 17°C, respectively, but it was observed that these fish overwintered in these areas. This study demonstrates that the recent rise in winter ocean temperatures has extended the period of activity of herbivorous fish. The results contradict the hypothesis that herbivorous fish species migrate southward during colder periods
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Approximating Minimum Common Supertrees for Complete k-Ary Trees
For a set T of complete k-ary trees, we give a polynomial-time approximation algorithm for the problem of finding a k-ary common supertree with the minimum number of edges. This algorithm constructs a common supertree that has at most (5/3)l edges, where l is the number of edges in a minimum common ... [more] For a set T of complete k-ary trees, we give a polynomial-time approximation algorithm for the problem of finding a k-ary common supertree with the minimum number of edges. This algorithm constructs a common supertree that has at most (5/3)l edges, where l is the number of edges in a minimum common supertree if $ k \leq 2 $.
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鷹島町における健康調査-第3報- : (2)栄養調査(脂質と食物摂取状況)
Two hundred and fifty-six young subjects 143 males and 113 females, aged from 20 to 39 years participated in the nutrient survey. The nutrient intakes and food consumption structures were analysed by means of the questionnaires. Daily physical activity index was calculated based on the basal metabol... [more] Two hundred and fifty-six young subjects 143 males and 113 females, aged from 20 to 39 years participated in the nutrient survey. The nutrient intakes and food consumption structures were analysed by means of the questionnaires. Daily physical activity index was calculated based on the basal metabolic rates of individual activities. The intakes of rice, soybeans, fishes, alcohol and pickles were greater and those of bread, oil, meat, eggs and milk were smaller in Takashima than the intakes of the National Nutrition Survey in 1979. Subjects were divided into 3 groups by means of the serum lipid level; low(L)-, normal (N)- and high(H)-group, and the characteristics of diet composition and life style of the three groups were compared. Of the male subjects, 20.4, 61.3 and 18.3% fell into L-, N- and H-group, whereas 52.2, 39.8 and 8.0% of the female subjects fell into L-, N- and H-group, respectively. The intakes of the food groups such as soybeans, eggs, milk and fruits were lower in L -group than in the other two groups. Energy and protein intakes were the same in the three. Fat intakes, however, were higher in H-group than in L- or N-group. Cereal energy ratio with the average of 60.2% was significantly higher in L-group than in H. In conlusion, the food consumption structure was more traditional diet style in L-group than in the other two. This is probably due to the high cereal intakes and smaller amount of sidedish. (Journal of Health Science Kyushu University 10: 9-16, 1988)
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鷹島町における健康調査 : 第４報 : （2）栄養調査（アポ蛋白と食物摂取）
Two hundred and ninety-seven subjects (88 males and 209 females) , age 40 to 69 years old, participated in the nutrient survey. The nutrient intakes and food consumption structure were analysed by means of the questionnaires. Daily physical activity index was calculated based on the basal metabolic ... [more] Two hundred and ninety-seven subjects (88 males and 209 females) , age 40 to 69 years old, participated in the nutrient survey. The nutrient intakes and food consumption structure were analysed by means of the questionnaires. Daily physical activity index was calculated based on the basal metabolic rates of individual activities. The intakes of rice, soybeans, fishes, alcohol and pickles were greater and those of bread, oil, meat and milk were smaller in Takashima island than the intakes of the National Nutrition Survey in 1986. Subjects were divided into 3 groups by means of the apolipoprotein B/AI ratio level : low(L)-, normal(N)-and high(H)-group, and the characteristics of diet composition were compared. Energy and protein intakes were the same in the three groups. Fat intakes were significantly lower in females in H-group than in L-group. Cereal energy ratio was significantly higher in males in H-group than in L-group. In conclusion, the food consumption structure was more traditional diet style in H-group than in L-group. This is probably due to the high cereal intakes and smaller amount of side dish.
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鷹島町における健康調査 : 第５報 : （2）栄養調査（血圧と食物摂取）
Four hundred and eight subjects (145 males and 263 females), age 23 to 82 years old, participated in the nutrient survey. The nutrient intake and food consumption structrure were analysed by means of the questionnaires. Daily physical activity index was calculated based on the basal metabolic rates ... [more] Four hundred and eight subjects (145 males and 263 females), age 23 to 82 years old, participated in the nutrient survey. The nutrient intake and food consumption structrure were analysed by means of the questionnaires. Daily physical activity index was calculated based on the basal metabolic rates of individual activites. The intakes of rice, soybeans, fishes, alcohol and pickles in Takashima island were greater and those of bread, oil and meat were smaller than those of the National Nutrition Survey in 1986. Subjects were divided into 3 groups based on WHO blood pressure criteria : normotensive(N), borderline hypertensive(BH) and hypertensive (H) group, and the characteristics of diet composition were compared. The intakes of fat, potassium and Vitamin-A were lower in H-group than in N-group. However, energy and protein intakes were the same in the three groups. Cereal energy ratio for females was significantly higher in H-group than in N-group. In conclusion, the food consumption pattern was more traditional diet style in H-group than in N-group. This is probably due to the high cereal intakes and smaller amount of side dish.
Following (12)
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Mark J Schreiber
Novartis -
Richard Holland
Eagle Genomics Ltd. -
Jessica Severin
RIKEN yokohama -
Shujiro Okuda
Ritsumeikan University -
Jan Aerts
Catholic University Leuven
