Automatic semantic annotation using unsupervised information extraction and integration

In this paper we propose a methodology to learn to automatically annotate domain-specific information from large repositories (e.g. Web sites) with minimum user intervention. The methodology is based on a combination of information extraction, information integration and machine learning techniques. Learning is seeded by extracting information from structured sources (e.g. databases and digital libraries). Retrieved information is then used to partially annotate documents. These annotated documents are used to bootstrap learning for simple Information Extraction (IE) methodologies, which in turn will produce more annotations used to annotate more documents. It will be used to train more complex IE engines and the cycle will keep on repeating itself until the required information is obtained. The user intervention is limited to providing an initial URL and to correct information if it is the case when the computation is finished. The revised annotation can then be reused to provide further training and therefore getting more information and/or more precision.peer-reviewe

Rice TOGO Browser: A Platform to Retrieve Integrated Information on Rice Functional and Applied Genomics

The Rice TOGO Browser is an online public resource designed to facilitate integration and visualization of mapping data of bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) clones, genes, restriction fragment length polymorphism (RFLP)/simple sequence repeat (SSR) markers and phenotype data represented as quantitative trait loci (QTLs) onto the genome sequence, and to provide a platform for more efficient utilization of genome information from the point of view of applied genomics as well as functional genomics. Three search options, namely keyword search, region search and trait search, generate various types of data in a user-friendly interface with three distinct viewers, a chromosome viewer, an integrated map viewer and a sequence viewer, thereby providing the opportunity to view the position of genes and/or QTLs at the chromosomal level and to retrieve any sequence information in a user-defined genome region. Furthermore, the gene list, marker list and genome sequence in a specified region delineated by RFLP/SSR markers and any sequences designed as primers can be viewed and downloaded to support forward genetics approaches. An additional feature of this database is the graphical viewer for BLAST search to reveal information not only for regions with significant sequence similarity but also for regions adjacent to those with similarity but with no hits between sequences. An easy to use and intuitive user interface can help a wide range of users in retrieving integrated mapping information including agronomically important traits on the rice genome sequence. The database can be accessed at http://agri-trait.dna.affrc.go.jp/

ORegAnno 3.0: A community-driven resource for curated regulatory annotation

The Open Regulatory Annotation database (ORegAnno) is a resource for curated regulatory annotation. It contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. ORegAnno differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information. The current release is an update of the database previously featured in the NAR Database Issue, and now contains 1 948 307 records, across 18 species, with a combined coverage of 334 215 080 bp. Complete records, annotation, and other associated data are available for browsing and download at http://www.oreganno.org/

校注『慈鎮和尚自歌合』稿（Ⅰ）

We prove that Priest Jichin's poems (慈鎮和尚自歌合) were composed at the end of 1198 (建久九年). His postscript reveals the process of their composition. Also, it is known that Fujiwara Shunzei (藤原俊成), the judge of the poem's competition, developed his theory of making poems. This study deals with the first half (大比叡・小比叡・聖真子), and gives annotations for difficult phrases and poetic expressions.原著Original国立情報学研究所で電子

Tackling hypotheticals in helminth genomes

Advancements in genome sequencing have led to the rapid accumulation of uncharacterized ‘hypothetical proteins’ in the public databases. Here we provide a community perspective and some best-practice approaches for the accurate functional annotation of uncharacterized genomic sequences

In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice

Microarray analysis of tiny amounts of RNA extracted from plant section samples prepared by laser microdissection (LM) can provide high-quality information on gene expression in specified plant cells at various stages of development. Having joined the LM-microarray analysis project, we utilized such genome-wide gene expression data from developing rice pollen cells to identify candidates for cis-regulatory elements for specific gene expression in these cells. We first found a few clusters of gene expression patterns based on the data from LM-microarrays. On one gene cluster in which the members were specifically expressed at the bicellular and mature pollen mitotic stages, we identified gene cluster fingerprints (GCFs), each of which consists of a short nucleotide representing the gene cluster. We expected that these GCFs would contain cis-regulatory elements for stage- and tissue-specific gene expression, and we further identified groups of GCFs with common core sequences. Some criteria, such as frequency of occurrence in the gene cluster in contrast to the total tested gene set, flanking sequence preference and distribution of combined GCF sets in the gene regions, allowed us to limit candidates for cis-regulatory sequences for specific gene expression in rice pollen cells to at least 20 sets of combined GCFs. This approach should provide a general purpose algorithm for identifying short nucleotides associated with specific gene expression

『厳島宝前和歌』『厳島社奉納和歌』 校注

I annotate two different waka poems dedicated to Itsukushima Shrine. The first one is the poems written supposedly in 1568 by fourteen people including one aristocrat, Masanori Asukai, This waka poem was dedicated to Itsukushima Shrine on his way to Kyoto. The second one is the poem written by thirty-six people including the Ex-Prime Minister Hideyoshi Toyotomi. It was dedicated to the shrine on their way to the Kyushu Front in March. 1587

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

Background The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas. Findings High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome. Conclusions This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture