Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japan Society of Information and Knowledge  

<p>　The National Institute of Informatics has been developing an environment called "Integrated Log Platform" for cross-sectional analysis of logs from the Research Data Cloud provided by the Institute. In this presentation, we will introduce some of the results of log analysis using the functions of this platform, especially for CiNii logs. The features of this platform are (1) creating a user action label (vocabulary) for a log (URI), and (2) organizing access logs into meaningful units ("access graph"). This research shows the possibility of these functions to model the behavior of individual users.</p>

DOI： 10.2964/jsik_2024_006

CiNii Research

Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japan Society of Information and Knowledge  

<p>　The National Institute of Informatics has developed and operates CiNii, an online database and search service for accessing Japanese academic information, but since the majority of its content is in Japanese, its current main users are from within Japan. In order to expand the use of CiNii to overseas, this research aims to make it easier to find content using languages other than Japanese. We have developed a service for evaluation by using machine translation to add English meta-data to the existing CiNii meta-data in batches. This paper describes the outline of the evaluation service, and reports on its effectiveness in improving content findability, issues it faces, and future plans for development.</p>

DOI： 10.2964/jsik_2024_007

CiNii Research

Language：Japanese   Publisher：19th International Conference on Scientometrics and Informetrics Issi 2023 Proceedings  

Scopus

Language：Japanese   Publishing type：Part of collection (book)   Publisher：Springer Nature Singapore  

DOI： 10.1007/978-981-99-8088-8_7

Scopus

Language：English   Publishing type：Research paper (international conference proceedings)  

DOI： 10.5281/zenodo.10652220

Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/pra2.660

Scopus

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/pra2.660

Language：Japanese   Publishing type：Research paper (conference, symposium, etc.)   Publisher：Japan Society of Information and Knowledge  

<p>The demand for academic information retrieval services is increasing due to the growing trend toward more active research data sharing and reexamination of research evaluation, but the constituent functions of these services are not clear. Therefore, this study focused on the screen functions of 59 domestic and foreign academic information retrieval services. We extracted and itemized the functions from these services, and conducted a comparative analysis. The itemization yielded 31 items, which were expressed as a 0/1 vector according to the presence or absence of the corresponding function. In this report, we describe the quantitative analysis based on the item vectors and the characteristics obtained by observing each service.</p>

DOI： 10.2964/jsik_2022_014

CiNii Research

Language：Japanese  

Language：Japanese   Publisher：Japan Society of Information and Knowledge  

<p>　Since the homogenized bipartite graph was proposed as a structure that can represent the knowledge information structure, there has been little discussion on its formal description and parser implementation. In this paper, we show that the representation of the structure is difficult in a conventional language, and propose a new language to represent a homogenized bipartite graph structure and its parser implementation. In addition, we describe some applications using the proposed mechanism and the perspectives on structuring knowledge and interpreting structured (formalized) knowledge. We also describe the tools implemented for the proof of concept. This tool is the first language that can formally describe a homogenized bipartite graph structure. This paper uses a style in which facts and considerations are mixed.</p>

DOI： 10.2964/jsik_2021_018

CiNii Research

Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/pra2.398

Scopus

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/pra2.398

Language：English   Publishing type：Research paper (other academic)  

Language：English   Publishing type：Research paper (international conference proceedings)  

Language：English  

Language：Japanese   Publisher：Proceedings of the Association for Information Science and Technology  

This study investigated papers posted on bioRXiv. In 2013–19, 17,818 papers were published in academic journals, accounting for 40.67% of the total publication. Among them, the Web of Science (WoS) Core Collection recorded journals of 16,525 published papers, accounting for 92.74% of the total. The following conclusions can be drawn. (1) Results indicate scientists' attention to the preprint system. (2) A large number of papers still use traditional publishing as the ultimate goal. (3) Because the posted papers scrutinized in this study were published in journals with a high impact factor, they have attracted the attention of many scientists. Nevertheless, we believe that the preprint platform will play a greater role from the academic exchange perspective.

DOI： 10.1002/pra2.175

Scopus

Language：English   Publishing type：Thesis (other)  

Language：Japanese  

Language：Japanese   Publisher：Information Science and Technology Association, Japan  

DOI： 10.18919/jkg.68.2_80

CiNii Research

Language：Japanese   Publisher：Society of Computer Chemistry, Japan  

<p>A cluster validity index (CVI) called "simplicity index" (SI) is newly proposed to enhance the accuracy of data clustering in machine learning. This index is derived to emphasize the importance of simplicity in cluster structures. The characteristics ofSI and its advantages over the known methods in the literature are discussed. SI is applied to classification of nucleotide sequences of nitrogen-fixing genes.</p>

DOI： 10.2477/jccj.2017-0062

CiNii Research

Language：Japanese   Publisher：Japan Society of Information and Knowledge  

DOI： 10.2964/jsik_2017_045

CiNii Research

CiNii Research

Language：Japanese   Publisher：Japan Society of Information and Knowledge  

DOI： 10.2964/jsik_2016_005

CiNii Research

CiNii Research

Language：Japanese   Publisher：Japan Society for Information and Media Studies  

Purpose: We analyze the mutual impact relationships among various research fields in the Natural Sciences using a field classification with a large granularity. Here, Natural Sciences include application fields such as engineering, medicine, and agriculture. On the basis of the classification used in this study, inter-field citations account for approximately 30% of the total citations. The objective of this study is to reveal the research structure of the Natural Science field by analyzing in detail the inter-field citations. Data Source: The data source of this study is Journal Citation Reports (JCR) 2004 Science Edition (CD-ROM). From this data source, we selected 5964 journals that contained articles published in 2000-2004 and cited at least once in 2004. Using the selected journals, we constructed an inter-journal citation matrix, from which we then constructed an inter-field citation matrix. Method: We used the field classification consisting of 21 fields; this classification is the same as that developed in our previous study, except that this classification united an extremely small field to the nearest field. The inter-field citation matrix based on these 21 fields was used for the analyses of the following indexes: 1. The extent that citations in the individual fields were made from/toward other fields. 2. Hierarchical relation of the 21 fields. 3. Impact strength between each field pair (symmetric/asymmetric linkage). 4. Total influence by the individual fields on other fields (based on the field Eigenfactor indicator). Results: In general, biomedical fields had a larger size than others, in terms of the number of articles. A synergistic effect was recognized between the size of a field and the impact of the articles in the field, by considering the Spearman rank correlation between them. There was a weaker synergistic effect between the size of a field and the cited/citing ratio of the field with other fields. The result of hierarchical clustering among the fields based on their citation patterns revealed interesting information about the inter-field relationships; for example, analytical chemistry was found to be nearer to agriculture than to other chemical fields. The result of symmetric linkage mostly supported the hierarchical structure; however, we observed some differences; for instance, the similarity between the condensed matter physics field and the chemistry field was the highest in the hierarchical structure but not so high in the symmetric linkage. In the analysis of the field influence based on the Eigenfactor, a large influence of biomedical fields on all other fields was observed. Additionally, we analyzed the effect of , which tunes the influence ratio between publications and citations, and observed that α is an important parameter for determining the influence ranking of the fields.

DOI： 10.11304/jims.12.28

CiNii Research

Other Link： https://jlc.jst.go.jp/DN/JALC/10022404557?from=CiNii

Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

This paper proposes a methodology which discriminates the articles by the target authors ("true" articles) from those by other homonymous authors ("false" articles). Author name searches for 2,595 "source" authors in six subject fields retrieved about 629,000 articles. In order to extract true articles from the large amount of the retrieved articles, including many false ones, two filtering stages were applied. At the first stage any retrieved article was eliminated as false if either its affiliation addresses had little similarity to those of its source article or there was no citation relationship between the journal of the retrieved article and that of its source article. At the second stage, a sample of retrieved articles was subjected to manual judgment, and utilizing the judgment results, discrimination functions based on logistic regression were defined. These discrimination functions demonstrated both the recall ratio and the precision of about 95% and the accuracy (correct answer ratio) of 90-95%. Existence of common coauthor(s), address similarity, title words similarity, and interjournal citation relationships between the retrieved and source articles were found to be the effective discrimination predictors. Whether or not the source author was from a specific country was also one of the important predictors. Furthermore, it was shown that a retrieved article is almost certainly true if it was cited by, or cocited with, its source article. The method proposed in this study would be effective when dealing with a large number of articles whose subject fields and affiliation addresses vary widely.

DOI： 10.1002/asi.21491

Web of Science

Scopus

Language：Japanese   Publisher：一般社団法人 日本土壌肥料学会  

DOI： 10.20710/dohikouen.57.0_187_2

CiNii Research

Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC BREEDING  

We applied the full-length cDNA overexpressor (FOX) gene-hunting system for systematic and genome-wide functional analysis of rice genes. In this study, we constructed a novel binary vector carrying the Gateway site-specific recombination cassette and then constructed rice FOX libraries containing a maximum of 13,823 independent, full-length cDNAs (fl-cDNAs) that correspond to approximately half the total number of rice fl-cDNA clones. By introducing the FOX libraries via Agrobacterium, we generated 2,586 FOX-rice lines exhibiting various visible alterations (e.g., plant height, tillers, leaves, and heading dates). The introduced fl-cDNAs, integrated into individual transgenic rice genomes, were amplified by genomic PCR and identified using sequencing analysis. The fl-cDNAs were PCR-amplified in 2,251 (94.2%) of the 2,389 FOX-rice lines that were examined, identifying 1,920 independent fl-cDNAs in the FOX lines. In addition to the previously generated FOX-rice plants, our new collection of FOX-rice lines produced through the Gateway system should be a useful tool for the efficient identification of gene functions in rice. Moreover, this Gateway-based technology should be applicable to other species in which a collection of fl-cDNA clones is available.

DOI： 10.1270/jsbbs.60.575

Web of Science

Scopus

Publisher：The Japanese Society of Plant Physiologists  

For systematic and genome-wide functional analysis of rice genes, we are taking advantage of the <U>F</U>ull-length cDNA <U>O</U>ver-e<U>X</U>presser (FOX) gene-hunting system. We collected the plasmid DNAs of 13,980 independent clones from RIKEN to produce a FOX library by placing individual cDNA under the control of <I>ZmUbi-1</I> promoter. Then the FOX library was transformed into rice via <I>Agrobacterium</I>. So far, we have generated approximately 12,000 RIKEN-FOX-rice lines. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8,615 FOX-rice lines identified FL-cDNAs in 8,225 lines, and a database search classified the cDNAs into 5,462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. We also have constructed rice FOX libraries containing 13,823 independent FL-cDNAs from the Foundation for Advancement of International Science (FAIS), and are generating FAIS-FOX-rice lines. Our collection of the FOX-rice lines should be a valuable tool to efficiently identify agronomically important genes.

DOI： 10.14841/jspp.2008.0.1003.0

CiNii Research

Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

The latest report has estimated the number of rice genes to be similar to 32 000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13 980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12 000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene, confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.

DOI： 10.1007/s11103-007-9243-y

Web of Science

Scopus

PubMed

Language：English   Publisher：OXFORD UNIV PRESS  

Web of Science

Publisher：The Japanese Society of Plant Physiologists  

To uncover functions of a large population of rice genes efficiently, we are employing <U>F</U>ull-length cDNA <U>O</U>ver-e<U>X</U>presser gene (FOX) hunting system. Producing FOX-rice lines, we have observed phenotypes of over 25,000 independent FOX-rice calli. Among them, two calli showed a green color on a 2,4-D-containing medium, on which wild-type rice calli are ivory yellow. In the two calli, <I>OsGLK1</I> gene, which encodes a GARP-transcription factor, was ectopically overexpressed. After transfer of wild-type calli to the regeneration medium, greening of calli and an increase in the <I>OsGLK1</I> mRNA level occurred synchronously. Transmission electron microscopy showed that chloroplasts with grana stacks were differentiated in the <I>OsGLK1</I>-FOX calli. However, in darkness, both the <I>OsGLK1</I>-FOX calli and plants did not show the green color and the differentiation of grana stacks. These data strongly suggest that OsGLK1 is a key regulator of chloroplast development under the control of light and phytohormones.

DOI： 10.14841/jspp.2007.0.403.0

CiNii Research

Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japan Society for Information and Media Studies  

Objective: In this paper, we propose a novel method to classify scientific journals into subject fields based on interjournal citation data. Object: Citation data of 5964 journals from JCR2004 Science Edition CD-ROM. Cited ratio vectors of the journals were used for analysis. Method: Our original clustering programs based on k-means were used. For the clustering, cosine distance (1-cos<I>θ</I>) was used. Results: In the cited-ratio-vector space, the spike-like-regions which appear to correspond to particular scientific fields were observed. And we succeeded to extract each spike-like-region by our clustering method. The number of fields (clusters identified) was 22. It was revealed that the cited feature of prominent multidisciplinary (general) science journals was similar to that of biochemistry journals.

DOI： 10.11304/jims.7.63

CiNii Research

Other Link： http://hdl.handle.net/2241/102370

Publishing type：Research paper (scientific journal)   Publisher：Information Processing Society of Japan  

DOI： 10.2197/ipsjdc.3.193

Language：English   Publisher：Information and Media Technologies Editorial Board  

Recently, clustering has been recognized as an important and fundamental method that analyzes and classifies large-scale sequence data to provide useful information. We developed a novel clustering method designated as Self-organizing clustering (SOC) that uses oligonucleotide frequencies for large-scale DNA sequence data. We implemented SOC as a command-line program package, and developed a server that provides access to it enabling visualization of the results.SOC effectively and quickly classifies many sequences that have low or no homology to each other. The command-line program is downloadable at http://rgp.nias.affrc.go.jp/programs/. The on-line web site is publicly accessible at http://rgp.nias.affrc.go.jp/SOC/. The common gateway interface (CGI) for the server is also provided within the package.

DOI： 10.11185/imt.2.523

CiNii Research

Language：English   Publisher：Japanese Society for Bioinformatics  

DOI： 10.11234/gi1990.14.575

CiNii Research

Language：Japanese  

Language：Japanese  

Language：Japanese  

Language：English  

Language：English