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Age-related changes of visual field size for detection : detection rate
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is a database that can display a visual target detection field in consideration of luminance contrast, target size and color. |
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| Data type | Visual data |
Age-related changes of visual field size for detection : size of visual field
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this is the database that it is able to display the field of view range in consideration of the influence of luminance contrast of the background and indicators, the influence of the color of the indicator, the influence of the size of the index and the influence of the brightness of the environment. |
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| Data type | Visual data |
Age-related relative luminance
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is the database that it is possible to display and to chart the optimal brightness contrast to another age. |
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| Data type | Visual data |
AIST Dance Video Database
| Summary | AIST Dance Video Database (AIST Dance DB) is a shared database containing original street dance videos with copyright-cleared dance music. This is the first large-scale shared database focusing on street dances to promote academic research regarding Dance Information Processing. |
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| Data type | Movie |
AIST Gait Database
| Summary | One of AIST's human body size and shape database, it is a database that publishes walking data of about 200 people. In addition to the increase in the number of subjects compared to the 2013 edition, the published data has been changed from 1 trial to 5 trials for each subject. You can download the data by agreeing to the data license conditions and entering your personal information and questionnaire. AIST Gait Database is one of the AIST has 214 people gait data (5 trials per capita) |
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| Data type | Ambulation data |
AIST Japanese Body Demention Data, 1991-92
| Summary | One of AIST's human body size and shape databases, which publishes the results of measurement surveys conducted by the Institute of Advanced Industrial Science and Technology at the Institute of Advanced Industrial Science and Technology in 1991-1992 for approximately 500 Japanese adults and men. The data is released free of charge for the purpose of acquiring basic data for the design support system construction. You can download the data by agreeing to the data license conditions and entering your personal information and questionnaire. |
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| Data type | Human body data |
AIST Japanese Body Demention Data, 1997-98
| Summary | In one of AIST human body size and shape database, this is a database to publish the data of the integrated measurement of the young men and women about 200 people and the elderly men and women 100 people, as data such as human body dimensions, mass of Japanese and center of gravity position. |
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| Data type | Human body data |
AJCSD
| Summary | The ASEAN-Japan Chemical Safety Database (AJCSD) is a database co-developed by ASEAN countries and Japan based on an agreement reached at ASEAN Economic Ministers and METI Economic and Industrial Cooperation Committee(AMEICC) Working Group on Chemical Industry (WG-CI). The AJCSD contains regulatory information on chemical substances provided directly by the governments of ASEAN countries, hazardous information, GHS Classification results, sample SDS, etc. |
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| Data type | Chemical Substance |
Anthropometric Database of Japanese Head 2001
| Summary | One of AIST's human body size and shape database, about 120 Japanese adolescent men and women measured between November and December 2001, and about 200 Japanese people over the age of 60 measured between January and March 2002 It is a database that exposes the head dimensions of. The data is released free of charge for the purpose of acquiring data for use in designing industrial products that fit the head of Japanese. You can download the data by agreeing to the data license conditions and entering your personal information and questionnaire. |
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| Data type | Head data |
Arch GeNet
| Summary | This database, Arch GeNet, aims at summarizing experimentally identified profiles of expression of individual genes in a thermophilic archaeon, Thermoplasma volcanium GSS1, upon adapting to different environments. In vivo not all genes coded in a genome are used at any moment. While keeping the same genomic information, organisms adapt to different environments by re-selecting appropriate populations of genes. With visual aids Arch GeNet will help understanding the network of genes, which enables environmental adaptation. |
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| Data type | Gene expression |
ARMLiPDB
| Summary | ARMLiPDB is a database of Age Related Expressions of Murine Liver Genes and Proteins. |
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| Data type | Gene expression |
ARTRA
| Summary | ARTRA is an Arabidopsis transcriptome and microarray database, which developed by Takara Bio inc, that contains transcriptome sequences and gene-specific sequences for a DNA microarray and RNAi knockdown triggers. |
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| Data type | Gene expression microarray |
ATTED II
| Summary | ATTED-II provides predicted cis elements and co-regulated gene relationships in Arabidopsis thaliana to estimate gene functions. Data source of coexpressed genes is publicly available microarray data (58 experiments, 1388 slides) collected by AtGenExpress. Coexpression measure is mutual rank (MR) based on weighted Pearson's correlation coefficients. CoexSearch function is newly supplied as "CoexSearch" in Search menu at Mar 2010. NEDO project products are included in ATTEDⅡ. |
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| Data type | Gene expression | microarray | Pathway |
Brain Atlas Database of Japanese Monkey for WWW.
| Summary | No brain atlas of a Japanese monkey, which is used widely in these experiments, was made except detail maps of the brain stem. They have made magnetic resonance images as well as histological sections of a Japanese monkey brain. For the purpose of the practical and efficient use of these images, they will construct computer database for WWW, in which we can display, magnify, and compare these images by easy mouse operations. (from original site) |
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| Data type | Morphology , MRI image |
CellMontage
| Summary | CellMontage is a system for searching gene expression databases for cells or tissues similar to the query gene expression profile. The similarity of two profiles is computed by comparing the order of genes ranked by expression. |
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| Data type | Gene expression | Cell | Tissue |
CELLPEDIA
| Summary | CELLPEDIA is a database for human cells, exhaustively collecting various types of information on cells.With a systematic classification of more than 2,000 cells based on their physical locations, each entry is organized with three types of basic information: cell morphological information with ontology, gene expression information, and related document information on cell differentiation, providing users all information requied for cell study at once (cited from original site). |
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| Data type | Cell |
CGH Data Base
| Summary | CGH Database is a database for array CGH (Comparative Genomic Hybridization)analysis data of various cancer cell lines. NEDO project products is includes in CGH Data Base. |
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| Data type | Disease-cancer |
Chemical hazard assessment document
| Summary | Chemical hazard assessment document is the data only briefly summarizes the main points of "written hazard assessment of chemical substances" has been published by NITE. By simplifying, we can provide a clue to the approximate overhead view that a hazard to quickly determine the risk of chemical substances. The data has been classified CAS number , PRTR number and materials name. |
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| Data type | Chemical compound |
Colour combinations based of fundamental colours
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this is a database that outputs the combination of colors based on the basic color region by entering the age, the environment and the color you want to examine. |
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| Data type | Visual data |
Contrast sensitivity
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is a database that can be displayed contrast sensitivity in photopic, mesopic and every presentation time conditions in one eye. |
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| Data type | Visual data |
CoP
| Summary | CoP is an integrated database for co-expressed genes and biological processes in plants. The information of biological processes is based on the biological process aspect of Gene Ontology. The genomic data in this database, including such information, were obtained from the TAIR database. The co-expression analyses in this database were executed using the Confeito algorithm, an approach for co-expression network analysis. The renewal version has been released at March 12, 2009, upgraded from the CoexProcess database. It includes co-expression analyses in 5257, 3654, and 1388 assays ofArabidopsis DNA microarray datasets and 95 assays of Populus DNA microarray datasets. This database will be reinforced every month. (cited from original site) |
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| Data type | Gene expression |
DAGViz
| Summary | DAGViz is a database to search and view ontology of 43 species, including Arabidopsis thaliana. You can search from GO term or gene product name. In the search screen, you can get detailed information through PubMed and links of gene products. It is possible to display DAG (the path from each GO term to the top term such as Biological Process). Each GO term can be displayed in a color chart representing each color. By arranging multiple color charts, you can easily compare GO terms observed in control experiments. |
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| Data type | Annotation GO |
Data and Biological Resource Platform
| Summary | DBRP is a data platform that can use information on biological resources (collection information, biological characteristic information, omics information, etc.). In addition to the microbial collections owned by NITE, you can search the collections of external organizations registered with DBRP. DBRP Stanza also allows you to search RIKEN JCM Microbial Resource Metadata microbial information and NITE collections in an integrated manner. |
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| Data type | nformation on biological resources (microbial strain information, isolation sources, etc.), data (genome, experimental data, images, etc.) |
Database for environmental microbiology
| Summary | Collaboration with each local government is indispensable to promote the environmental microbial database project for municipal sewage treatment process. We have established a collaboration system with 16 city sewage treatment plants managed by nine municipalities. We collect sludge samples from activated sludge tanks and digestion tanks about once a month. We regularly collect sludge samples and monitor the diversity of the microorganisms that make up the sludge and the types of genes that these microorganisms develop at the site of treatment. Therefore we would like to use it to investigate the causes of various troubles occurring suddenly in urban sewage treatment facilities. We will make full use of Japan's rich diversity of climate. By analyzing municipal wastewater treatment facilities that operate in various areas of Hokkaido in the north and Okinawa prefecture in the south, it is possible to create new wastewater treatment processes that can deal with various aspects, improve existing processes We are hoping for feedback on technological development aimed at. |
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| Data type | Unknown |
Database for genetic engineering of microalgae
| Summary | Useful information for genetic engineering of microalgae is collected in the database.The information is categorized as follows;1. host - vector (structure of vector, promoter, research institute, papers)2. gene transfer technique (organism, method, papers)3. production of useful materials (product, host, transferred genes, papers)4. inhibitor tolerant mutants (organism, inhibitor, mutant gene, papers)5. synthetic transposon6. selective marker(from original site) |
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| Data type | DNA-regration-region |
Database of genomes and transcriptional regulations for filamentous fungi
| Summary | The filamentous fungus, Aspergillus oryzae, plays an important role in the Japanese sake and fermentation industry, and many industrial enzymes are produced by this organism. We hope this database will provide you useful information for your research and industrial applications. |
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| Data type | DNA-sequence |
Development of a Drug Discovery Informatics System
| Summary | The Initiative 'Development of a Drug Discovery Informatics System' was conducted for five years from 2015 to support drug discovery and development in Japan. In this project, in order to improve the pharmacokinetics and toxicity which was bottleneck in academia drug discovery, in silico prediction systems of drug metabolism and pharmacokinetics, cardiotoxicity and hepatotoxicity were constructed. These in silico prediction systems are expected to be a practical tool for prioritization and optimization of compound synthesis in the early stage of drug discovery. |
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| Data type | Metadata |
DIAM
| Summary | DIAM (DataBiosafety for Industrial Applications of Microbes) was established to help meet the needs for convenience and safety and security of businesses use recombinant DNA technology.This system is intended to enhance the usefulness of Biosafety in the industry as a source of information, two databases were developed independently of each other ("JBAM" and "Biosafty-database") which was integrated.(the former URL:http://diam-jba.jp/diam/index.jsp) |
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| Data type | Journal , Biosafety infomation |
DNA ProbeLocator
| Summary | DNAProbeLocator is a web-based display for the mapping of DNA array probes onto the human full-length cDNAs (cited from the original site). |
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| Data type | Gene expression probe |
DoBISCUIT
| Summary | Secondary metabolites such as those produced by bacteria have pharmacologically important activities and attract attentions as lead-compounds and/or candidates for drug development.Although we can find many INSDC entries describing either complete or partial sequences of such secondary metabolite biosynthetic gene clusters, gene descriptions in each entry varies wildly.DoBISCUIT enables easy access to comprehensive information related to biosynthesis clusters and browsing standardized up-to-date gene descriptions. DoBISCUIT will thus serve as a useful reference for the analysis of secondary metabolite synthesis. |
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| Data type | Annotation | secondary metabolite |
Elderly Behavior Library
| Summary | The Elderly Behavior Library is a library on elderly behavior developed by the Ministry of Economy, Trade and Industry in fiscal year 29, which was developed by business related to commerce transaction optimization / product safety (action data acquisition project of elderly people, etc. for the realization of the vintage society). In this project, with the arrival of a super-aged society of "100 years of life" approaching, in order to realize an economic and social environment in which the elderly can work for a long time and can live, from the existing economic and social system, We aim to advance correspondence (vintage shift) to a new era in various societies and layers in society, ranging from services and products to be used, so as to produce highly safe product development for the elderly We have acquired and analyzed necessary data. The elderly behavior library collects behavior data (video data and attitude data) for elderly people living in nursing homes and elderly people living in ordinary households, and comprehends physical and cognitive functions, behavior types, behaviors It is related to information such as products related to the library and made it. Behavior data can be searched under the condition of body / cognitive function, behavior type, product related to behavior, etc. By aiming to grasp the behavioral characteristics of the elderly and how to use the products, we aim to use it for developing highly safe products and developing products that support the lives of elderly people. |
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| Data type | Movie |
Equal-loudness-level contours
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, an equal sense of curve of the magnitude of sound (equal loudness level curve), is a database to be displayed in graph for the young and the elderly.When you want to use, because you will be asked the first intended use, please choose those that fall from the choices. |
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| Data type | Hearing data |
Escherichia coli Multi-omics Database
| Summary | To understand the highly complex nature of living systems, a comprehensive knowledge of the quantitative information regarding the inner molecular components of cells is necessary. Here at the Institute for Advanced Biosciences, Keio University located in Tsuruoka city of Japan, we are dedicated to a collaborative grand challenge to gather multi-omics data of the model organism Escherichia coli for these purposes. |
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| Data type | Gene expression , Protein, Metabolities |
Estimation of minimum legible font size
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is the database that it is possible to estimate the readable character size from a variety of conditions.Under the conditions of the white background and black text, and you can guess the minimum readable font size for reading character, depending on the age, viewing distance, brightness and character types. |
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| Data type | Visual data |
Evola
| Summary | Evola (Evolutionary annotation database) is a database providing ortholog information of H-InvDB human genes. Evola contains orthologs among human and 14 vertebrates (chimpanzee, macaque, mouse, rat, dog, horse, cow, opossum, chicken, zebrafish, medaka, Tetraodon, and fugu). Evolutionary bioligical information such as protein multiple alignments, phylogenetic trees, transcript variants, and the degree of natural selection (dN/dS) are implemented. |
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| Data type | Comparative genomics |
Example of structured manuals for elderly care
| Summary | A structured manual for nursing care is a work procedure manual that arranges the necessary actions and their relationships for the purpose to be achieved, and expresses them using figures such as lines and squares. |
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| Data type | Structured manual for elderly care |
EzCatDB
| Summary | The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB). Each data set contains corresponding enzyme information, such as E.C. number, PDB entries with their annotated ligand information and active site residues, information on catalytic mechanisms, and links to other databases, such as Swiss-prot, CATH, KEGG, PDBsum, and PubMed. |
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| Data type | Protein-structure Enzyme |
GGDB
| Summary | Glycogene includes genes associated with glycan synthesis such as glycosyltransferase, sugar nucleotide synthases, sugar-nucleotide transporters, sulfotransferases, etc. In "Construction of GlycoGene Library Project " (April, 2001 - March, 2004), we collected and compiled the data on such glycogenes as GlycoGene Database (GGDB), which is the first database to store information on substrate specificity. |
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| Data type | DNA-sequence Substrates, Expression |
GHS Classification Results
| Summary | The GHS classification results with Hazard statement codes and Precautionary statements and codes are available in Excel and HTML format at "Substances List". |
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| Data type | Chemical Substance |
Glycoforum
| Summary | Glycoforum? was established in 1997, with the aim of introducing rapidly developing carbohydrate research in an understandable way not only to specialists but also widely to those who are interested in the field through publication of review articles, research introductions, etc. by front-line glycoscience researchers, thereby contributing to development of the carbohydrate research field. |
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| Data type | Documents | Journals |
GlycoProtDB
| Summary | GlycoProtDB -a glycoprotein database- is a searchable database to provide information of N-glycoproteins which are identified experimentally from C. elegans N2 and mouse tissues (strain C52BL/6J, male). These data were obtained and supplied by the Lab of Biochemistry at Tokyo Metropolitan University (TMU) in Tokyo Japan, and the Research Center for Medical Glycoscience (RCMG) at the AIST in Tsukuba Japan. The studies of C.elegans and mouse tissues were supported in part by grants for the Integrated Proteomics System Project, Pioneer Research on Genome the Frontier, from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan, and for the Structural Glycomics Project from the New Energy and Industrial Technology Development Organization (NEDO) of Japan, respectively. |
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| Data type | Protein-motif |
GMDB
| Summary | Glycomics has lagged far behind proteomics because of analytical difficulties arising from the structural complexity of glycans, such as variations in branching, linkage and stereo-chemistry. Recently, tandem mass spectrometry has revealed that different glycan structures show their own fragment patterns in their collision-induced dissociation (CID) spectra. We are constructing a multistage tandem mass spectral database using a variety of structurally defined glycans, some of which were prepared using glycosyltransferases in vitro. This database offers a novel tool for glycomics research as it enables users to identify glycans very easily and quickly by spectral matching. (cited from the original site) |
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| Data type | Sugar chain |
H-ANGEL
| Summary | H-ANGEL is a resource which provides information on human gene expression. H-ANGEL displays expression patterns of transcriptional products generated by the H-Invitational project in practical tissue categories based on tissue-specific expression data from several experimental platforms. H-ANGEL also displays information for the expression of different genes at their corresponding physical positions in the human genome. This information is linked to the corresponding transcript or locus annotation data stored in H-InvDB. |
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| Data type | Gene expression |
H-Exp
| Summary | This is a DB of Human Tissue-specific expression profile data and it was integrated and coordinated with H-InvDB. This system enables (1) fast search, sort, and view for gene cluster or isoform, (2) comparison of expression pattern for gene cluster or isoform, (3) display of detailed information for gene expression and related data.* Original site is now closed. |
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| Data type | Gene expression |
H-InvDB
| Summary | H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, protein functions, etc. |
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| Data type | RNA human full-length cDNA, mRNA |
Hand measurements DB
| Summary | One of AIST's human body size and shape database, this is a database that publishes gender-specific statistics of the size of the hand of 72 items measured for Japanese men and women 530 people in 2004-2011. Data can be downloaded for each measurement item. |
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| Data type | Hand data |
Healthy human micro-biome database
| Summary | In the human body, there are various microorganisms such as more than 1000 kinds and more than 100 trillion bacteria, and the population is called "microbiota". We will develop and build a healthy human microbiome database and microbiome research that will be the basis of that. |
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| Data type | Unknown |
Hearing threshold for low-frequency tones
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is a database that presents hearing thresholds for low-frequency tones, for young and older adults separately in graphical form. |
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| Data type | Hearing data |
High energy material crystal structure database
| Summary | It aims to provide crystal structure information which is the basis for considering physical property findings on high energy substances such as explosives and explosives. Furthermore, it is important to investigate the reaction process and structural change leading to the explosion to elucidate the explosion phenomenon. However, since it is difficult for experiments, the database also shows the result of predicting the crystal structure under high temperature and high pressure by computer simulation. |
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| Data type | Chemical Substance | Crystal structure |
High-energy chemical properties fact database
| Summary | Explosion accidents related to chemical substances are repeatedly occurring in every place in the world. This database maintains and publishes safety information on fire-fighting raw materials and compositions, in which accidents occur frequently. It is aimed at creating an encyclopediastic database which can comprehensively examine information related to explosion safety of chemical substances (UN numbers, physical properties, evaluation methods, past cases, prediction methods, etc.). We aim to contribute even a little to safety improvement in various industries and research activities. |
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| Data type | Chemical Substance, Explosion risk, Spectral analysis, Ion-exchange resin method, Exothermic decomposition energy measurement |
Human Body Properties Database
| Summary | In one of the AIST human body size and shape database, this database, compiled the foregoing literature concerning the human body mechanical properties, are organized into easy-to-read form.As the first step, organized database has been published about the human body size characteristics and joint characteristics and inertia characteristics. |
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| Data type | Literatures |
Identification rates of tactile symbols and letters
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this database presents correct identification rates for tactile symbols and letters, separately for groups with different properties, in graphical form. |
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| Data type | Touch data |
INOH Pathway Database
| Summary | INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form.(the former URL:http://www.inoh.org/) |
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| Data type | Protein-Proteome |
J-CHECK
| Summary | J-CHECK is a database developed to provide the information regarding "Act on the Evaluation of Chemical Substances and Regulation of Their Manufacture, etc. "(CSCL) by the authorities of the law, Ministry of Health, Labour and Welfare, Ministry of Economy, Trade and Industry, and Ministry of the Environment.J-CHECK provides the information regarding CSCL, such as the list of CSCL, chemical safety information obtained in the existing chemicals survey program, Japan Challenge Program, etc.in cooperation with eChemPortal by OECD.(cited from original site)J-CHECK related with CHRIP in chemical compound name. |
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| Data type | Chemical compound |
Japan Paleobiology Database
| Summary | This is the information on sample databases of domestic universities, museums, and museums holding archaeological specimens. |
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| Data type | Paleobiology |
KATANA
| Summary | Genomic information of Arabidopsis thaliana can be obtained from various public databases. Given that naming conventions often vary between databases and that the same genes can be annotated differently, we developed a web-based tool, KATANA (Kazusa Arabidopsis thaliana Annotation Abstract; http://www.kazusa.or.jp/katana/), to guide users searching for Arabidopsis genomic information to the relevant public databases from a single site. The tool contains information and annotations of genes and proteins, gene families, gene ontology (GO) terms, metabolic pathways and gene expression data from the Massively Parallel Signature Sequencing (MPSS) experiments. Given that entries in the tool are hyper-linked to those of the databases, detailed information can be accessed at the original sites. Advanced searches for metabolic pathways and GO terms can also be performed.(cited from the original paper) |
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| Data type | Gene expression , Metabolic pathway, Gene ontoloby |
KNApSAcK
| Summary | The KNApSAcK package when installed in the user's computer provides tool for analyzing his/her own datasets of mass spectra that are prepared according to a particular format, as well as for retrieving information on metabolites by entering the name of a metabolite, the name of an organism, molecular weight or molecular formula. A list of metabolites that are associated to a taxonomic class can be obtained by search with the taxonomic name, from which information of individual metabolites can be retrieved. (cited from the original site) |
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| Data type | Metabolite repression mass spectra |
KNApSAck Family
| Summary | KNApSAck Family is integrated database ,which KNApSAcK is the core system.The gene annotation of Arabidopsis, Bacillus, Human has been released. In addition, metal ion binding site of protein database MetalMine, KAMPO medicine database and JAMU database works with KNApSAck.In addition, the 7356 records of plant species from 119 countries have data stored. These data have been collected and registered from published scientific reports.NEDO project detaset is includes in KNApSAck Family. |
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| Data type | Metabolite repression |
KomicMarket
| Summary | KomicMarket (Kazusa Omics Data Market) is the database of annotations of the metabolite peaks that were detected by mass spectroteters (MS) in metabolomics studies. Most of the data were obtained with high-resolution MSs connected to liquid chromatograpy (LC).(cited from original site) |
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| Data type | Metabolite repression , mass spectra |
LEGENDA
| Summary | Legenda is the system to find articles in which any pair of gene names, diseases, and substrates are co-occurred in the abstract in MEDLINE. Co-occurrence of the same types (e.g. genes) can be searched. Legenda has its own gene name dictionary. |
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| Data type | Journal , Gene, Disease, Substrate |
LfDB
| Summary | Lectin Frontier DataBase (LfDB) provides quantitative interaction data in terms of the affinity constants (Ka) of a series of lectins toward a panel of pyridylaminated (PA) glycans obtained by an automated frontal affinity chromatography with fluorescence detection (FAC-FD) system (Fig. 1). Since the data are accurate and reliable, providing the absolute values of sugar-protein interactions, LfDB would be a valuable resource in the studies of glycan-related biology.(cited from the original site) |
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| Data type | Sugar chain ,Lectin |
LigandBox
| Summary | LigandBox(LIGANDs Data Base Open and eXtensible) is a 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies. It contains the 3D molecular structures including full hydrogen atoms with atomic charges for each compounds. LigandBox has been developed by JBIC, as one component of the molecular simulation system myPresto, supported by NEDO. 3D conformations of compounds were generated from 2D structural data, kindly provided by Namiki Shoji Co.,Ltd. Compounds from Namiki Shoji Co.,Ltd can be ordered to each company through each inquiry web page. Chemical structures in this database were computationally generated, may not be identical to structures of compounds stored in supplying companies. |
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| Data type | Small molecule structure |
MassBank
| Summary | MassBank has been developed with the Institute for Advanced Biosciences, Keio University (IAB) Analytical Chemistry Group, RIKEN Plant Science Center (PSC) Metabolomics Research Group as a high-resolution mass spectral database by JST-BIRD project. MassBank provides the similar spectrum search, the compound search, and peak search services. Also, MassBank was recognized as the official mass spectral database of Mass Spectrometry Society of Japan at 2008. The results of the NEDO project was contained. (Excerpt from the original site) |
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| Data type | mass spectral data |
MassBase
| Summary | The concept of metabolomics is emerged as a new omics layer of system biology in this several years, but a flood of publicly available data for bioinformatics research is not observed yet. MassBase is an archive of a huge amount of mass spectrum tags (MST) include both known and unknown assigned (or predicted) peaks which are found in biological samples (mainly from plants) and standard chemical reagents for peak annotation. The aim of the database is to enhance the bioinformatics research of metabolomics using a huge metabolomics dataset. Over 39,100,000 peaks from 7,600 MSTs by GC-MS, 7,100 MSTs by LC-MS, and 28,800 MSTs by CE-MS are archived as text format files with its binary raw data files. Scanned mass spectra (SMS), a text format list of mass signals in all scans of a binary raw data are also archived. It should help to verify a computational peak assignment and to study an improvement of a quality of peak assignment. All dataset is freely downloadable from this site. To expand the dataset by using another type of MS instruments (e.g. CE-MS) are planned in near future. MassBase developed at Kazusa DNA research institute and supported by the NEDO project. (cited from the original site) |
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| Data type | Metabolite repression |
MEDALS
| Summary | The outcome is this portal site. This provides various informationon databases and analysis tools for life science which weredeveloped by the projects directly sponsored by METI (Ministry of Economy, Trade and Industry), or developedby the Institutes sponsored by METI. The name of the site, "MEDALS",stands for METI Database portal for Life Science. It opened on October 29, 2008. |
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| Data type | metadata |
mFAERS
| Summary | mFAERS provides information on intractable diseases designated by the Ministry of Health, Labor and Welfare in a coordination with side effects reported in the FDA Adverse Event Reporting System (FAERS). FAERS is a drug adverse event (side effect) reporting system operated by the US Food and Drug Administration (FDA). mFAERS system creates a database of FAERS public data and provides searches by drug name, disease name, and side effect name. It also scores and displays the association between medications and side effects. |
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| Data type | Adverse event reports of drugs |
MFSearcher
| Summary | Kazusa Molecular Formula Searcher is a RESTful Web service, by which researchers can promptly get possible molecular formulae from accurate mass as a query(cited from original site). |
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| Data type | Metabolite repression |
Microbial Risk Information Database
| Summary | Microbial Hazard Information Database (M-RINDA) is a comprehensive site for harmful information on microorganisms (bacteria and fungi) provided by NBRC. |
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| Data type | Microbiological risk | DNA-sequence | Amino acid sequence |
Microbiological risk information list
| Summary | It is a unified list of domestic and overseas information which is the criteria for judging the risk / hazard of microorganisms (bacteria, fungi). It is possible to retrieve information such as the biosafety level (BSL) classification of each microorganism and the application of domestic laws and regulations from the scientific name (including old name and heterogeneous name). In addition to the Web version, downloadable Excel version is installed. |
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| Data type | Microbiological risk |
Microorganism database system
| Summary | This database allows users to search microorganisms and to see the various biological information. This database is available only in Japanese. |
|---|---|
| Data type | Journal old species name (if any), philogenetic position, type strain, isolation origin, chemical components as chemical taxonomic index, substrate availability, energy gain type, accession number of 16S rDNA to DDBJ/EMBL/GenBank and so on. |
MS-MS Fragment Viewer
| Summary | 'MS-MS Fragment Viewer' is a database for metabolomics which consists of the FT-MS, IT- and FT-MS/MS spectral data with predicted structures of fragment ion observed in LC-FT/ICR-MS analysis (cited from original site). |
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| Data type | Chemical compound , mass spectra |
Natural compound library
| Summary | Natural compounds produced by microorganisms possess abundant biological activities and diverse structures. It has great appeal as a new drug candidate compound. In addition, it can be said that natural chemical chemistry is unique to Japan. In order for each pharmaceutical company to cooperate to promote drug discovery research with natural products, companies holding excellent natural product libraries gathered and established the next generation natural chemical technology research association in 2011. We will store and manage unified libraries of natural products independently developed by each company and promote mutual use by other partner companies and academia. By mutual use of this natural product library, each company can maximize the utilization of the library possessed. Both library providers and users benefit. As a result, many drug candidate compounds are discovered and are expected to contribute to the development of natural drug discovery in Japan. |
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| Data type | Chemical Substance | Product of nature |
NBRC (Biological Resource Center, NITE)
| Summary | NBRC (NITE Biological Resource Center) collects and stores about 90,000 shares of filamentous fungi, yeast, bacteria, actinomyces, microalgae, etc. as a biological resource center, We offer it for a wide range of applications from research to industrial use. |
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| Data type | Data |
NBRC culture catalogue search
| Summary | Microorganisms (15,400 clones) held by NBRC of NITE can be searched. There are four ways to search, the first is NBRC number, the second is keyword, the third is scientific name or numberof other institutions, and last is homology search. The results can provide the scientific name, history, agency numbers, culture conditions and the paper information. In addition, prokaryotic (16SrDNA) and eukaryotic (28rDNA) for the registration of the sequence to confirm the identity resources search from the search sequence information. (Own translation) |
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| Data type | DNA-sequence |
Network Database System for Thermophysical Property Data
| Summary | So far, a plenty of material / matter databases have been developed, but those databases are so called databases. In those databases, it was general that only one organization that played a roll as a data center collects, deals with all transaction to register, to administrate, to supply data. The other hand, NMIJ (National Metrology Institute of Japan) suggests a concept of "Network Database System for Thermophysical Property Data", in which each institute that supplies data is responsible for its own thermophysical property database continuously and user can access to each database by one client interface "InetDBGV" through internet. And NMIJ has been developing the database that unifies each database and holds thermophysical properties like thermal conductivity, thermal diffusivity, specific heat, emissivity and so on. This is based on the research achievements of "Research on Prototype Thermophysical Property Database System", one of the task of "Research on Measurement Technology and Reference Materials for Thermophysical Properties of Solids" which was supported by the Special Coordination Funds from Science and Technology Agency (Special Coordination Funds for Promoting Science and Technology) during 5 years from 1997 to 2001. |
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| Data type | Chemical Substance | Thermophysical property |
NITE-CHRIP
| Summary | CHRIP has been developed as part of the "Foundation of Safety Management Infrastructure for Chemical Substances" based on "The Intellectual Infrastructure Installation Project" of METI. You can search the comprehensive information on a target chemical substance (information on hazardous property/hazard assessments or regulations, etc.) by entering its number or name as a keyword |
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| Data type | Chemical compound chemical substance |
Nucleic Acid Drug Database
| Summary | DB is focused on nucleic acid drugs known as biopharmaceuticals and displayed approval drugs and information on three phases of clinical trial stage. |
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| Data type | Nucleic acid drug |
OpenPML
| Summary | The study of correlations between genome variation and phenotype diversity is a key theme in the current biosciencefield. This has lead to a large number of different studies generating huge amounts of data, which typically must be shared amongst many collaborators and researchers. To store and use such data efficiently, it is paramount that biomedical researchers describe the data in a compatible and similar way. The Japan Biological Informatics Consortium has developed a data model(PaGE-OM:Phenotype and Genotype-Object Model), which have validated PaGE-OM by applying it to various existing phenotype and genotype databases, and will demonstrating how further databases can be expressed in the PaGE-OM. (cited from original site) |
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| Data type | DNA-polymol |
PoSSuM
| Summary | PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures. Basically, the users can search similar binding pockets using two search modes(cited from original site). |
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| Data type | Protein-structure |
PPI view
| Summary | The PPI view displays H-InvDB human protein-protein interaction (PPI)information. PPI data were collected from five major public PPI databases (BIND, DIP, MINT, HPRD, IntAct) and integrated them as a non-redundant PPI dataset. As the result, we got 32,198 human PPIs comprised of 9,268 proteins. (at H-InvDB version 5.0) The PPI view displays proteins which interact with the usersCHR(39) query proteins (or gene products), and provides links to H-InvDB locus view and cDNA view, which guide you to the gene locations and the detailed gene functional annotations of these interacting proteins, respectively.PPI view: http://www.h-invitational.jp/hinv/ppi/ PPI view sample:http://h-invitational.jp/hinv/ppi/ppi_view.cgi?hip=HIP000084307 |
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| Data type | Protein-Proteome |
Preferred kerning and leading of text and sentences
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is the database that it can estimate appropriate kerning and leading values for designing the form of text and sentences.The preferred kerning and leading values can be estimated by setting design parameters of the text (font and size of letters) and the conditions of use (user’s age and viewing distance). |
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| Data type | Visual data |
Preferred sound level for listening to spoken announcements
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this database presents the sound pressure level at which spoken announcements sound comfortably loud in noisy conditions, for young and older adults separately in graphical form. |
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| Data type | Hearing data |
Preferred sound level for watching TV programs
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this database presents, in graphical form, the average sound pressure levels of various TV programs at which young and older adults hear them as comfortably loud. |
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| Data type | Hearing data |
Properties Data base
| Summary | This database contains physical property data (standard enthalpy of formation, standard enthalpy of formation, standard entropy, specific heat capacity, transition enthalpy, transition entropy) for heat-related materials and basic materials. |
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| Data type | Heat-related materials | Basic materials |
PRTR map
| Summary | The PRTR map consists of an emission map and a concentration map, and the emission map shows the emissions of PRTR notification data from 2002 to 2018 (ascertained from 2001 to 2017) announced by the government. , It is color-coded by prefecture, city (local government), or town name according to the scale. The concentration map is a 5-fold mesh (5km x 5km) (scale 1) of the annual average daily concentration of chemical substances in Japan from 2002 to 2018 (ascertained from 2001 to 2017). For 200,000 or more, each mesh of the tertiary mesh (1km x 1km *) is color-coded according to the density. The estimated concentration in the atmosphere is the amount of PRTR notification data emitted from FY2002 to FY2018 (ascertained from FY2001 to FY2017) announced by the national government and the amount of data not reported by PRTR (businesses below the skirt). AIST developed by the National Institute of Advanced Industrial Science and Technology based on annual meteorological data, etc., in addition to emission data for each mesh, which is the sum of emissions from businesses, mobile bodies, and households that are not subject to PRTR. -Calculated with ADMER. (AIST-ADMER Ver, 2.6 is used for estimation up to 2013, and AIST-ADMER Ver, 3.0 is used from 2014) * The 1km x 1km mesh is an estimated value based on PRTR data from 2010 onwards.Emissions (business establishments, 3rd mesh, 5x mesh), estimated atmospheric concentration (3rd mesh, 5x mesh), and input data for AIST-ADMER calculation, which are published on the PRTR map, can be downloaded from here. is. |
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| Data type | Emissions dat | Concentration data |
Rat Brain Sections
| Summary | This database provides whole section images of rat brain recorded in ultra high resolution. You can see each neuron if you zoom in the images. The database was created by AIST, Eizou Bijutsuin, and PFU Limited.(cited from the original site) |
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| Data type | Morphology image |
Reference database for gene Expression Analysis
| Summary | RefExA is a exhaustive gene expression database for human normal tissue, normal cell and cancer cell. |
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| Data type | Disease-cancer gene expression |
RISCAD
| Summary | Relational Information System for Chemical Accidents Database |
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| Data type | Chemical Disaster Case |
Rminfo
| Summary | RMinfo is a portal site for reference materials operated by the National Metrology Institute of Japan (NMIJ), National Institute of Advance Industrial Science and Technology (AIST), Japan. More than 8,000 certified reference materials (CRMs) and reference materials (RMs) produced in Japan are registered. |
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| Data type | Reference material |
RnR
| Summary | Here is a database for the prediction of gene-transcriptional and metabolite-accumulative regulation in T87 cultured cells. The database is based on 214 DNA microarray, 222 GC-MS, and 202 UPLC-MS assays. (cited from the original site) |
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| Data type | Metabolite repression |
Size and contrast threshold for legibility
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is a database that can estimate the legible font size of a letter and a digit by setting design parameters of the display character (font, characters, and luminance contrast between a character and background) and their conditions of use (user’s age and viewing distance). In addition, this database can estimate the legible luminance contrast between a character and background by setting design parameters of the display characters (font, characters, and size) and their conditions of use. |
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| Data type | Visual data |
Solid-State NMR Spectral Database
| Summary | Solid-State NMR Spectral Database (SSNMR_SD) is a spectral database, which includes NMR spectra of mainly solid samples. Most of the spectra have been measured by solid-state NMR researchers in our institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan (or the former Institutes, National Chemical Laboratory for Industry and National Institute of Materials and Chemical Research). |
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| Data type | Chemical Substance, Formula, Spectra |
Sound pressure level of auditory signals
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is a database that provides a sound pressure level range of auditory signal that is audible and comfortably loud when heard in noise.The range is determined by taking the effects of age-related hearing loss.Based on the range, this application judges whether the level of auditory signal is suitable for use in the noise that is specified. |
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| Data type | Hearing data |
Spectral Database
| Summary | In this database, NMR, IR, MS, ESR, and Raman spectra for more than 33,000 organic compounds are provided through the internet (free).Spectral data that has been recorded are all original . |
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| Data type | Spectral data for Organic compounds |
Speech recognition scores related to hearing ability
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this database presents a relation between speech-to-noise ratio in decibels and the percentage correct of word recognition measured using high-familiarity word lists.Both test panels and test words were Japanese.The graph is displayed the sound pressure level difference between the noise and the sound as a parameter. |
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| Data type | Hearing data |
Statistical distribution of hearing threshold levels as a function of age (ISO 7029)
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, it is a database that presents statistics of the hearing-threshold-level distribution as a function of age.The values are displayed for men and women separately in the form of an audiogram.For retrieving data of Japanese people only, see Statistical distribution of hearing threshold levels as a function of age (Japanese data). |
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| Data type | Hearing data |
Statistical distribution of hearing threshold levels as a function of age (Japanese data)
| Summary | In one of the sensory characteristics database of elderly persons and persons with disabilities, this is the database that presents statistics of the hearing-threshold-level distribution of Japanese individuals as a function of age. The values are displayed for men and women separately in the form of an audiogram. For international data adopted in ISO 7029[1], see Statistical distribution of hearing threshold levels as a function of age (ISO 7029). |
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| Data type | Hearing data |
TOT-DB
| Summary | TOT-DB (The Theileria orientalis Genome Annotation Database) ia a database of the genome information of parasitic protists Theileria orientalis.Genes annotated by an integration of expression data and gene prediction by several software are displayed on the G-integra genome browser.TOT-DB also offers the BLAST homolgy search service and data downloads of the genome sequences and gene annotation of T. orientalis. |
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| Data type | Comparative genomics |
ToxBay
| Summary | This system evaluate repeated Dose Toxicity by Bayesian Net, which access two data (toxicity knowledge database and metabolism knowledge database). |
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| Data type | Chemical compound toxicity knowledge |
toxBridge
| Summary | toxBridge ? a statistical interpretation of building relationship between in vivo and in vitro for the purpose of constructing a panel as a marker group for predicting hepatotoxicity. Based on the rat in vivo and human in vitro gene expression data, the significance of gene signatures and pathways were analyzed for about 170 medical compounds at four dose levels and time points. The characteristics of toxBridge are focused on in vivo-in vitro and in vitro human-rat bridging, and various correlation indices between the bridges in the expression profile are stored in the database. It has the function of searching for compounds and searching for genes and pathways. This function allows the selection of which compounds are significant as bridging using correlation indices and creates a molecular panel in bridging by selecting a compound having a superior correlation index. |
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| Data type | Chemical compound | Gene | Pathway |
TraP
| Summary | The metabolic pathways were compared, such as glycolysis, the TCA cycle, amino acid biosynthesis, and nucleic acid biosynthesis among 7 archaea. It is possible to highlight the differences between different archaea. (cited from the original site) |
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| Data type | Metabolite repression |
３-D scanning methodologies for internationally compatible anthropometric databases
| Summary | One of AIST's human body size and shape databases, it is a database that releases data for 97 persons obtained as a result of human body size and shape measurement carried out at Digital Human Research Center, AIST. In order to investigate the use promotion of 3D human body shape data, the data is released for free. |
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| Data type | Morphological characteristic data |
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