Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain).

Time-course transcriptome expression data were constructed for four parts of the silk gland (anterior, middle, and posterior parts of the middle silk gland, along with the posterior silk gland) in the domestic silkworm, Bombyx mori, from days 0 to 7 of the last-instar larvae. For sample preparation, silk glands were extracted from one female and one male larva every 24 hours accurately after the fourth ecdysis. The reliability of these transcriptome data was confirmed by comparing the transcripts per million (TPM) values of the silk gene and quantitative reverse transcription PCR results.

TogoID: an exploratory ID converter to bridge biological datasets.

Motivation: Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.

TogoGenome/TogoStanza: modularized Semantic Web genome database.

TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches. All the information is stored as Resource Description Framework (RDF) data, and the reporting web pages are generated on the fly using SPARQL Protocol and RDF Query Language (SPARQL) queries. TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies.

MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.

The Microbial Genome Database for Comparative Analysis (MBGD) is a database for comparative genomics based on comprehensive orthology analysis of bacteria, archaea and unicellular eukaryotes. MBGD now contains 6318 genomes. To utilize the database for both closely related and distantly related genomes, MBGD previously provided two types of ortholog tables: the standard ortholog table containing one representative genome from each genus covering the entire taxonomic range and the taxon specific ortholog tables for each taxon.

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

Background: Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary.

The Orthology Ontology: development and applications.

Background: Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides establishing evolutionary relations among genes of organisms and allows functional inference of gene products. However, the wide variations in current orthology databases necessitate the research toward the shareability of the content that is generated by different tools and stored in different structures.

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data.

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score.

Background: Identification of ortholog groups is a crucial step in comparative analysis of multiple genomes. Although several computational methods have been developed to create ortholog groups, most of those methods do not evaluate orthology at the sub-gene level. In our method for domain-level ortholog clustering, DomClust, proteins are split into domains on the basis of alignment boundaries identified by all-against-all pairwise comparison, but it often fails to determine appropriate boundaries.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data.

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.

CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses.

CELLPEDIA is a repository database for current knowledge about human cells. It contains various types of information, such as cell morphologies, gene expression and literature references. The major role of CELLPEDIA is to provide a digital dictionary of human cells for the biomedical field, including support for the characterization of artificially generated cells in regenerative medicine.

PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs.

How to identify true transcription factor binding sites on the basis of sequence motif information (e.g., motif pattern, location, combination, etc.

Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.

Background: Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial.

Cation-controlled assembly of Na+-linked lacunary alpha-Keggin tungstosilicates.

Two novel salts of lacunary tungstosilicates with guanidinium and alkali metal cations, (CH6N3)7Na[SiW11O39].(CH3)2CO.8H2O (1) and (CH6N3)K6Na[SiW11O39].

A new 19-metal-atom cluster [(Me2PhP)10Au12Ag7(NO3)9] with a nearly staggered-staggered M5 ring configuration.

New mixed metal clusters with M19 metal frameworks have been synthesized by NaBH4 reduction of Au(NO3)(PMe2Ph) together with AgNO3 in ethanol. Single crystal X-ray diffraction has revealed Au12Ag7 and Au17Ag2 metal skeletons for these clusters, which are best described in terms of bicapped pentagonal antiprismatic cages with a staggered-staggered M(5) ring configuration. These clusters connect the missing link between M13 icosahedral and M25 biicosahedral clusters providing a view of the cluster growth process.