{ "title": { "path": "Path of the page URL", "name": "Database name", "alias": "Alternative name", "dbcat_id": "Integbio Database Catalog ID", "doi": "DOI", "creators": "Creator", "creator_name": "Creator Name", "creator_affiliation": "Creator Affiliation", "creator_jglobal_id": "J-GLOBAL ID of creator", "creator_researchmap_id": "researchmap ID of creator", "creator_orcid": "ORCID of creator", "creator_is_representative": "Representative", "contact_address": "Contact address", "categories": "Database classification", "categories_free_style": "Database classification (Free style)", "organisms": "Organism", "organism_name": "Taxonomy Name", "taxonomy_id": "Taxonomy ID", "organism_free_style": "Organism (Free style)", "description": "Database description", "features": "Features and manner of utilization of database", "fundings": "Background and funding", "funding_name": "Funding", "funding_jglobal_id": "J-GLOBAL ID of funding", "funding_lsdb_project_id": "LSDB project ID of funding", "funding_free_style": "Background and funding (Free style)", "references": "Reference(s)", "reference_title": "Article title", "reference_authors": "Author name(s)", "journal": "Journal", "reference_pubmed_id": "PubMed ID of Article", "reference_jglobal_id": "J-GLOBAL ID of Article", "maintenance_site": "Database maintenance site", "original_sites": "URL of the original website", "operation_start_date": "Operation start date", "last_updated_date": "Last update date", "upper_level_site": "URL of the portal site", "whole_data_download": "Whole data download", "referenced_site": "Referenced database", "list_search": "Entry list", "query_search": "Query search", "web_services": "Web services", "webservice_url": "URL of Web services", "user_registration": "Need for user registration" }, "data": [ { "path": "en\/metagenomerefdb\/desc.html", "name": "16S RNA sequence set for metagenomic analysis", "alias": "", "dbcat_id": [ "nbdc02583" ], "doi": "10.18908\/lsdba.nbdc02583-000", "creators": [ { "creator_name": "Naoya Oec", "creator_affiliation": "Dogrun Inc.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hidemasa Bono", "creator_affiliation": "Graduate School of Integrated Sciences for Life, Hiroshima University", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "RNA sequence databases" ], "categories_free_style": [ "RNA data" ], "organisms": [], "organism_free_style": "", "description": "16S RNA sequence set for metagenomic analysis using kraken2.", "features": "", "fundings": [], "funding_free_style": "", "references": [], "maintenance_site": "Graduate School of Integrated Sciences for Life, Hiroshima University", "original_sites": [ "https:\/\/dbarchive.biosciencedbc.jp\/jp\/metagenomerefdb\/desc.html" ], "operation_start_date": "2021", "last_updated_date": "2021", "upper_level_site": "", "whole_data_download": "https:\/\/dbarchive.biosciencedbc.jp\/en\/metagenomerefdb\/download.html", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/acest\/desc.html", "name": "AcEST", "alias": "Adiantum capillus-veneris EST", "dbcat_id": [ "nbdc00839" ], "doi": "10.18908\/lsdba.nbdc00839-000", "creators": [ { "creator_name": "Hiromi Kanegae", "creator_affiliation": "Tokyo Metropolitan University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Eri Kibukawa", "creator_affiliation": "Science & Technology Systems Inc.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takeshi Kanegae", "creator_affiliation": "Tokyo Metropolitan University)", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Nucleotide Sequence Databases", "Plant databases - Other plants" ], "categories_free_style": [], "organisms": [ { "organism_name": "Adiantum capillus-veneris", "taxonomy_id": 13818 } ], "organism_free_style": "", "description": "This is a database of EST sequences of Adiantum capillus-veneris determined by Tokyo Metropolitan University, and the results of the blastx search between these sequences and UniProtKB\/Swiss-Prot and TrEMBL databases. Although various plant genomes have been analyzed, the research concerning fern plants has not progressed among land plants (including seed plants, fern and moss). Considering Adiantum capillus-veneris, which has been used for photomorphogenesis research, as a model fern plant, EST sequence analysis of Adiantum was performed.", "features": "AcEST is a database comprising about 30,000 items of EST sequence data of Adiantum capillus-veneris and additional secondary information. The database can be used to look for new genes in fern plants, to elucidate gene evolution and to collect gene information specific to fern plants.", "fundings": [ { "funding_name": "Research funded by the basic research budget of Tokyo Metropolitan University", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Analysis of expressed sequence tags in prothallia of Adiantum capillus-veneris.", "reference_authors": "Yamauchi, D., Sutoh, K., Kanegae, H., Horiguchi, T., Matsuoka, K., Fukuda, H., Wada, M.", "journal": "J. Plant Res. 118 (3): 223-227.", "reference_pubmed_id": 15940394, "reference_jglobal_id": "200902214433760982" } ], "maintenance_site": "Plant Environmental Responses Laboratory, Department of Biological Sciences, Tokyo Metropolitan University Graduate School of Science and Engineering", "original_sites": [ "http:\/\/togodb.biosciencedbc.jp\/togodb\/view\/acest\/" ], "operation_start_date": "2009-06-12", "last_updated_date": "2009-11", "upper_level_site": "", "whole_data_download": "http:\/\/togodb.biosciencedbc.jp\/togodb\/view\/acest\/", "referenced_site": "", "list_search": true, "query_search": true, "web_services": true, "webservice_url": "", "user_registration": false }, { "path": "en\/aoe\/desc.html", "name": "AOE", "alias": "All Of gene Expression", "dbcat_id": [ "nbdc00467" ], "doi": "10.18908\/lsdba.nbdc00467-000", "creators": [ { "creator_name": "Hidemasa Bono", "creator_affiliation": "Database Center for Life Science", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "bonohu", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "201401171089187777", "creator_is_representative": true } ], "categories": [ "Microarray Data and other Gene Expression Databases" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "An index of public gene expression database.", "features": "Direct data access from the histogram, and make the table with selecte entries.\r\nUpdated data ranking by organisms and by methods enhances searchability of archived data.\r\nDynamic histogram for selected organisms and methods can be produced only by click operation.", "fundings": [ { "funding_name": "MEXT Integrated Database Project", "funding_jglobal_id": "", "funding_lsdb_project_id": 0 }, { "funding_name": "Life Science Database Integration Project", "funding_jglobal_id": "201304069785935332", "funding_lsdb_project_id": 0 }, { "funding_name": "Development of fundamental technologies related to integration of databases", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 0 } ], "funding_free_style": "", "references": [ { "reference_title": "All of gene expression (AOE): integrated index for public gene expression databases", "reference_authors": "Hidemasa Bono", "journal": "bioRxiv https:\/\/doi.org\/10.1101\/626754", "reference_pubmed_id": 0, "reference_jglobal_id": "" } ], "maintenance_site": "Database Center for Life Science", "original_sites": [ "https:\/\/aoe.dbcls.jp\/en" ], "operation_start_date": "2014-10-01", "last_updated_date": "2019-04-12", "upper_level_site": "https:\/\/dbcls.rois.ac.jp\/index-en.html", "whole_data_download": "", "referenced_site": "ArrayExpress, Gene Expression Omnibus(GEO), Genomic Expression Archive", "list_search": true, "query_search": true, "web_services": true, "webservice_url": "https:\/\/github.com\/dbcls\/AOE\/blob\/master\/API_documentation.md", "user_registration": false }, { "path": "en\/arabidopsis-phenome\/desc.html", "name": "Arabidopsis Phenome Database", "alias": "", "dbcat_id": [ "NBDC01509" ], "doi": "10.18908\/lsdba.nbdc01509-000", "creators": [ { "creator_name": "Hiroshi Masuya", "creator_affiliation": "RIKEN BioResource Center", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100317799465", "creator_is_representative": false }, { "creator_name": "Koji Doi", "creator_affiliation": "Institute of Crop Science, NARO", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100377855305", "creator_is_representative": false } ], "categories": [ "Plant databases - Arabidopsis thaliana" ], "categories_free_style": [], "organisms": [ { "organism_name": "Arabidopsis thaliana", "taxonomy_id": 3702 } ], "organism_free_style": "", "description": "The Arabidopsis thaliana phenome is the whole set of characteristics expressed in response to genomic, environmental and experimental factors of the most major experimental plant. The huge variety of published data have been accumulated, which is an indispensable resource to improve plant omics studies both on basic and applied research fields. It is also important to link information of bioresources such as mutant lines to the phenome to improve experimental research. Inconstancy among them however has inhibited their effective application. We developed the new Arabidopsis Phenome Database integrating two novel databases. One is the “RIKEN Phenome Integration of Arabidopsis Mutants”, that allows researchers to search mutants developed in RIKEN according to their interests in specified phenotypes to find useful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing on the Arabidopsis phenome collected by human curation of published papers, is designed to realize easily both phenotype-to-genome and genome-to-phenotype association studies.", "features": "", "fundings": [], "funding_free_style": "Database Integration Coordination Program \"Development of the integrated database of phenome\" (2014\/4-2017\/3)", "references": [], "maintenance_site": "RIKEN BioResource Center", "original_sites": [ "http:\/\/jphenome.info\/?page_id=95" ], "operation_start_date": "", "last_updated_date": "2016-12", "upper_level_site": "http:\/\/metadb.riken.jp\/metadb\/front", "whole_data_download": "http:\/\/metadb.riken.jp\/metadb\/db\/SciNetS_ria143i", "referenced_site": "Ds tagging line, Ac activation tagging line, Fox-hunting line", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/astra\/desc.html", "name": "ASTRA", "alias": "Alternative Splicing and Transcription Archives (ASTRA)", "dbcat_id": [ "nbdc00371" ], "doi": "10.18908\/lsdba.nbdc00371-000", "creators": [ { "creator_name": "Hideki Nagasaki", "creator_affiliation": "National Institute of Advanced Industrial Science and Technology, AIST. Current affiliation: Kazusa DNA Research Institute", "creator_jglobal_id": "201301021943203731", "creator_researchmap_id": "nagasaki", "creator_orcid": "", "creator_jglobal_jgpn": "201201100231289206", "creator_is_representative": false }, { "creator_name": "Osamu Gotoh", "creator_affiliation": "National Institute of Advanced Industrial Science and Technology, AIST", "creator_jglobal_id": "200901010240453294", "creator_researchmap_id": "read0081671", "creator_orcid": "", "creator_jglobal_jgpn": "200901100337614682", "creator_is_representative": false }, { "creator_name": "Masanori Arita", "creator_affiliation": "National Institute of Advanced Industrial Science and Technology, AIST. Current affiliation: National Institute of Genetics", "creator_jglobal_id": "200901068111061442", "creator_researchmap_id": "arita", "creator_orcid": "", "creator_jglobal_jgpn": "200901100359062330", "creator_is_representative": false } ], "categories": [ "Nucleotide Sequence Databases - Gene structure, introns and exons, splice sites" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Drosophila melanogaster", "taxonomy_id": 7227 }, { "organism_name": "Caenorhabditis elegans", "taxonomy_id": 6239 }, { "organism_name": "Arabidopsis thaliana", "taxonomy_id": 3702 }, { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "The database represents classified patterns of alternative splicing (AS) and alternative transcriptional initiation (ATI) in six eukaryotic genomes.", "features": "This database enables to search and represent alternative splicing\/transcriptional initiation genes and their patterns (ex: cassette) based on mapping results between full-length cDNA and genomic sequences. Furthermore the database output translated sequences of their isoforms.", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.", "reference_authors": "Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O.", "journal": "Gene. 2005 Dec 30;364:53-62.", "reference_pubmed_id": 16219431, "reference_jglobal_id": "201302256390587758" }, { "reference_title": "Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.", "reference_authors": "Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O.", "journal": "Bioinformatics. 2006 May 15;22(10):1211-6.", "reference_pubmed_id": 16500940, "reference_jglobal_id": "201002289269382085" } ], "maintenance_site": "National Institute of Advanced Industrial Science and Technology, AIST.", "original_sites": [ "" ], "operation_start_date": "2005", "last_updated_date": "2006", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/atatlas\/desc.html", "name": "AT Atlas", "alias": "Advanced Technologies Atlas", "dbcat_id": [ "nbdc01162" ], "doi": "10.18908\/lsdba.nbdc01162-000", "creators": [ { "creator_name": "Sei Miyamoto", "creator_affiliation": "Fujitsu Co., Ltd.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Yasumasa Shigemoto", "creator_affiliation": "Fujitsu Co., Ltd.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hisashi Mizutani", "creator_affiliation": "National Institute of Genetics", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takao Iwayanagi", "creator_affiliation": "National Institute of Genetics", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hideaki Sugawara", "creator_affiliation": "National Institute of Genetics", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Other Molecular Biology Databases" ], "categories_free_style": [ "Experimental Methodology" ], "organisms": [], "organism_free_style": "Homo sapiens, mouse and Arabidopsis thaliana et al. as organisms of synthesized protein.\r\nE. coli, wheat, human, yeast et al. as organisms using protein biosynthesis.", "description": "AT Atlas will make you familiar with the accomplishments by research groups of \"Protein Production\", \"Structural Analysis\" and \"Chemical Regulation\" in the Targeted Proteins Research Program. AT Atlas is composed of graphical abstract (flow chart) , information in text including actual application of the method and link to PRotein Experimental Information Management System (PREIMS). You will be able to find experimental methods used to elucidate the structure and\/or functions of proteins that you are interested in. Further, you will be able to reproduce the experimental process to study corresponding entries of PREIMS. (Most of the graphical abstracts have been drawn by use of Cell Illustrator that is a pathway-drawing software developed by Prof. Satoru Miyano and his colleagues at the U. Tokyo)", "features": "The database provides techniques in protein production (hardly-soluble proteins, membrane proteins, protein complexes etc.), structural analysis of proteins and chemical library for protein regulation technology, which were worked in Targeted Proteins Research Program (TPRP). It is a practical database including graphical abstracts and links to detailed protocols in PREIMS (Protein Experimental Information Management System).", "fundings": [ { "funding_name": "The Targeted Proteins Research Program (2007-2011) promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.\r\nProject ID: IPC1 Creation and management of information platform in Targeted Proteins Research Program\r\nhttp:\/\/www.tanpaku.org\/e_pf.php", "funding_jglobal_id": "", "funding_lsdb_project_id": 34 } ], "funding_free_style": "", "references": [], "maintenance_site": "Platform for Drug Discovery, Informatics, and Structural Life Science\r\nResearch Organization of Information and Systems\r\nNational Institute of Genetics", "original_sites": [ "http:\/\/www.tanpaku.org\/atatlas\/index_e.html" ], "operation_start_date": "2011-08", "last_updated_date": "2012-03-31", "upper_level_site": "http:\/\/www.tanpaku.org\/e_index.php", "whole_data_download": "", "referenced_site": "Protein Experimental Information Management System (PREIMS)", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/bodyparts3d\/desc.html", "name": "BodyParts3D", "alias": "3D structure database for anatomical concepts", "dbcat_id": [ "nbdc00837" ], "doi": "10.18908\/lsdba.nbdc00837-000", "creators": [ { "creator_name": "Kousaku Okubo", "creator_affiliation": "The Database Center for Life Science", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [], "categories_free_style": [ "Organ" ], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 } ], "organism_free_style": "", "description": "Dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a three-dimensional whole-body model for an adult human male", "features": "The biggest feature is that a three-dimensional whole-body model for an adult human male is available for free. The database is not only useful as an electronic atlas to three-dimensionally confirm the position and shape of human organ, but also useful in reusing the available data as the input data for human-body simulation and data mapping.\r\nA tool called \"Anatomogram\" is also made available to the public (http:\/\/lifesciencedb.jp\/bp3d\/) to readily generate an anatomical image of human body by selecting body parts from BodyParts3D and setting desired viewpoint, zoom, color and opacity.", "fundings": [ { "funding_name": "MEXT Integrated Database Project", "funding_jglobal_id": "201410043352900536", "funding_lsdb_project_id": 25 } ], "funding_free_style": "", "references": [ { "reference_title": "BodyParts3D: 3D structure database for anatomical concepts.", "reference_authors": "Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K.", "journal": "Nucleic Acids Res. 2008 Oct 3.", "reference_pubmed_id": 18835852, "reference_jglobal_id": "201302297372077317" } ], "maintenance_site": "The Database Center for Life Science", "original_sites": [ "http:\/\/lifesciencedb.jp\/bp3d\/" ], "operation_start_date": "2007-10", "last_updated_date": "2013-05", "upper_level_site": "http:\/\/lifesciencedb.jp\/lsdb.cgi?lng=en", "whole_data_download": "http:\/\/dbarchive.biosciencedbc.jp\/en\/bodyparts3d\/download.html", "referenced_site": "Foundational Model of Anatomy", "list_search": true, "query_search": true, "web_services": true, "webservice_url": "http:\/\/lifesciencedb.jp\/bp3d\/info_en\/webapi\/", "user_registration": false }, { "path": "en\/yeast-cdna\/desc.html", "name": "Budding yeast cDNA sequencing project", "alias": "", "dbcat_id": [ "nbdc00838" ], "doi": "10.18908\/lsdba.nbdc00838-000", "creators": [ { "creator_name": "Fumihito Miura", "creator_affiliation": "Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo(when creating)", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takashi Ito", "creator_affiliation": "Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo(when creating)", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Genomics Databases (non-vertebrate) - Fungal genome databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Saccharomyces cerevisiae", "taxonomy_id": 4932 } ], "organism_free_style": "", "description": "5'-end sequences of full-length cDNA clones generated from the budding yeast full-length cDNA library by the vector-capping method and the sequence quality score generated by the Phred software.", "features": "Since the vector-capping method allows to prepare cDNA possessing a genuine 5'-end, mapping the 5'-end sequence to the genome will lead to accurate identification of the transcription start site.", "fundings": [ { "funding_name": "KAKENHI (Grant-in-Aid for Scientific Research) on Priority Areas \"Systems Genomics\" from the Ministry of Education, Culture, Sports, Science and Technology of Japan", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Institute for Bioinformatics Research and Development, Japan Science and Technology Agency", "funding_jglobal_id": "200904072106278644", "funding_lsdb_project_id": 24 } ], "funding_free_style": "", "references": [ { "reference_title": "A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.", "reference_authors": "Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T.", "journal": "Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17846-51.", "reference_pubmed_id": 17101987, "reference_jglobal_id": "200902252672155526" } ], "maintenance_site": "Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo", "original_sites": [ "http:\/\/itolab.med.kyushu-u.ac.jp\/GCap\/" ], "operation_start_date": "2006-11-14", "last_updated_date": "2006-11-14", "upper_level_site": "", "whole_data_download": "http:\/\/itolab.med.kyushu-u.ac.jp\/GCap\/download.html", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/chemtheatre\/desc.html", "name": "ChemTHEATRE", "alias": "", "dbcat_id": [ "nbdc01632" ], "doi": "10.18908\/lsdba.nbdc01632-000.V002", "creators": [ { "creator_name": "Kei Nakayama", "creator_affiliation": "Center for Marine Environmental Studies, Ehime University", "creator_jglobal_id": "200901047447388990", "creator_researchmap_id": "read0144296", "creator_orcid": "0000-0002-0247-757X", "creator_jglobal_jgpn": "200901100575204999", "creator_is_representative": true } ], "categories": [], "categories_free_style": [ "Monitoring of chemical substances" ], "organisms": [], "organism_free_style": "", "description": "Existing data on the environmental concentration of chemical substances has been digitized as academic papers or public institution reports. But most of them are stored as text or excel files. They are never easy to use for modeling and risk analysis. The prediction of global chemical contamination is much delayed compared with the climate change research. It is probably due to the fact that monitoring data as an input of the prediction model and verification material is not prepared. It is a great loss that valuable research results obtained by investing a large amount of research expenses are not fully utilized. In order to make effective use of these valuable information in the future, I think that building a highly versatile database is an essential task. For that reason, we would like to create a database on concentration information on chemical substances in the environment and create a platform (ChemTHEATRE) that stores and view monitoring data on all chemical substances. Utilizing this platform makes it possible to ensure traceability of chemical substances, facilitate prediction of behavior and fate in the environment, and to cooperate with external databases on chemical substance emissions and toxicity information, etc. It ensure ecological risk assessments of highly seasoned chemical substances with high precision and transparency. Also, with advanced visualization technology of information, we can expect the return of monitoring research to society, especially contribution to environmental education and open science.", "features": "", "fundings": [], "funding_free_style": "", "references": [], "maintenance_site": "Center for Marine Environmental Studies, Ehime University", "original_sites": [ "https:\/\/chem-theatre.com\/" ], "operation_start_date": "2016-05-31", "last_updated_date": "2020-07-28", "upper_level_site": "", "whole_data_download": "", "referenced_site": "PubChem", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/chip-atlas\/desc.html", "name": "ChIP-Atlas", "alias": "", "dbcat_id": [ "nbdc01558" ], "doi": "10.18908\/lsdba.nbdc01558-000.V020", "creators": [ { "creator_name": "Shinya Oki", "creator_affiliation": "Kyoto University", "creator_jglobal_id": "201501040753326194", "creator_researchmap_id": "okishinya", "creator_orcid": "0000-0002-4767-3259", "creator_jglobal_jgpn": "200901100345522495", "creator_is_representative": false }, { "creator_name": "Tazro Ohta", "creator_affiliation": "Database Center for Life Science", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0003-3777-5945", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Human and other Vertebrate Genomes - Human genome databases, maps and viewers", "Nucleotide Sequence Databases - Transcriptional regulator sites and transcription factors", "Genomics Databases (non-vertebrate) - Genome annotation terms, ontologies and nomenclature" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Drosophila melanogaster", "taxonomy_id": 7227 }, { "organism_name": "Caenorhabditis elegans", "taxonomy_id": 6239 }, { "organism_name": "Saccharomyces cerevisiae", "taxonomy_id": 4932 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "ChIP-Atlas is the database and its web interface to provide the result of analysis processed from the entire ChIP-Seq data archived in Sequence Read Archive. We have curated metadata described by original data submitter to enable further data analysis. See details here: https:\/\/github.com\/inutano\/chip-atlas\/wiki", "features": "Users can browse all peaks from published ChIP-Seq data, and the result of target gene analysis and Colocalization analysis. Users also can perform enrichment analysis by querying user data.", "fundings": [], "funding_free_style": "", "references": [], "maintenance_site": "Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine", "original_sites": [ "https:\/\/chip-atlas.org\/" ], "operation_start_date": "2015-12-01", "last_updated_date": "2020-09-04", "upper_level_site": "", "whole_data_download": "https:\/\/github.com\/inutano\/chip-atlas\/wiki#downloads_doc", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/clest\/desc.html", "name": "ClEST", "alias": "Cimex lectularius EST", "dbcat_id": [ "nbdc01137" ], "doi": "10.18908\/lsdba.nbdc01137-000", "creators": [ { "creator_name": "Minoru Moriyama", "creator_affiliation": "National Institute of Advanced Industrial Science and Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Nucleotide Sequence Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Cimex lectularius", "taxonomy_id": 79782 } ], "organism_free_style": "", "description": "Expressed sequence tags (EST) database of unique organs and whole bodies of the bedbug, Cimex lectularius", "features": "The bedbug Cimex lectularius is a blood-feeding exoparasite of humans and other warm-blooded animals. They have unique biological traits including the obligate nutritional mutualism with a Wolbachia endosymbiont, and the peculiar mating habit called traumatic insemination. The novel insect organs, the bacteriome for endosymbiosis and the spermalege for traumatic insemination, have evolved in the bedbug lineage. This database includes transcriptome of these unique organs, and can offer the basic information for evolutionary biology and medical and hygienic applications.", "fundings": [ { "funding_name": "The Program for Promotion of Basic and Applied Research for Innovations in Bio-oriented Industry (BRAIN).", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Comparative transcriptomics of the bacteriome and spermalege of the bedbug Cimex lectularius (Hemiptera: Cimicidae)", "reference_authors": "Minoru Moriyama, Ryuichi Koga, Takahiro Hosokawa, Naruo Nikoh, Ryo Futahashi, Takema Fukatsu", "journal": "Appl Entomol Zool. 2012 Aug; 47(3):233-243.", "reference_pubmed_id": null, "reference_jglobal_id": "201202212690555357" } ], "maintenance_site": "Symbiotic Evolution and Biological Functions Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)", "original_sites": [], "operation_start_date": "", "last_updated_date": "", "upper_level_site": "http:\/\/staff.aist.go.jp\/t-fukatsu\/BRAINHome.html", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/confc\/desc.html", "name": "ConfC", "alias": "Database of conformation changes in protein structures", "dbcat_id": [ "nbdc00400" ], "doi": "10.18908\/lsdba.nbdc00400-000", "creators": [ { "creator_name": "Tamotsu Noguchi", "creator_affiliation": "Meiji Pharmaceutical University", "creator_jglobal_id": "200901022790957522", "creator_researchmap_id": "read0205922", "creator_orcid": "", "creator_jglobal_jgpn": "201550000299995880", "creator_is_representative": false } ], "categories": [ "Structure Databases - Protein structure", "Structure Databases - Small molecules", "Structure Databases - Nucleic acid structure" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "This database extracts this dynamic information from the protein structure being obtained now and is consist of three kinds of sub-database, that is, 1) evolutional structure change, 2) conformation changes by some binding and 3) structural flexibility, which were individually classified respectively.", "features": "This database will be used to 1) study protein structure stability, functional expression based on sequence changes, 2) study mechanism of gene disease based on protein structure, and 3) develop prediction methods for the protein function, disorder region and domain linker, and the method of drug design by considering the protein the movement.", "fundings": [], "funding_free_style": "This database project was supported by the Grant-in-Aid for Publication Scientific Research Results from Japan Society for the Promotion of Science(JSPS) in 2004", "references": [], "maintenance_site": "National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront\r\n*The original website was terminated.", "original_sites": [ "http:\/\/mbs.cbrc.jp\/ConfC\/" ], "operation_start_date": "2005-05-01", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/create-portal\/desc.html", "name": "CREATE portal", "alias": "", "dbcat_id": [ "nbdc00403" ], "doi": "10.18908\/lsdba.nbdc00403-000", "creators": [ { "creator_name": "Hisashi Koga", "creator_affiliation": "Kazusa DNA Research Institute (KDRI)", "creator_jglobal_id": "200901092683460338", "creator_researchmap_id": "read0132746", "creator_orcid": "", "creator_jglobal_jgpn": "200901100479841929", "creator_is_representative": false } ], "categories": [ "Proteomics Resources" ], "categories_free_style": [], "organisms": [ { "organism_name": "Mus musculus", "taxonomy_id": 10090 } ], "organism_free_style": "", "description": "KDRI has cloned ~2000 mouse homologs of human KIAA genes and prepared ~2000 rabbit polyclonal antibodies against respective mouse KIAA (mKIAA) proteins. In the CREATE portal, you can see the results of experiments exploring the expression levels of mRNA and protein for 274 mKIAA genes in the InGaP database. You can also see the results of protein-protein interaction of 50 mKIAA proteins of which interaction interactions were identified by mass spectrometry analysis following immuno-precipitation with anti-mKIAA antibodies.", "features": "You can see the results of tissue-specific expression of mKIAA proteins. These data are useful to find out the sensitivity and specificity of the anti-mKIAA antibodies, because parts of anti-mKIAA antibodies prepared in the project can be obtained from the ProteinExpress. In the InCeP database, you can see protein-protein interaction data of mKIAA proteins, useful to predict their functions.", "fundings": [], "funding_free_style": "CREATE Program (Collaboration of Regional Entities for the Advancement of Techno- logical Excellence) (2001-2006)", "references": [ { "reference_title": "A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene\/protein expression profiles for 127 mouse KIAA genes\/proteins", "reference_authors": "Koga H, Yuasa S, Nagase T, Shimada K, Nagano M, Imai K, Ohara R, Nakajima D, Murakami M, Kawai M, Miki F, Magae J, Inamoto S, Okazaki N, Ohara O.", "journal": "DNA Res. 2004 Aug 31;11(4):293-304.", "reference_pubmed_id": 15500254, "reference_jglobal_id": "200902275729419053" }, { "reference_title": "InCeP: intracellular pathway based on mKIAA protein-protein interactions", "reference_authors": "Murakami M, Shimada K, Kawai M, Koga H.", "journal": "DNA Res. 2005;12(5):379-87.", "reference_pubmed_id": 16769695, "reference_jglobal_id": "200902204953292293" } ], "maintenance_site": "", "original_sites": [], "operation_start_date": "", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/dhaplodb\/desc.html", "name": "D-HaploDB", "alias": "Definitive Haplotype Database", "dbcat_id": [ "nbdc00036" ], "doi": "10.18908\/lsdba.nbdc00036-000", "creators": [ { "creator_name": "Kenshi Hayashi", "creator_affiliation": "Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "Tomoko Tahira", "creator_affiliation": "Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Human Genes and Diseases - General polymorphism databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 } ], "organism_free_style": "", "description": "This database presents true haplotypes and LD structures of Japanese genome, determined using DNA samples obtained from complete hydatidiform moles.", "features": "The genome of complete hydatidiform mole is derived from a single sperm. Therefore, the haplotypes described in DHaploDB are true haplotypes. This is in contrast to the haplotypes of Asians described by the HapMap Project, which are haplotypes deduced from genotypes of diploid materials using computational method that yields haplotypes with error at a certain level.\r\n\r\nG-browse function is implemented at the original website (see below), where updated version (D4) is available.", "fundings": [ { "funding_name": "\"Research Revolution 2002\" (RR2002) initiative from the Ministry of Education, Culture, Sports, Science and Technology, Japan.", "funding_jglobal_id": "", "funding_lsdb_project_id": 67 }, { "funding_name": "A Grant-in-Aid for Scientific Research on Priority Areas “Applied Genomics\" from the Ministry of Education, Culture, Sports, Science and Technology, Japan.", "funding_jglobal_id": "201410076767231384", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles.", "reference_authors": "Kukita Y, Miyatake K, Stokowski R, Hinds D, Higasa K, Wake N, Hirakawa T, Kato H, Matsuda T, Pant K, Cox D, Tahira T, Hayashi K.", "journal": "Genome Res. 2005 Nov;15(11):1511-8.", "reference_pubmed_id": 16251461, "reference_jglobal_id": "201302245829785100" }, { "reference_title": "D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.", "reference_authors": "Higasa K, Miyatake K, Kukita Y, Tahira T, Hayashi K.", "journal": "Nucleic Acids Res. 2007 Jan;35(Database issue):D685-9.", "reference_pubmed_id": 17166862, "reference_jglobal_id": "201302229677297311" }, { "reference_title": "Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions.", "reference_authors": "Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K.", "journal": "PLoS Genetics, 2009 May;5(5):e1000468.", "reference_pubmed_id": 19424418, "reference_jglobal_id": "201302291339498520" }, { "reference_title": "A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.", "reference_authors": "Kukita Y, Yahara K, Tahira T, Higasa K, Sonoda M, Yamamoto K, Kato K, Wake N, Hayashi K.", "journal": "Am. J. Hum. Genet. 2010 Jun;86(6):918-28.", "reference_pubmed_id": 20537301, "reference_jglobal_id": "201002292632978646" } ], "maintenance_site": "Division of Genome Analysis,Research Center for Genetic Information,　Medical Institute of Bioregulation, Kyushu University\r\n* The original website was terminated.", "original_sites": [ "http:\/\/orca.gen.kyushu-u.ac.jp\/" ], "operation_start_date": "2005-07-20", "last_updated_date": "2011-06-23", "upper_level_site": "http:\/\/www.gen.kyushu-u.ac.jp\/~genome\/database.html", "whole_data_download": "http:\/\/orca.gen.kyushu-u.ac.jp\/download.html", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/dbspire\/desc.html", "name": "DB-SPIRE", "alias": "", "dbcat_id": [ "nbdc00411" ], "doi": "10.18908\/lsdba.nbdc00411-000", "creators": [ { "creator_name": "Tamotsu Noguchi", "creator_affiliation": "Meiji Pharmaceutical University", "creator_jglobal_id": "200901022790957522", "creator_researchmap_id": "read0205922", "creator_orcid": "", "creator_jglobal_jgpn": "201550000299995880", "creator_is_representative": false } ], "categories": [ "Structure Databases - Protein structure" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "This database has the positional information in the amino acid motif structure. The information is identified by experiments or sequence analysis (homology search and multiple alignment). We use PROSITE and BLOCKS as amino acid motif databases. PROSITE has motives from experiments, and BLOCKS has motives from both experiments and sequence analysis. We use PDB as the protein structure database and decide the motif position from SEQRES and ATOM sequences. The reason we need SEQRES and ATOM sequences is because those are not matched in some PDB entries.", "features": "This database is aimed to make researchers in bioinformatics, biochemistry or structural biology understand quickly protein function structures.\r\nYou can use this database together with “Database of conformation changes in protein structures” (ConfC) to get the picture of protein structure-function relationship dynamically and predict function sites.", "fundings": [], "funding_free_style": "", "references": [], "maintenance_site": "National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront\r\n*The original website was terminated.", "original_sites": [ "http:\/\/mbs.cbrc.jp\/DB-SPIRE" ], "operation_start_date": "2005-04-01", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "PROSITE, BLOCKS, PDB", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/dbqsnp\/desc.html", "name": "dbQSNP", "alias": "Database of SNPs in human genome with allele frequency information", "dbcat_id": [ "nbdc00042" ], "doi": "10.18908\/lsdba.nbdc00042-000", "creators": [ { "creator_name": "Kenshi Hayashi", "creator_affiliation": "Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University (when creating)", "creator_jglobal_id": "200901095483023110", "creator_researchmap_id": "read0043291", "creator_orcid": "", "creator_jglobal_jgpn": "200901100543281134", "creator_is_representative": true }, { "creator_name": "Tomoko Tahira", "creator_affiliation": "Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University (when creating)", "creator_jglobal_id": "200901050296431120", "creator_researchmap_id": "read0043292", "creator_orcid": "", "creator_jglobal_jgpn": "200901100472372281", "creator_is_representative": false }, { "creator_name": "Koichiro Higasa", "creator_affiliation": "Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University (when creating)", "creator_jglobal_id": "200901083988185648", "creator_researchmap_id": "read0106390", "creator_orcid": "", "creator_jglobal_jgpn": "200901100532168360", "creator_is_representative": false } ], "categories": [ "Human Genes and Diseases - General polymorphism databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 } ], "organism_free_style": "", "description": "SNP discovery and determination of their allele frequency in various sample groups using pooled DNA-quantitative fluorescent SSCP analysis", "features": "Most of SNPs described here were collected around the transcription start sites of many genes, and their allele frequencies were precisely determined by quantitative fluorescent SSCP analysis of pooled DNA constructed using various populations. These data is useful for the determination of genetic background of various quantitative variation of phenotypes of populations.", "fundings": [ { "funding_name": "\"Research Revolution 2002\" (RR2002) initiative from the Ministry of Education, Culture, Sports, Science and Technology, Japan.", "funding_jglobal_id": "", "funding_lsdb_project_id": 67 } ], "funding_free_style": "", "references": [ { "reference_title": "dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation", "reference_authors": "Tahira T, Baba S, Higasa K, Kukita Y, Suzuki Y, Sugano S, Hayashi K", "journal": "Human Mutation 2005 Aug. 26(2) 69-77", "reference_pubmed_id": 15977179, "reference_jglobal_id": "201002297369680698" }, { "reference_title": "Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA.", "reference_authors": "Sasaki T, Tahira T, Suzuki A, Higasa K, Kukita Y, Baba S, Hayashi K.", "journal": "Am J Hum Genet. 2001 Jan;68(1):214-8.", "reference_pubmed_id": 11083945, "reference_jglobal_id": "201302128039807034" }, { "reference_title": "Single-stranded conformational polymorphism analysis using automated capillary array electrophoresis apparatuses.", "reference_authors": "Baba S, Kukita Y, Higasa K, Tahira T, Hayashi K.", "journal": "Biotechniques. 2003 Apr;34(4):746-50.", "reference_pubmed_id": 12703299, "reference_jglobal_id": "200902228111090460" }, { "reference_title": "Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA)", "reference_authors": "Higasa K, Kukita Y, Baba S, Hayashi K.", "journal": "Biotechniques. 2002 Dec;33(6):1342-8.", "reference_pubmed_id": 12503322, "reference_jglobal_id": "200902117784892251" }, { "reference_title": "Association of polymorphisms in complement component C3 gene with susceptibility to systemic lupus erythematosus.", "reference_authors": "Miyagawa H, Yamai M, Sakaguchi D, Kiyohara C, Tsukamoto H, Kimoto Y, Nakamura T, Lee JH, Tsai CY, Chiang BL, Shimoda T, Harada M, Tahira T, Hayashi K, Horiuchi T.", "journal": "Rheumatology (Oxford). 2008 Feb;47(2):158-64", "reference_pubmed_id": 18174230, "reference_jglobal_id": "201102219065884269" }, { "reference_title": "Estimation of SNP allele frequencies by SSCP analysis of pooled DNA", "reference_authors": "Tahira T, Kukita Y, Higasa K, Okazaki Y, Yoshinaga A, Hayashi K", "journal": "Methods in Molecular Biology 578:193-207 (2009)", "reference_pubmed_id": 19768595, "reference_jglobal_id": "" }, { "reference_title": "Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics", "reference_authors": "Jespersgaard C, Larsen LA, Baba S, Kukita Y, Tahira T, Christiansen M, Vuust J, Hayashi K, Andersen PS", "journal": "Electrophoresis 27: 3816-3822 (2006)", "reference_pubmed_id": 16941449, "reference_jglobal_id": "200902255425395254" }, { "reference_title": "Multicolor post-PCR labeling of DNA fragments with fluorescent dideoxynucleotides.", "reference_authors": "Kukita Y, Hayashi K", "journal": "BioTechniques 33: 502-506 (2002)", "reference_pubmed_id": 12238759, "reference_jglobal_id": "" }, { "reference_title": "Hemi-stranded SSCP analysis of single-nucleotide polymorphisms in short sequence-tagged sites.", "reference_authors": "Kukita Y, Manago S, Baba S, Hayashi K", "journal": "BioTechniques 33:1118-1121 (2002)", "reference_pubmed_id": 12449392, "reference_jglobal_id": "" }, { "reference_title": "SSCP analysis of point mutations by multicolor capillary electrophoresis.", "reference_authors": "Hayashi K, Wenz HM, Inazuka M, Tahira T, Sasaki T, Atha DH", "journal": "Methods in Molecular Biology 163: 109-126 (2001)", "reference_pubmed_id": 11242937, "reference_jglobal_id": "" }, { "reference_title": "Recent enhancements in SSCP.", "reference_authors": "Hayashi K", "journal": "Genetic Analysis: Biomolecular Engineering 14: 193-196 (1999)", "reference_pubmed_id": 10084114, "reference_jglobal_id": "" }, { "reference_title": "SSCP analysis of long DNA fragments in low pH gel", "reference_authors": "Kukita Y, Tahira T, Sommer SS, Hayashi K", "journal": "Human Mutation 10: 400-407 (1997)", "reference_pubmed_id": 9375857, "reference_jglobal_id": "201002139486511142" }, { "reference_title": "One-tube post-PCR fluorescent labeling of DNA fragments", "reference_authors": "Inazuka M, Tahira T, Hayashi K", "journal": "Genome Research 6: 551-557 (1996)", "reference_pubmed_id": 8828044, "reference_jglobal_id": "200902189119838174" }, { "reference_title": "PCR-SSCP: A method for detection of mutations", "reference_authors": "Hayashi K", "journal": "Genetic Analsysis: Techniques and Applications 9: 73-79 (1992)", "reference_pubmed_id": 1476794, "reference_jglobal_id": "201302012182084479" }, { "reference_title": "PCR-SSCP: A simple and sensitive method for detection of mutations in the genomic DNA", "reference_authors": "Hayashi, K", "journal": "PCR Methods and Applications 1: 34-38 (1991)", "reference_pubmed_id": 1842918, "reference_jglobal_id": "" }, { "reference_title": "Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction", "reference_authors": "Orita M, Suzuki Y, Sekiya T, Hayashi K", "journal": "Genomics 5: 874-879 (1989)", "reference_pubmed_id": 2687159, "reference_jglobal_id": "200902069950476844" } ], "maintenance_site": "Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University\r\n*The original website was terminated.", "original_sites": [ "http:\/\/qsnp.gen.kyushu-u.ac.jp\/" ], "operation_start_date": "2002-10-23", "last_updated_date": "2008-09-22", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/dgby\/desc.html", "name": "DGBY", "alias": "Database for Gene function and expression of Baker's Yeast", "dbcat_id": [ "nbdc00953" ], "doi": "10.18908\/lsdba.nbdc00953-000", "creators": [ { "creator_name": "Akira Ando", "creator_affiliation": "National Food Research Institute, National Agriculture and Food Research Organization", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Microarray Data and other Gene Expression Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Saccharomyces cerevisiae", "taxonomy_id": 4932 } ], "organism_free_style": "", "description": "Baker’s yeast Saccharomyces cerevisiae is an essential ingredient in bakery products. Baker’s yeast is exposed to severe environmental stresses during bread making and the production of commercial yeast products. During bread making, yeast in frozen dough is exposed to freeze-thaw stress, and yeast in high-sugared dough is exposed to high osmolarity. In dried yeast preparation, yeast cells are exposed to air-drying stress.\r\n\r\nFigure: https:\/\/dbarchive.biosciencedbc.jp\/images\/dbarchive_images\/mail_address\/about_eg.jpg\r\n\r\nWe have investigated the stress tolerance of baker’s yeast by utilizing post-genome research. We collected a wealth of data regarding genes that may be involved in stress tolerance by using two post-genomic approaches, that is, genome-wide gene expression analysis using DNA microarrays (transcriptomics), and genome-wide screening of S. cerevisiae deletion mutant collection (so-called phenomics). We uploaded these data on this website which is designated DGBY(Database for Gene expression and function of Baker's yeast).", "features": "This database is applicable to retrieve infomation on gene expression of baker's yeast and growth data of the deletion strain set of S. cerevisiae under baking associated stresses.", "fundings": [ { "funding_name": "This work was supported by a grant from the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN).", "funding_jglobal_id": "201110030737911494", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation.", "reference_authors": "Tanaka F, Ando A, Nakamura T, Takagi H, Shima J.", "journal": "Food Microbiol. 2006 Dec;23(8):717-28. Epub 2006 Apr 4.", "reference_pubmed_id": 16943074, "reference_jglobal_id": "200902242754081770" }, { "reference_title": "Functional genomics of commercial baker's yeasts that have different abilities for sugar utilization and high-sucrose tolerance under different sugar conditions.", "reference_authors": "Tanaka-Tsuno F, Mizukami-Murata S, Murata Y, Nakamura T, Ando A, Takagi H, Shima J.", "journal": "Yeast. 2007 Oct;24(10):901-11.", "reference_pubmed_id": 17724779, "reference_jglobal_id": "200902286186846900" }, { "reference_title": "Changes in gene expression of commercial baker's yeast during an air-drying process that simulates dried yeast production.", "reference_authors": "Nakamura T, Mizukami-Murata S, Ando A, Murata Y, Takagi H, Shima J.", "journal": "J Biosci Bioeng. 2008 Oct;106(4):405-8.", "reference_pubmed_id": 19000619, "reference_jglobal_id": "200902243563683882" }, { "reference_title": "Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae.", "reference_authors": "Ando A, Tanaka F, Murata Y, Takagi H, Shima J.", "journal": "FEMS Yeast Res. 2006 Mar;6(2):249-67.", "reference_pubmed_id": 16487347, "reference_jglobal_id": "200902242232742955" }, { "reference_title": "Identification and classification of genes required for tolerance to freeze-thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.", "reference_authors": "Ando A, Nakamura T, Murata Y, Takagi H, Shima J.", "journal": "FEMS Yeast Res. 2007 Mar;7(2):244-53. Epub 2006 Sep 21.", "reference_pubmed_id": 16989656, "reference_jglobal_id": "200902296147274830" }, { "reference_title": "Possible roles of vacuolar H+-ATPase and mitochondrial function in tolerance to air-drying stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains.", "reference_authors": "Shima J, Ando A, Takagi H.", "journal": "Yeast. 2008 Mar;25(3):179-90.", "reference_pubmed_id": 18224659, "reference_jglobal_id": "200902276052598793" } ], "maintenance_site": "National Food Research Institute, National Agriculture and Food Research Organization (NARO)", "original_sites": [ "http:\/\/www.naro.affrc.go.jp\/org\/nfri\/english\/Useful\/yeast\/index.html" ], "operation_start_date": "2006-10-02", "last_updated_date": "2009-07-29", "upper_level_site": "http:\/\/www.naro.affrc.go.jp\/english\/index.html", "whole_data_download": "", "referenced_site": "GEO, SGD, PubMed", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/dicty-cdb\/desc.html", "name": "Dicty_cDB", "alias": "Dictyostelium cDNA Database", "dbcat_id": [ "nbdc00419" ], "doi": "10.18908\/lsdba.nbdc00419-000", "creators": [ { "creator_name": "Hideko Urushihara", "creator_affiliation": "University of Tsukuba", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "Yoshihiro Ugawa", "creator_affiliation": "", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Yuji Shimizu", "creator_affiliation": "", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Genomics Databases (non-vertebrate) - Unicellular eukaryotes genome databases" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "Dicty_cDB is a publicly available gene information database comprising the primary information obtained by EST analysis of Dictyostelium discoideum, which is known as a social amoeba, and a variety of additional secondary information. This database represents the results of the Dictyostelium cDNA Project in Japan for Dictyostelium discoideum.", "features": "Sequences and BLAST search results of all ESTs and assembled unigenes are displayed for D. discoideum. Clones themselves are distributed by NBRP (http:\/\/nenkin.lab.nig.ac.jp\/).", "fundings": [ { "funding_name": "Grant-in-Aid for Scientific Research", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Grant-in-Aid for Publication of Scientific Research Results", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Research for the Future Program of the Japanese Society for Promotion of Science", "funding_jglobal_id": "", "funding_lsdb_project_id": 31 } ], "funding_free_style": "", "references": [ { "reference_title": "Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum", "reference_authors": "Urushihara H, Morio T, Saito T, Kohara Y, Koriki E, Ochiai H, Maeda M, Williams JG, Takeuchi I, Tanaka Y.", "journal": "Nucleic Acids Res. 2004 Mar 9;32(5):1647-53.", "reference_pubmed_id": 15010511, "reference_jglobal_id": "200902233851438803" } ], "maintenance_site": "Graduate School of Life and Environmental Sciences, University of Tsukuba", "original_sites": [ "" ], "operation_start_date": "1996-12", "last_updated_date": "2009-08", "upper_level_site": "", "whole_data_download": "", "referenced_site": "GENBANK\/DDBJ\/EBI", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/dmpd\/desc.html", "name": "DMPD", "alias": "Dynamic Macrophage Pathway CSML Database", "dbcat_id": [ "nbdc00558" ], "doi": "10.18908\/lsdba.nbdc00558-000", "creators": [ { "creator_name": "Masao Nagasaki", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Ayumu Saito", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Andre Fujita", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Kazuko Ueno", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Emi Ikeda", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Euna Jeong", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Satoru Miyano", "creator_affiliation": "The Institute of Medical Science, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "Nihon BIOBASE KK.", "creator_affiliation": "", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Metabolic and Signaling Pathways " ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mammalia", "taxonomy_id": 40674 } ], "organism_free_style": "", "description": "DMPD collects pathway models of transcriptional regulation and signal transduction in CSML format for dymamic simulation based on the curation of descriptions about LPS and PMA stimulation for macrophage from literature.", "features": "[Feature]\r\nThis is the world's largest pathway simulation model database for regulation of differentiation and activation of macrophage. Information on those pathways are extracted in the CSML format, one of the XML format, from selected literatures described about the macrophage differentiation and activation (a total of 200 articles).\r\n[Utility and Manner of Utilization]\r\nThe CSML format allows users to edit the model and perform simulation of the model by using Cell Illustrator which is one of the softwares for system biology. For experts in macrophage-related areas, it may be useful to search for pathway models related to their work, and also customize the models for further use. They can also take out part of a single pathway for further use or edit and integrate multiple pathways for use as a larger pathway model. Each model is also released in images such as the PNG format. So, you can still get the general picture of pathways by using ordinary browsers.", "fundings": [ { "funding_name": "Achievements of the Ministry of Education, Culture, Sports, Science and Technology - Genome Network Project (GNP)", "funding_jglobal_id": "", "funding_lsdb_project_id": 1 } ], "funding_free_style": "", "references": [], "maintenance_site": "The Institute of Medical Science, The University of Tokyo", "original_sites": [ "http:\/\/gnp.hgc.jp\/macrophage\/" ], "operation_start_date": "2009-03", "last_updated_date": "2009-08", "upper_level_site": "http:\/\/gnp.hgc.jp\/", "whole_data_download": "http:\/\/gnp.hgc.jp\/macrophage\/", "referenced_site": "PubMed", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/esol\/desc.html", "name": "eSOL", "alias": "Solubility database of all E.coli proteins", "dbcat_id": [ "NBDC00440" ], "doi": "10.18908\/lsdba.nbdc00440-000", "creators": [ { "creator_name": "Tatsuya Niwa", "creator_affiliation": "Department of Biomolecular Engineering, School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hideaki Sugawara", "creator_affiliation": "The Research and Development of Biological Databases Project, National Institute of Genetics", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuya Ueda", "creator_affiliation": "Department of Medical Genome Science, Graduate School of Frontier Sciences, The University of Tokyo", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hideki Taguchi", "creator_affiliation": "Department of Biomolecular Engineering, School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Protein sequence databases - Protein properties" ], "categories_free_style": [], "organisms": [ { "organism_name": "Escherichia coli", "taxonomy_id": 562 } ], "organism_free_style": "", "description": "The database of solubilities and synthetic yields of all E.coli proteins translated by using an in vitro reconstituted translation system. For 788 aggregation-prone proteins, the data of chaperone effects on the prevention of aggregate formation were added on May 2012.\r\nGene segments from plasmids of ASKA library (Kitagawa et al. 2005) , which is the library of all genes of the E. coli strain K-12, were amplified by PCR, and their proteins were synthesized by using an in vitro translation system (PURE system). The solubilities were evaluated by SDS-PAGE and autoradiography before and after centrifugation.\r\nFor aggregation-prone proteins (defined as the proteins with less than 30% solubility in the absence of any chaperone), observations of changes in solubility were made by adding the major chaperones of E. coli, Trigger Factor (TF), DnaK\/DnaJ\/GrpE (KJE) and GroEL\/ES (GroE), individually.", "features": "Since PURE system is a reconstituted chaperone-free translation system, it is possible to evaluate the solubilities of translated proteins and the chaperone effects accurately. The acquired data will form the basis of protein folding studies and be useful for planning researches and industries using protein expression and improving their efficiencies.", "fundings": [ { "funding_name": "Grant-in-Aid for Scientific Research on Priority Areas:\r\n- Regulation of Nano-systems in Cells 17049009, 19037007\r\n- Protein Community 19058002", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Grant-in-Aid for Research Activity Start-up:\r\n- 22870010", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Grant-in-Aid for Scientific Research(A):\r\n- 18201040", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Targeted Proteins Research Program by the Mext,\r\nTechnology Development Themes:\r\n- Protein Production PPC1\r\n- Information Platform IPC1", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Global analysis of chaperone effects using a reconstituted cell-free translation system.", "reference_authors": "Niwa T, Kanamori T, Ueda T, Taguchi H.", "journal": "Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):8937-42.", "reference_pubmed_id": 22615364, "reference_jglobal_id": "201202263784155208" }, { "reference_title": "Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins.", "reference_authors": "Niwa T, Ying BW, Saito K, Jin W, Takada S, Ueda T, Taguchi H.", "journal": "Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4201-6.", "reference_pubmed_id": 19251648, "reference_jglobal_id": "200902244689813257" } ], "maintenance_site": "The Targeted Proteins Research Program promoted by the MEXT", "original_sites": [ "http:\/\/www.tanpaku.org\/tp-esol\/index.php?lang=en" ], "operation_start_date": "2009-06-18", "last_updated_date": "2012-05-02", "upper_level_site": "http:\/\/www.tanpaku.org\/e_index.php", "whole_data_download": "http:\/\/www.tanpaku.org\/tp-esol\/download.php?lang=en", "referenced_site": "GenoBase", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/fantom5\/desc.html", "name": "FANTOM5", "alias": "Functional Annotation of the Mammalian Genome", "dbcat_id": [ "nbdc01389" ], "doi": "10.18908\/lsdba.nbdc01389-000.V003", "creators": [ { "creator_name": "Yoshihide Hayashizaki", "creator_affiliation": "RIKEN Preventive Medicine and Diagnosis Innovation Program \/ Omics Science Center", "creator_jglobal_id": "200901051272882144", "creator_researchmap_id": "read0117945", "creator_orcid": "", "creator_jglobal_jgpn": "200901100413883043", "creator_is_representative": false }, { "creator_name": "Hideya Kawaji", "creator_affiliation": "RIKEN Preventive Medicine and Diagnosis Innovation Program \/ RIKEN Advanced Center for Computing and Communication \/ Center for Life Science Technologies \/ Omics Science Center \/ Center for Integrative Medical Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "201550000279179415", "creator_is_representative": false }, { "creator_name": "Takeya Kasukawa", "creator_affiliation": "RIKEN Center for Life Science Technologies \/ Center for Integrative Medical Sciences", "creator_jglobal_id": "201301049355449068", "creator_researchmap_id": "kasukawa", "creator_orcid": "", "creator_jglobal_jgpn": "200901100594999048", "creator_is_representative": false } ], "categories": [], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Canis lupus familiaris", "taxonomy_id": 9615 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 }, { "organism_name": "Macaca mulatta", "taxonomy_id": 9544 }, { "organism_name": "Gallus gallus", "taxonomy_id": 9031 } ], "organism_free_style": "", "description": "FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM has since developed and expanded over time to encompass the fields of transcriptome analysis. The object of the project is moving steadily up the layers in the system of life, progressing thus from an understanding of the 'elements' - the transcripts - to an understanding of the 'system' - the transcriptional regulatory network, in other words the 'system' of an individual life form. In FANTOM5, we have systematically investigated exactly what are the sets of genes used in virtually all cell types across the human body, and the genomic regions which determine where the genes are read from. We aim to use this information to build transcriptional regulatory models for every primary cell type that makes up a human. The resource provides raw and processed data obtained in the FANTOM5 project.", "features": "The FANTOM5 resources provides a comprehensive map of gene activity across the human body, and provides a holistic view of the complex networks that regulate gene expression across the wide variety of cell types that make up a human being. The resource can be a foundamental tool to define normal cells in human bodies. These findings will help in the identification of genes involved in disease and the development of personalized and regenerative medicine.", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "A promoter-level mammalian expression atlas.", "reference_authors": "FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Lassmann T, Itoh M, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.", "journal": "Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038\/nature13182.", "reference_pubmed_id": 24670764, "reference_jglobal_id": "201402275043578678" }, { "reference_title": "An atlas of active enhancers across human cell types and tissues.", "reference_authors": "Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.", "journal": "Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038\/nature12787.", "reference_pubmed_id": 24670763, "reference_jglobal_id": "201402230098400688" }, { "reference_title": "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.", "reference_authors": "Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.", "journal": "Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126\/science.1259418. Epub 2015 Feb 12.", "reference_pubmed_id": 25678556, "reference_jglobal_id": "201502215990188624" }, { "reference_title": "An atlas of human long non-coding RNAs with accurate 5' ends", "reference_authors": "Chung-Chau Hon, Jordan A. Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J. L. Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M. Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A. Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A. Medvedeva, Alison C. Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A. Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O. Daub, Michiel J. L. de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci & Alistair R. R. 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You can use it in Web (https:\/\/GGGenome.dbcls.jp\/) and as a distributed Docker container. If you use the Docker container, you have to set this dataset in it. Contact the above \"Contact address\" about the distribution of GGGenome container.\r\nAbout the reference sequence data (fasta format) in this dataset, you can use it for another purpose.", "features": "GGGenome exhaustively searches short sequences allowing mismatches and gaps.", "fundings": [ { "funding_name": "MEXT Integrated Database Project", "funding_jglobal_id": "", "funding_lsdb_project_id": 0 }, { "funding_name": "Life Science Database Integration Project", "funding_jglobal_id": "201304069785935332", "funding_lsdb_project_id": 0 }, { "funding_name": "Development of fundamental technologies related to integration of databases", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 0 } ], "funding_free_style": "", "references": [], "maintenance_site": "Database Center for Life Science", "original_sites": [ "https:\/\/GGGenome.dbcls.jp\/" ], "operation_start_date": "2012-07-04", "last_updated_date": "2019-07-31", "upper_level_site": "https:\/\/dbcls.rois.ac.jp\/", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": true, "web_services": true, "webservice_url": "https:\/\/GGGenome.dbcls.jp\/", "user_registration": false }, { "path": "en\/jam-coral-img\/desc.html", "name": "Image collection in the Coral Reef Network WEB System", "alias": "", "dbcat_id": [], "doi": "10.18908\/lsdba.nbdc02655-000", "creators": [ { "creator_name": "Akira Sonoda", "creator_affiliation": "Japan Agency for Marine-Earth Science and Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takashi Hosono", "creator_affiliation": "Japan Agency for Marine-Earth Science and Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "The Global Oceanographic Data Center (GODAC) collected pictures of marine organisms around the coral reefs in the Ryukyu Islands from citizen divers during 2002 to 2013. GODAC also collected videos through GODAC’s research activities using a small remotely-operated vehicle “Niraikanai 150”. These image collection of the pictures and videos had been published on the website of Coral Reef Network WEB System (http:\/\/www.godac.jp\/coral\/). The image collection can become a valuable snapshot to know a past fauna or flora in the Ryukyu Island. The metadata of images provided to the system is used to extract scientific names and locations (latitude and longitude), which are then organized as biological occurrence records and published in BISMaL, a database for marine biodiversity information (http:\/\/www.godac.jamstec.go.jp\/bismal\/).", "features": "・Understanding the geographical distribution of marine organisms\r\n・evaluation or predication for marine biodiversiy", "fundings": [], "funding_free_style": "", "references": [], "maintenance_site": "", "original_sites": [], "operation_start_date": "", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "https:\/\/www.godac.jamstec.go.jp\/bismal\/e\/dataset\/jamstec_godac_coralreef_web", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/asteraceae-chr-index\/desc.html", "name": "Index to Chromosome numbers in Asteraceae", "alias": "", "dbcat_id": [ "nbdc02601" ], "doi": "10.18908\/lsdba.nbdc02601-000", "creators": [ { "creator_name": "Watanabe, Kuniaki", "creator_affiliation": "Kobe University (Professor Emeritus)", "creator_jglobal_id": "200901011265522610", "creator_researchmap_id": "read0014875", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Other plants" ], "categories_free_style": [], "organisms": [ { "organism_name": "Alangiaceae", "taxonomy_id": 42219 }, { "organism_name": "Alseuosmiaceae", "taxonomy_id": 49929 }, { "organism_name": "Argophyllaceae", "taxonomy_id": 57707 }, { "organism_name": "Asteraceae", "taxonomy_id": 4210 }, { "organism_name": "Calyceraceae", "taxonomy_id": 41860 }, { "organism_name": "Campanulaceae", "taxonomy_id": 4381 }, { "organism_name": "Carpodetaceae", "taxonomy_id": 85554 }, { "organism_name": "Goodeniaceae", "taxonomy_id": 16472 }, { "organism_name": "Menyanthaceae", "taxonomy_id": 24579 }, { "organism_name": "Pentaphragmataceae", "taxonomy_id": 41864 }, { "organism_name": "Phellinaceae", "taxonomy_id": 57708 }, { "organism_name": "Rousseaceae", "taxonomy_id": 85554 }, { "organism_name": "Stylidiaceae", "taxonomy_id": 41865 } ], "organism_free_style": "", "description": "The title of Asteraceae “Index to Chromosome numbers in Asteraceae” has been used for the representative of families in Asterales due to the largest and most familiar for many researchers. 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This Database includes taxon name, chromosome number (n and 2n), DNA contents, genbank accession numbers (for the nuclear or chloroplast DNA sequences：You can know that taxa used for molecular phylogenetic analyses), habit (life form) and size of plant, reproductive system, collection locality (Nation), Author (s) and the title of paper and published journal names.\r\n　　The classification of the Asteraceae (= Compositae) follows on Susanna, A. et al (2020) is followed in this database.　Sixteen subfamilies (Barnadesioideae, Famatinanthioideae, Stifftioideae, Mutisioideae, Gochnatioideae, Wunderlichioideae, Hacastocleideideae, Perytyoideae, Tarchonanthoideae, Dicomoideae, Carduoideae, Gymnarrhenoideae, Vernonioideae, Cichorioideae, Corymboideae, Asteroideae.) + 49 tribes + 116 subtribes are included.", "features": "", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "An Overview to the Index to Chromosome Numbers in Asteraceae Database: Revisiting Base Chromosome Numbers, Polyploidy, Descending Dysploidy, and Hybridization", "reference_authors": "Semple, J. C. ＆Watanabe, K.", "journal": "Methods in Molecular Biology (Springer Humana Press) 2023, Vol. 2703, pp.161-171", "reference_pubmed_id": 37646944, "reference_jglobal_id": "" }, { "reference_title": "A review of chromosome numbers in Asteraceae with hypotheses on chromosomal base number evolution.\r\nISBN:978-3-9501754-3-1", "reference_authors": "Semple, J. C. ＆Watanabe, K.", "journal": "Systematics, evolution and biogeography of Compoditae (Funk, V. A et al. (ed.)pp.61-72. (2009)", "reference_pubmed_id": null, "reference_jglobal_id": "" } ], "maintenance_site": "", "original_sites": [], "operation_start_date": "", "last_updated_date": "2024-06-05", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/inoh\/desc.html", "name": "INOH", "alias": "Integrating Network Objects with Hierarchies", "dbcat_id": [ "nbdc00107" ], "doi": "10.18908\/lsdba.nbdc00107-000.V003", "creators": [ { "creator_name": "Toshihisa Takagi", "creator_affiliation": "School of Science, The University of Tokyo", "creator_jglobal_id": "201101052485930732", "creator_researchmap_id": "takagi", "creator_orcid": "", "creator_jglobal_jgpn": "200901100503133582", "creator_is_representative": true }, { "creator_name": "Ken-ichiro Fukuda", "creator_affiliation": "Information and Communication Infrastructure Division, National Institute of Advanced Industrial Science and Technology", "creator_jglobal_id": "200901050332753032", "creator_researchmap_id": "read0205812", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Satoko Yamamoto", "creator_affiliation": "Institute for Bioinformatics Research and Development, Japan Science and Technology Agency", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Noriko Sakai", "creator_affiliation": "Institute for Bioinformatics Research and Development, Japan Science and Technology Agency", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hiromi Nakamura", "creator_affiliation": "Information and Mathematical Science and Bioinformatics Co., Ltd.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Metabolic and Signaling Pathways - Metabolic pathways", "Metabolic and Signaling Pathways - Protein-protein interactions", "Metabolic and Signaling Pathways - Signalling pathways" ], "categories_free_style": [], "organisms": [], "organism_free_style": "Model species (Homo sapiens, Mus musculus, Rattus norvegicus) etc.", "description": "INOH database is a highly structured, manually curated database of signal transduction pathways. The database focuses on curating and encoding textual knowledge in scientific articles into a machine-processable form.", "features": "INOH database provides signal transduction pathway data which is well-annotated by the INOH ontology terms.\r\nINOH curators who have a biological background created pathways and annotated every pathway component by a set of uniquely developed ontologies.\r\nThe INOH Client tool, which is a pathway navigation\/editor tool, is freely downloadable.\r\nINOH pathway diagrams are freely available in INOH XML and BioPAX formats.", "fundings": [ { "funding_name": "Institute for Bioinformatics Research and Development, Japan Science and Technology Agency", "funding_jglobal_id": "200904046071000167", "funding_lsdb_project_id": 24 } ], "funding_free_style": "", "references": [ { "reference_title": "INOH: ontology-based highly structured database of signal transduction pathways.", "reference_authors": "Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T.", "journal": "Database (Oxford). 2011 Nov 26;2011:bar052. Print 2011.", "reference_pubmed_id": 22120663, "reference_jglobal_id": "" }, { "reference_title": "INOH pathway database: Curation, Annotation, Integration.", "reference_authors": "Fukuda K.", "journal": "InterOntology08, 1(1), pp.47-50 (2008).", "reference_pubmed_id": null, "reference_jglobal_id": "" }, { "reference_title": "Graphical Syntax and Query for Pathway Database", "reference_authors": "Fukuda, K., Yamamoto, S., Sakai, N., Nakanishi, Y., Nakamura, H., Takagi, T.", "journal": "The 10th World Multi-Conference on Systemics, Cybernetics and Infrmatics, pp7-10 (2006).", "reference_pubmed_id": null, "reference_jglobal_id": "201002224083332342" }, { "reference_title": "Event ontology: a pathway-centric ontology for biological processes.", "reference_authors": "Kushida T, Takagi T, Fukuda K.", "journal": "Pac Symp Biocomput. 2006:152-63.", "reference_pubmed_id": 17094236, "reference_jglobal_id": "" }, { "reference_title": "Research on biological pathways peculiar to woody perennial Plants using a pathway database : P-INOH.", "reference_authors": "Kushida, T., Yamamoto, S., Yamagata, Y., Asanuma, T., Hattori, E., Takagi, T. and Fukuda, K.", "journal": "Proceedings of International Workshop on Knowledge Discovery and Data Management in Biomedical Science. 2005.5, pp.56-67", "reference_pubmed_id": null, "reference_jglobal_id": "" }, { "reference_title": "Higher Order Knowledge Proceeding : Pathway Database and Ontologies.", "reference_authors": "Fukuda, K.", "journal": "Genomics & Informatics, vol.3, No.2, ISSN 1598-866X, 2005.6, pp.47-51", "reference_pubmed_id": null, "reference_jglobal_id": "" }, { "reference_title": "The Molecule Role Ontology: An Ontology for Annotation of Signal Transduction Pathway Molecules in the Scientific Literature.", "reference_authors": "Yamamoto S, Asanuma T, Takagi T, Fukuda K.", "journal": "Comp Funct Genomics. 2004;5(6-7):528-36.", "reference_pubmed_id": 18629146, "reference_jglobal_id": "201002290449983344" }, { "reference_title": "A Pathway Editor for Literature-based Knowledge Curation.", "reference_authors": "Ken-ichiro Fukuda, Toshihisa Takagi.", "journal": "APBC 2004, pp.339-344.", "reference_pubmed_id": null, "reference_jglobal_id": "" }, { "reference_title": "Pathway Database: Higher Order Knowledge in Biology.", "reference_authors": "Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi.", "journal": "nformation Processing Society of Japan (IPSJ), Transactions on Databases, vol.45 No.SIG7(TOD 22) June 2004, pp.77-84", "reference_pubmed_id": null, "reference_jglobal_id": "200902201795333018" }, { "reference_title": "FREX: a query interface for biological processes with hierarchical and recursive structures.", "reference_authors": "Fukuda K, Yamagata Y, Takagi T.", "journal": "In Silico Biol. 2004;4(1):63-79. Epub 2004 Feb 22.", "reference_pubmed_id": 15089754, "reference_jglobal_id": "" }, { "reference_title": "Knowledge representation of signal transduction pathways.", "reference_authors": "Fukuda K, Takagi T.", "journal": "Bioinformatics. 2001 Sep;17(9):829-37.", "reference_pubmed_id": 11590099, "reference_jglobal_id": "200902170364409120" } ], "maintenance_site": "The Institute of Medical Science, The University of Tokyo\r\n*The original website was terminated.", "original_sites": [ "http:\/\/inoh.hgc.jp\/" ], "operation_start_date": "2006-02-01", "last_updated_date": "2011-03-29", "upper_level_site": "", "whole_data_download": "http:\/\/inoh.hgc.jp\/download.html", "referenced_site": "", "list_search": true, "query_search": true, "web_services": true, "webservice_url": "http:\/\/inoh.hgc.jp\/inoh_api_manual.html", "user_registration": false }, { "path": "en\/jedisystem-oceansdb\/desc.html", "name": "JEDI System\/OCEANS DB", "alias": "Joint Environmental Data Integration System\/Oshima Coastal Environmental data Acquisition Network System database", "dbcat_id": [], "doi": "10.18908\/lsdba.nbdc02629-000.V001", "creators": [ { "creator_name": "Hidekatsu Yamazaki", "creator_affiliation": "Tokyo University of Marine Scinece and Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [], "categories_free_style": [ "Others (Marine plankton data)", "Others (Marine environmental monitoring data)" ], "organisms": [], "organism_free_style": "", "description": "The physical, chemical, biological and engineering data observed by OCEANS (Oshima Coastal Environmental data Acquisition Network Sysmtem) of JEDI (Joint Environmental Data Integration) System at Habu port of Izu Oshima, Tokyo, Japan, from August 10, 2014 to August 10, 2018. See www2.kaiyodai.ac.jp\/~hide\/JEDI\/ for more information.", "features": "Dataset for biodiversity study and prediction model development, Plankton image dataset for classification", "fundings": [], "funding_free_style": "Novel technologies to evaluate multi-scale variations of pelagic marine communities and biodiversity under the influence of the Kuroshio and internal waves in coastal habitats (CREST\/JST, 2012-2018)", "references": [ { "reference_title": "A cable observatory system for integrated long term, high-frequency biological, chemical, physical measurement for understanding planktonic ecosystem", "reference_authors": "Yamazaki, H., S. M. Gallager, M. Tanaka and K. Yamaguchi.", "journal": "IEEE Techno-Ocean’16 429-434. doi:10.1109\/Techno-Ocean.2016.7890692", "reference_pubmed_id": 0, "reference_jglobal_id": "201702274013224002" } ], "maintenance_site": "", "original_sites": [], "operation_start_date": "", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/jpostdb\/desc.html", "name": "jPOST database", "alias": "", "dbcat_id": [ "nbdc01594" ], "doi": "10.18908\/lsdba.nbdc01594-02-000", "creators": [ { "creator_name": "Yasushi Ishihama", "creator_affiliation": "Graduate School of Pharmaceutical Sciences, Kyoto University", "creator_jglobal_id": "200901055328608810", "creator_researchmap_id": "yasishihama", "creator_orcid": "0000-0001-7714-203X", "creator_jglobal_jgpn": "200901100350399979", "creator_is_representative": true }, { "creator_name": "Susumu Goto", "creator_affiliation": "Database Center for Life Science, Research Organization of Information and Systems", "creator_jglobal_id": "200901003217633483", "creator_researchmap_id": "gotosusumu", "creator_orcid": "0000-0003-2989-8486", "creator_jglobal_jgpn": "200901100337621077", "creator_is_representative": false }, { "creator_name": "Norie Araki", "creator_affiliation": "Graduate School of Medical Scienses, Kumamoto University", "creator_jglobal_id": "200901000315656140", "creator_researchmap_id": "noriearaki", "creator_orcid": "", "creator_jglobal_jgpn": "200901100545851051", "creator_is_representative": false }, { "creator_name": "Masaki Matsumoto", "creator_affiliation": "Niigata University Graduate School of Medical and Dental Sciences", "creator_jglobal_id": "200901077148297194", "creator_researchmap_id": "read0067478", "creator_orcid": "", "creator_jglobal_jgpn": "201550000300102150", "creator_is_representative": false }, { "creator_name": "Shujiro Okuda", "creator_affiliation": "Niigata University Graduate School of Medical and Dental Sciences", "creator_jglobal_id": "200901054853171620", "creator_researchmap_id": "read0145560", "creator_orcid": "0000-0002-7704-8104", "creator_jglobal_jgpn": "201550000060651313", "creator_is_representative": false }, { "creator_name": "Shin Kawano", "creator_affiliation": "Faculty of Contemporary Society, Toyama University of International Studies", "creator_jglobal_id": "200901037038220690", "creator_researchmap_id": "read0065295", "creator_orcid": "0000-0002-7969-2972", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Proteomics Resources" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "jPOSTdatabase (Japan ProteOme STandard DataBase) is a database containing re-analysis results with unified criteria for proteome data from jPOSTrepository. It provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms.", "features": "", "fundings": [], "funding_free_style": "Life Science Database Integration Project \"Development of an Integrated Database for Proteomes\"(FY2015-FY2017)", "references": [ { "reference_title": "The jPOST environment: an integrated proteomics data repository and database", "reference_authors": "Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Yoshinori Yamanouchi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama", "journal": "Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1218–D1224. doi: 10.1093\/nar\/gky899", "reference_pubmed_id": null, "reference_jglobal_id": "" } ], "maintenance_site": "jPOST team", "original_sites": [ "https:\/\/globe.jpostdb.org\/" ], "operation_start_date": "2018-03-26", "last_updated_date": "", "upper_level_site": "https:\/\/jpost.org\/", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/jpost\/desc.html", "name": "jPOST repository", "alias": "", "dbcat_id": [ "nbdc01594" ], "doi": "10.18908\/lsdba.nbdc01594-000.V002", "creators": [ { "creator_name": "Yasushi Ishihama", "creator_affiliation": "Graduate School of Pharmaceutical Sciences, Kyoto University", "creator_jglobal_id": "200901055328608810", "creator_researchmap_id": "read0121778", "creator_orcid": "0000-0001-7714-203X", "creator_jglobal_jgpn": "200901100350399979", "creator_is_representative": true }, { "creator_name": "Susumu Goto", "creator_affiliation": "Database Center for Life Science, Research Organization of Information and Systems", "creator_jglobal_id": "200901003217633483", "creator_researchmap_id": "read0183910", "creator_orcid": "0000-0003-2989-8486", "creator_jglobal_jgpn": "200901100337621077", "creator_is_representative": false }, { "creator_name": "Norie Araki", "creator_affiliation": "Graduate School of Medical Scienses, Kumamoto University", "creator_jglobal_id": "200901000315656140", "creator_researchmap_id": "read0043428", "creator_orcid": "", "creator_jglobal_jgpn": "200901100545851051", "creator_is_representative": false }, { "creator_name": "Masaki Matsumoto", "creator_affiliation": "Niigata University Graduate School of Medical and Dental Sciences", "creator_jglobal_id": "200901077148297194", "creator_researchmap_id": "read0067478", "creator_orcid": "", "creator_jglobal_jgpn": "201550000300102150", "creator_is_representative": false }, { "creator_name": "Shujiro Okuda", "creator_affiliation": "Niigata University Graduate School of Medical and Dental Sciences", "creator_jglobal_id": "200901054853171620", "creator_researchmap_id": "read0145560", "creator_orcid": "0000-0002-7704-8104", "creator_jglobal_jgpn": "201550000060651313", "creator_is_representative": false }, { "creator_name": "Shin Kawano", "creator_affiliation": "Faculty of Contemporary Society, Toyama University of International Studies", "creator_jglobal_id": "200901037038220690", "creator_researchmap_id": "read0065295", "creator_orcid": "0000-0002-7969-2972", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Proteomics Resources" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "jPOST(Japan ProteOme STandard Repository\/Database) is the repository where users reposit mass spectrometry (MS) raw data, peak lists and analyzed data. jPOST joins the ProtemoeXchange (PX) Consortium, so it can issue PX ID users need in submitting their articles.", "features": "", "fundings": [ { "funding_name": "Life Science Database Integration Project \"Development of an Integrated Database for Proteomes\"(FY2015-FY2017)", "funding_jglobal_id": "201304096002265299", "funding_lsdb_project_id": null }, { "funding_name": "Life Science Database Integration Project \"Development of functional and interactive database for proteomics\"(FY2018-FY2023)", "funding_jglobal_id": "201304096002265299", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "jPOSTrepo: an international standard data repository for proteomes", "reference_authors": "Shujiro Okuda, Yu Watanabe, Yuki Moriya, Shin Kawano, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Akiyasu C. 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It allows users to search cDNAs by various methods, e.g. accession number, clone name, BLAST search score, GO (Gene Ontology) term and keywords. Clustering information and annotation of the EST can be referenced from the search results. The characteristic information of the cDNA libraries those are species of silkworm, organ \/ tissue, and developmental stage, etc., is described in \"cDNA libraries\".", "fundings": [ { "funding_name": "Grants-in-Aid for Scientific Research <KAKENHI> (No.506015, 1999; No.128102, 2000)", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Management Expenses Grants", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "Ministry of Agriculture, Forestry and Fisheries of Japan (MAFF) commissioned research project \"Integrated research project for plant, insect and animal using genome technology (basic insect genome research for creating and enhancing market demand)\"", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori", "reference_authors": "Suetsugu Y, Futahashi R, Kanamori H, Kadono-Okuda K, Sasanuma S, Narukawa J,Ajimura M, Jouraku A, Namiki N, Shimomura M, Sezutsu H, Osanai-Futahashi M,　Suzuki MG, Daimon T, Shinoda T, Taniai K, Asaoka K, Niwa R, Kawaoka S, Katsuma S,Tamura T, Noda H, Kasahara M, Sugano S, Suzuki Y, Fujiwara H, Kataoka H, Arunkumar KP, Tomar A, Nagaraju J, Goldsmith MR, Feng Q, Xia Q, Yamamoto K, Shimada T, Mita K.", "journal": "G3 (Bethesda) \/ 2013, Sep \/ vol.9", "reference_pubmed_id": 23821615, "reference_jglobal_id": "" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/sgp.dna.affrc.go.jp\/EST\/" ], "operation_start_date": "2004-04-12", "last_updated_date": "2011-11-11", "upper_level_site": "http:\/\/sgp.dna.affrc.go.jp\/", "whole_data_download": "", "referenced_site": "KAIKObase (http:\/\/sgp.dna.affrc.go.jp\/KAIKObase\/)\r\nInterPro (http:\/\/www.ebi.ac.uk\/interpro\/)\r\nSPRINT (http:\/\/www.bioinf.man.ac.uk\/dbbrowser\/sprint\/)\r\nPfam (http:\/\/pfam.xfam.org\/)\r\nPIR (http:\/\/pir.georgetown.edu\/pirwww\/index.shtml)\r\nProDom (http:\/\/prodom.prabi.fr\/prodom\/current\/html\/home.php)\r\nSMART (http:\/\/smart.embl-heidelberg.de\/)\r\nSUPERFAMILY (http:\/\/supfam.org\/SUPERFAMILY\/cgi-bin\/scop.cgi)\r\nCATH\/Gene3D (http:\/\/www.cathdb.info\/)\r\nPROSITE (http:\/\/prosite.expasy.org\/)\r\nHAMAP (http:\/\/hamap.expasy.org\/)\r\nPANTHER (http:\/\/www.pantherdb.org\/)\r\nNCBI (http:\/\/www.ncbi.nlm.nih.gov\/)\r\nWormBase (http:\/\/www.wormbase.org\/)\r\nVectorBase (https:\/\/www.vectorbase.org\/)", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/kegg-medicus\/desc.html", "name": "KEGG MEDICUS", "alias": "", "dbcat_id": [ "NBDC01185" ], "doi": "10.18908\/lsdba.nbdc01185-000.V005", "creators": [ { "creator_name": "Minoru Kanehisa", "creator_affiliation": "Institute for Chemical Research, Kyoto University", "creator_jglobal_id": "200901024319681897", "creator_researchmap_id": "read0082013", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Human Genes and Diseases", "Other Molecular Biology Databases - Drugs and drug design" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 } ], "organism_free_style": "", "description": "KEGG MEDICUS is an integrated information resource of diseases, drugs, and health-related substances, aiming to bring the genomic revolution to society.", "features": "Drug labels (package inserts) of all marketed drugs in Japan and the USA are integrated with the KEGG DRUG and KEGG DISEASE databases in KEGG MEDICUS. The resource can assist researchers to translate research results into practical applications and can also help medical professionals and people in society to better understand the scientific basis of diseases and drugs. (This archive version does not contain package inserts.)", "fundings": [ { "funding_name": "Genome-based integrated resource for diseases, drugs, and environmental substances", "funding_jglobal_id": "201304032293847208", "funding_lsdb_project_id": 0 }, { "funding_name": "Integrated database linking genomes to phenotypes, diseases and drugs", "funding_jglobal_id": "", "funding_lsdb_project_id": 0 }, { "funding_name": "Network database integrating genomes, diseases and drugs", "funding_jglobal_id": "", "funding_lsdb_project_id": 0 } ], "funding_free_style": "Life Science Database Integration Project\r\n\"Genome-based integrated resource for diseases, drugs, and environmental substances\"(FY2011-FY2013)\r\n\"Integrated database linking genomes to phenotypes, diseases and drugs\"(FY2014-FY2016)\r\n\"Network database integrating genomes, diseases and drugs\"(FY2017-FY2021)", "references": [ { "reference_title": "KEGG for representation and analysis of molecular networks involving diseases and drugs.", "reference_authors": "Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., Hirakawa, M.", "journal": "Nucleic Acids Res.\/ 2010\/ 38, D355-D360", "reference_pubmed_id": 19880382, "reference_jglobal_id": "" } ], "maintenance_site": "Kanehisa Laboratory, Institute for Chemical Research, Kyoto University", "original_sites": [ "http:\/\/www.kegg.jp\/kegg\/medicus\/" ], "operation_start_date": "2010-10-01", "last_updated_date": "2022-08-17", "upper_level_site": "http:\/\/www.kanehisa.jp\/ja\/", "whole_data_download": "ftp:\/\/ftp.genome.jp\/pub\/kegg\/medicus\/", "referenced_site": "", "list_search": true, "query_search": true, "web_services": true, "webservice_url": "http:\/\/www.kegg.jp\/kegg\/rest\/", "user_registration": false }, { "path": "en\/kome\/desc.html", "name": "KOME", "alias": "Knowledge-based Oryza Molecular biological Encyclopedia", "dbcat_id": [ "nbdc00120" ], "doi": "10.18908\/lsdba.nbdc00120-000", "creators": [ { "creator_name": "Shoshi Kikuchi", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "Information about approximately 38,000 full-length cDNA clones that were completely sequenced in the Rice full-length cDNA project is shown in the database. The full-length cDNA clones were collected from various tissues treated under various stress conditions. The database contains not only information about complete nucleotide sequences and encoded amino acid sequences, but also results of homology searches against public databases, mapping information, information about patterns of alternative splicing, protein domains and transmembrane structures, and information about cellular localizations and gene functions annotated with Gene Ontology.", "features": "The full-length cDNA libraries were constructed from randomly picked 170,000 clones derived from twenty types of stressed tissues of japonica rice. The clones were grouped into 28,000 independent classes according to their 3' terminal single-pass sequences. All of the representative clones were completely sequenced.", "fundings": [ { "funding_name": "The Rice Full-Length cDNA", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "The information about full-length cDNA clones were collected and completely sequenced by the joint collaboration of National Institute of Agrobiological Sciences (NIAS), Foundation of Advancement of International Science (FAIS), and RIKEN institute, under the supervision of BRAIN (Bio-oriented Technology Research Advancement Institution). This work has been undertaken through the project named \"The Rice Full-Length cDNA\".", "references": [ { "reference_title": "Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice", "reference_authors": "Rice Full-Length cDNA Consortium; National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team, Kikuchi S*, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T;\r\nFoundation of Advancement of International Science Genome Sequencing & Analysis Group, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K;\r\nRIKEN, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A.", "journal": "Science 2003 July 18; Vol.301 no.5631: pp.376-379", "reference_pubmed_id": 12869764, "reference_jglobal_id": "200902243136795840" }, { "reference_title": "Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray", "reference_authors": "Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S.", "journal": "PLoS One. 2007 Nov 28; 2(11):e1235.", "reference_pubmed_id": 18043742, "reference_jglobal_id": "201302253450484016" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/cdna01.dna.affrc.go.jp\/cDNA\/" ], "operation_start_date": "2003-07-18", "last_updated_date": "2010-03-31", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/cgi-bin\/sogo.cgi?class=719&lang=en", "whole_data_download": "", "referenced_site": "DDBJ\r\nNCBI-GenBank\r\nTIGR\r\nBGI RIS\r\nRice Microarray Opening Site (RMOS)\r\nRice mutant panel database (Tos17)\r\nA Database of Plant Cis-acting Regulatory DNA Elements (PLACE)\r\nPIR\r\nSWISS-PROT\r\nUniProt\r\nInterPro\r\nBlocks\r\nRice Proteome Database", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/leading-authors\/desc.html", "name": "Leading Author's", "alias": "", "dbcat_id": [ "NBDC01195" ], "doi": "", "creators": [ { "creator_name": "Keisuke Iida", "creator_affiliation": "Database Center for Life Science", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [], "categories_free_style": [ "Literature" ], "organisms": [], "organism_free_style": "", "description": "Open access and online review articles written by Japanese authors who lead several biological research areas.", "features": "", "fundings": [], "funding_free_style": "MEXT Integrated Database Project\r\nLife Science Database Integration Project \"Development of fundamental technologies related to integration of databases\"", "references": [ { "reference_title": "バイオインフォマティクスを使い尽くす秘訣教えます！【第3回】「DBCLSが提供する日本語コンテンツ」", "reference_authors": "飯田啓介、小野浩雅", "journal": "生物工学会誌 第95巻 第1号(2017\/1\/25)", "reference_pubmed_id": 0, "reference_jglobal_id": "" }, { "reference_title": "新しい日本語Webコンテンツ，「新着論文レビュー」と「領域融合レビュー」", "reference_authors": "飯田啓介", "journal": "情報管理, 56, 148-155 (2013)", "reference_pubmed_id": 0, "reference_jglobal_id": "" } ], "maintenance_site": "Database Center for Life Science", "original_sites": [ "http:\/\/leading.lifesciencedb.jp\/" ], "operation_start_date": "2012-09-01", "last_updated_date": "", "upper_level_site": "http:\/\/dbcls.rois.ac.jp\/", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/ligandbox\/desc.html", "name": "LigandBox", "alias": "LIGANDs Data Base Open and eXtensible", "dbcat_id": [ "nbdc00551" ], "doi": "10.18908\/lsdba.nbdc00551-000", "creators": [ { "creator_name": "Yoshifumi Fukunishi", "creator_affiliation": "Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)", "creator_jglobal_id": "200901030514498002", "creator_researchmap_id": "read0079249", "creator_orcid": "0000-0002-7264-250X", "creator_jglobal_jgpn": "200901100485862571", "creator_is_representative": true }, { "creator_name": "Takeshi Kawabata", "creator_affiliation": "Institute for Protein Research, Osaka University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-0032-9688", "creator_jglobal_jgpn": "201201109025563889", "creator_is_representative": false }, { "creator_name": "Yusuke Sugihara", "creator_affiliation": "Fujitsu Kyushu Systems, Ltd", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Kohta Sakai", "creator_affiliation": "Fujitsu Kyushu Systems, Ltd", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100371813481", "creator_is_representative": false }, { "creator_name": "Hiroshi Kusudo", "creator_affiliation": "Hitachi Solutions East Japan, Ltd.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "201550000285290590", "creator_is_representative": false }, { "creator_name": "Yoshiaki Mikami", "creator_affiliation": "Hitachi Solutions East Japan, Ltd.", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100519394947", "creator_is_representative": false }, { "creator_name": "Tadaaki Mashimo", "creator_affiliation": "IMSBIO Co., Ltd", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-8671-9934", "creator_jglobal_jgpn": "200901100540395015", "creator_is_representative": false }, { "creator_name": "Haruki Nakamura", "creator_affiliation": "Institute for Protein Research, Osaka University", "creator_jglobal_id": "200901059646726169", "creator_researchmap_id": "read0191257", "creator_orcid": "0000-0001-6690-5863", "creator_jglobal_jgpn": "200901100313066609", "creator_is_representative": false } ], "categories": [ "Structure Databases - Small molecules" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "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.\r\nLigandBox has been developed by JBIC, as one component of the molecular simulation system myPresto, supported by NEDO.\r\n3D 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.\r\nChemical structures in this database were computationally generated, may not be identical to structures of compounds stored in supplying companies.", "features": "The molecular files are in Sybyl mol2 file format for virtual drug screening, protein-compound docking, and chemo-informatics.The partial atomic charges of each compound is calculated by MOPAC AM1-BCC and the users can adopt these charges in the molecular dynamics simulations.Each compound has physical properties such as solubility and partition coefficient. These information is useful to avoid promiscuous compounds.The compound IDs are the vender’s ID to purchase the compounds and the inventory ratio is high.", "fundings": [], "funding_free_style": "The following projects of Japan Biological Informatics Consortium (JBIC):\r\n- Structural Proteomics Project (https:\/\/togodb.biosciencedbc.jp\/entry\/lsdb_project_en\/11)\r\n- Development of Basic Technology for Protein Structure Analysis Aimed at Acceleration of Drug Discovery Research (https:\/\/togodb.biosciencedbc.jp\/entry\/lsdb_project_en\/10)\r\n- Development of Innovative Drug Discovery Platform Utilizing Information Technology(http:\/\/www.jbic.or.jp\/english\/rd\/004.html)\r\n \r\nSupport by New Energy and Industrial Technology Development Organization (NEDO) and Ministry of Economy, Trade and Industry (METI)The following projects of Technology Research Association for Next generation natural products chemistry\r\n- Development of core technologies for innovative drug development based upon IT(https:\/\/www.amed.go.jp\/en\/program\/list\/06\/01\/005.html)\r\n \r\nSupport by Japan Agency for Medical Research and Development (AMED)", "references": [ { "reference_title": "LigandBox : a database for 3D structures of chemical compounds.", "reference_authors": "Kawabata,T., Sugihara, Y., Fukunishi, Y., Nakamura, H.", "journal": "BIOPHYSICS,9,113-121.", "reference_pubmed_id": 27493549, "reference_jglobal_id": "200901030514498002" } ], "maintenance_site": "Technology Research Association for Next generation natural products chemistry", "original_sites": [ "http:\/\/www.mypresto5.com\/ligandbox\/cgi-bin\/index.cgi?LANG=en" ], "operation_start_date": "", "last_updated_date": "2018-08-13", "upper_level_site": "", "whole_data_download": "", "referenced_site": "PDB,KEGG", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/mecab\/desc.html", "name": "MeCab user dictionary for science technology term", "alias": "", "dbcat_id": [ "NBDC02358" ], "doi": "10.18908\/lsdba.nbdc02358-000.V002", "creators": [ { "creator_name": "Yuka Tateisi", "creator_affiliation": "National Bioscience Database Center", "creator_jglobal_id": "200901004043498359", "creator_researchmap_id": "read0125210", "creator_orcid": "", "creator_jglobal_jgpn": "201550000083251746", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "dictionary" ], "organisms": [], "organism_free_style": "", "description": "We have made a user dictionary of morphological analysis engine MeCab (http:\/\/taku910.github.io\/mecab\/) headwords and synonyms of JST Thesaurus (2015 edition) . The dictionary items are based on IPA dictionary and encoded in UTF-8. Entries with zenkaku alphabets, numerals and symbols converted into corresponding hankaku characters are also included.\r\nPlease note that this dictionary can not be used as a thesaurus because information on relations between words is not included in the dictionary.", "features": "", "fundings": [ { "funding_name": "Life Science Database Integration Project", "funding_jglobal_id": "201304069785935332", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "JST科学技術用語シソーラスに基づくMeCab用専門用語辞書", "reference_authors": "建石由佳, 信定知江, 高木利久", "journal": "言語処理学会第23回年次大会、P7-1 (予稿集 pp485-488）、2017年3月", "reference_pubmed_id": null, "reference_jglobal_id": "201702253099150088" } ], "maintenance_site": "National Bioscience Database Center", "original_sites": [], "operation_start_date": "2018-06-04", "last_updated_date": "2019-05-17", "upper_level_site": "", "whole_data_download": "", "referenced_site": "IPA dictionary, JST Thesaurus (2015 edition)", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/metabolonote\/desc.html", "name": "Metabolonote", "alias": "", "dbcat_id": [ "nbdc01324" ], "doi": "10.18908\/lsdba.nbdc01324-000", "creators": [ { "creator_name": "Nozomu Sakurai", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100570339845", "creator_is_representative": false }, { "creator_name": "Takeshi Ara", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "200901083593941290", "creator_researchmap_id": "read0116102", "creator_orcid": "", "creator_jglobal_jgpn": "200901100349725323", "creator_is_representative": false }, { "creator_name": "Mitsuo Enomoto", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Experimental Metadata (Materials and Methods)" ], "organisms": [], "organism_free_style": "whole organism", "description": "A database specified for managing information on experimental methods (metadata) which is accompanied with the experimental data obtained from metabolomics studies. This system aims to promote the publication and utilization of metabolomics data by simplifying the metadata record process.\r\nNote: Archived data has been downloaded from the original site in 2016\/5\/18.", "features": "Separation of the management of metadata from that of experimental data has the following two advantages: (1) Multiple databases that stores experimental data can share the same metadata, and (2) the submitter can manage the metadata at one site. The Wiki-based recording system helps submitters to prepare metadata with ease. The system allowes submitters to attach additional information such as image files of the sample, movie files of tricky experiments, and hyperlinks to the related web resources. Such a user-centric design of the system contributes to accelarate publication of metabolomics data.", "fundings": [ { "funding_name": "This work is supported by the project of promotion of integration of life science databases by National Bioscience Database Center（NBDC）, Japan Science and Technology Agency （JST）.", "funding_jglobal_id": "201304029921302010", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.", "reference_authors": "Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S and Sakurai N (2015)", "journal": "Front Bioeng Biotechnol 3: 38", "reference_pubmed_id": 25905099, "reference_jglobal_id": "" } ], "maintenance_site": "Kazusa DNA Research Institute\r\n2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan", "original_sites": [ "http:\/\/metabolonote.kazusa.or.jp\/" ], "operation_start_date": "2012-12-28", "last_updated_date": "2016-05-20", "upper_level_site": "http:\/\/www.kazusa.or.jp\/komics\/", "whole_data_download": "", "referenced_site": "KOMICS\r\nMassBase\r\nKomicMarket\r\nNEW KomicMarket Temporary Website\r\nBio-MassBank\r\nMassBank\r\nKNApSAcK Family", "list_search": true, "query_search": true, "web_services": true, "webservice_url": "http:\/\/metabolonote.kazusa.or.jp\/Help:Use_Data_From_External_System", "user_registration": false }, { "path": "en\/microbedb\/desc.html", "name": "MicrobeDB.jp", "alias": "", "dbcat_id": [ "NBDC01181" ], "doi": "10.18908\/lsdba.nbdc01181-000.V002", "creators": [ { "creator_name": "Ken Kurokawa", "creator_affiliation": "Center for Information Biology, National Institute of Genetics", "creator_jglobal_id": "200901090038088057", "creator_researchmap_id": "read0119484", "creator_orcid": "", "creator_jglobal_jgpn": "200901100451208317", "creator_is_representative": true }, { "creator_name": "Yasukazu Nakamura", "creator_affiliation": "Center for Information Biology, National Institute of Genetics", "creator_jglobal_id": "201001025273786718", "creator_researchmap_id": "yaskaz", "creator_orcid": "", "creator_jglobal_jgpn": "200901100313069420", "creator_is_representative": false }, { "creator_name": "Ikuo Uchiyama", "creator_affiliation": "National Institute for Basic Biology", "creator_jglobal_id": "200901081292717901", "creator_researchmap_id": "read0061570", "creator_orcid": "", "creator_jglobal_jgpn": "200901100476958892", "creator_is_representative": false }, { "creator_name": "Hiroshi Mori", "creator_affiliation": "Center for Information Biology, National Institute of Genetics", "creator_jglobal_id": "201601016277811550", "creator_researchmap_id": "himori", "creator_orcid": "", "creator_jglobal_jgpn": "201550000025436922", "creator_is_representative": false }, { "creator_name": "Takatomo Fujisawa", "creator_affiliation": "Center for Information Biology, National Institute of Genetics", "creator_jglobal_id": "201301018781550644", "creator_researchmap_id": "takatomo", "creator_orcid": "", "creator_jglobal_jgpn": "201550000165064448", "creator_is_representative": false }, { "creator_name": "Hirokazu Chiba", "creator_affiliation": "National Institute for Basic Biology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "201550000300011619", "creator_is_representative": false }, { "creator_name": "Nozomi Yamamoto", "creator_affiliation": "School of Life Science, Tokyo Institute of Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Shinya Suzuki", "creator_affiliation": "School of Life Science, Tokyo Institute of Technology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hiroyo Nishide", "creator_affiliation": "National Institute for Basic Biology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Integrated database of microbiological" ], "organisms": [ { "organism_name": "Archaea", "taxonomy_id": 2157 }, { "organism_name": "Bacteria", "taxonomy_id": 2 }, { "organism_name": "Fungi", "taxonomy_id": 4751 } ], "organism_free_style": "", "description": "MicrobeDB.jp is an integrated database of several microbiological datasets (e.g., genes, taxa, and environments) using semantic web technology with a gene\/genome -centric approach.", "features": "MicrobeDB.jp version 2 (doi: 10.18908\/lsdba.nbdc01181-000.V002) is an updated version of MicrobeDB.jp version 1 (doi: 10.18908\/lsdba.nbdc01181-000.V001). Since version 1 contains microbial genome, ortholog, metagenome, and culture collection data that were obtained before 2013, we updated these data with reorganizing RDF data structures. Microbial environmental ontology and other ontologies were also updated. These ontologies were used for annotation of the data. The data format of MicrobeDB.jp version 2 are RDF and OWL. Users can use these data by (i) loading the data to Triplestore, and (ii) searching the data using SPARQL.", "fundings": [], "funding_free_style": "Database Integration Coordination Program, National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST).", "references": [], "maintenance_site": "National Institute of Technology", "original_sites": [ "http:\/\/microbedb.jp\/" ], "operation_start_date": "2012-12-12", "last_updated_date": "2017-02-01", "upper_level_site": "http:\/\/microbedb.jp\/", "whole_data_download": "", "referenced_site": "NCBI RefSeq, INSDC GenBank, INSDC SRA, NBRC, JCM, NCBI BioProject, NCBI BioSample, NCBI Taxonomy, JGI GOLD, UniProt, PubMed", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/mouse-basement-membrane-bodymap\/desc.html", "name": "Mouse Basement Membrane Bodymap", "alias": "", "dbcat_id": [ "nbdc00574" ], "doi": "10.18908\/lsdba.nbdc00574-000", "creators": [ { "creator_name": "Kiyotoshi Sekiguchi", "creator_affiliation": "Institute for Protein Research, Osaka University", "creator_jglobal_id": "200901047247681811", "creator_researchmap_id": "read0054833", "creator_orcid": "", "creator_jglobal_jgpn": "200901100454736667", "creator_is_representative": true }, { "creator_name": "Ko Tsutsui", "creator_affiliation": "RIKEN Center for Developmental Biology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100417896336", "creator_is_representative": false }, { "creator_name": "Ri-ichiroh Manabe", "creator_affiliation": "RIKEN Center for Life Science Technologies", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "201550000272342043", "creator_is_representative": false } ], "categories": [ "Protein sequence databases - Protein localization and targeting" ], "categories_free_style": [ "画像データベース" ], "organisms": [ { "organism_name": "Mus musculus", "taxonomy_id": 10090 } ], "organism_free_style": "", "description": "This is a database of body-wide localizations of basement membrane proteins in developing mouse embryos. The database consists of hundreds of high resolution virtual slides created from gigapixel digital images representing immunohistochemically stained whole mouse sagittal and head frontal sections and hematoxylin\/eosin stained adjacent sections.", "features": "This database provides immunohistochemically stained virtual slides in which visitors can observe and compare expression patterns of 42 different ECM proteins in the interesting developing organs on the same platform with hematoxylin\/eosin stained adjacent slides.", "fundings": [], "funding_free_style": "JST Exploratory Research for Advanced Technology (ERATO) SEKIGUCHI Biomatrix Signaling (2000-2005)", "references": [ { "reference_title": "Transcriptome-based systematic identification of extracellular matrix proteins.", "reference_authors": "Manabe R, Tsutsui K, Yamada T, Kimura M, Nakano I, Shimono C, Sanzen N, Furutani Y, Fukuda T, Oguri Y, Shimamoto K, Kiyozumi D, Sato Y, Sado Y, Senoo H, Yamashina S, Fukuda S, Kawai J, Sugiura N, Kimata K, Hayashizaki Y, Sekiguchi K.", "journal": "Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12849-54. doi: 10.1073\/pnas.0803640105. Epub 2008 Aug 29.", "reference_pubmed_id": 18757743, "reference_jglobal_id": "" } ], "maintenance_site": "Japan Science and Technology Agency", "original_sites": [ "http:\/\/dbarchive.biosciencedbc.jp\/archive\/matrixome\/bm\/home.html" ], "operation_start_date": "2008-08-18", "last_updated_date": "2015-07-21", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rice-tos17-insertion\/desc.html", "name": "Mutant Panel", "alias": "Rice Tos17 Insertion Mutant Database", "dbcat_id": [], "doi": "10.18908\/lsdba.nbdc00229-000.V001", "creators": [ { "creator_name": "Akio Miyao", "creator_affiliation": "NARO (formerly NIAS)", "creator_jglobal_id": "200901044216238759", "creator_researchmap_id": "0000043309", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "The Mutant Panel is a database of rice (Nipponbare) Tos17 insertion mutant lines. These lines were created by activation of the endogenous retrotransposon Tos17. This database enables users to search sequences adjacent to the transposon, as well as strain names from the results of PCR screening using a three-dimensional DNA pool.", "features": "The Tos17 insertion sites and corresponding phenotypes for each line are organized, allowing for the investigation of the relationship between the disrupted gene caused by the insertion and the resulting phenotype.", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome", "reference_authors": "Akio Miyao, Katsuyuki Tanaka, Kazumasa Murata, Hiromichi Sawaki, Shin Takeda, Kiyomi Abe, Yoriko Shinozuka, Katsura Onosato, Hirohiko Hirochika", "journal": "Plant Cell\/2003\/15(8):1771-1780", "reference_pubmed_id": 12897251, "reference_jglobal_id": "" }, { "reference_title": "A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes", "reference_authors": "Akio Miyao, Yukimoto Iwasaki, Hidemi Kitano, Jun-Ichi Itoh, Masahiko Maekawa, Kazumasa Murata, Osamu Yatou, Yasuo Nagato, Hirohiko Hirochika", "journal": "Plant Mol. Biol.\/2007\/63(5):625-635", "reference_pubmed_id": 17180734, "reference_jglobal_id": "" } ], "maintenance_site": "National Agriculture and Food Research Organization (NARO)", "original_sites": [ "https:\/\/tos.nias.affrc.go.jp\/" ], "operation_start_date": "1997-12-05", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": true }, { "path": "en\/nikkaji\/desc.html", "name": "NBDC Nikkaji RDF", "alias": "NBDC Japan Chemical Substance Dictionary (Nikkaji) RDF", "dbcat_id": [ "nbdc01530" ], "doi": "10.18908\/lsdba.nbdc01530-02-000.V011", "creators": [ { "creator_name": "Japan Science and Technology Agency (JST)", "creator_affiliation": "", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Chemical Database" ], "organisms": [], "organism_free_style": "", "description": "NBDC NikkajiRDF is RDF data of Japan Chemical Substance Dictionary (Nikkaji), which is one of the largest chemical substance databases in Japan.", "features": "NikkajiRDF is described by standard ontologies, such as Chemical Information Ontology (CHEMINF) and Semanticscience Integrated Ontology (SIO). The users can perform SPARQL search by uploading the downloaded RDF into their own triplesore.", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "Openness of Nikkaji RDF data and integration of chemical information by Nikkaji acting as a hub. (written in Japanese)", "reference_authors": "Takahiro KIMURA, Tatsuya KUSHIDA", "journal": "Journal of Information Processing and Management Vol. 58 (2015) No. 3 p. 204-212. (http:\/\/doi.org\/10.1241\/johokanri.58.204)", "reference_pubmed_id": null, "reference_jglobal_id": "201502280673286170" } ], "maintenance_site": "Japan Science and Technology Agency (JST)", "original_sites": [ "http:\/\/doi.org\/10.18908\/lsdba.nbdc01530-02-000" ], "operation_start_date": "2005-03-31", "last_updated_date": "2025-04-21", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/nikkaji-inchi-mapping\/desc.html", "name": "Nikkaji-InChI Mapping Table", "alias": "", "dbcat_id": [ "nbdc01530" ], "doi": "10.18908\/lsdba.nbdc01530-01-001.V004", "creators": [ { "creator_name": "Japan Science and Technology Agency (JST)", "creator_affiliation": "", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Chemical Database" ], "organisms": [], "organism_free_style": "", "description": "This is mapping data of Nikkaji Number (chemical substances identifier), InChI, and InChIKey in Nikkaji (http:\/\/doi.org\/10.15079\/NIKKAJI) which is one of the largest chemical substances database in Japan.", "features": "InChI which was developed by IUPAC (International Union of Pure and Applied Chemistry) and NIST (National Institute of Standards and Technology) is a non-proprietary identifier for chemical substances. The InChIKey is a hashed version of the full InChI. Mapping between chemical database IDs may become easy by using InChI (InChIKey).", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "“Nikkaji Web” has been released.", "reference_authors": "Yumiko TOMIKAWA, Mimiko KIMURA, Chikako MAEDA", "journal": "Journal of Information Processing and Management Vol. 48 (2005) No. 4 p. 220-225. (http:\/\/doi.org\/10.1241\/johokanri.48.220)", "reference_pubmed_id": null, "reference_jglobal_id": "200902296169308991" }, { "reference_title": "Openness of Nikkaji RDF data and integration of chemical information by Nikkaji acting as a hub", "reference_authors": "Takahiro KIMURA, Tatsuya KUSHIDA", "journal": "Journal of Information Processing and Management Vol. 58 (2015) No. 3 p. 204-212. (http:\/\/doi.org\/10.1241\/johokanri.58.204)", "reference_pubmed_id": null, "reference_jglobal_id": "201502280673286170" } ], "maintenance_site": "Japan Science and Technology Agency (JST)", "original_sites": [ "http:\/\/doi.org\/10.18908\/lsdba.nbdc01530-01-000" ], "operation_start_date": "2005-03-31", "last_updated_date": "2018-03-28", "upper_level_site": "", "whole_data_download": "", "referenced_site": "Japan Existing Chemical Data Base (JECDB)\r\nSpectral Database for Organic Compounds (SDBS)\r\nPolymer Database (PoLyInfo)\r\nKis-net (Written in Japanese)", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/nucleic-acid-drug\/desc.html", "name": "Oligonucleic Acid Drug Database", "alias": "", "dbcat_id": [ "NBDC02343" ], "doi": "10.18908\/lsdba.nbdc02343-000.V003", "creators": [ { "creator_name": "Kazuhiko FUKUI", "creator_affiliation": "Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)", "creator_jglobal_id": "200901017295507576", "creator_researchmap_id": "read0120683", "creator_orcid": "0000-0002-2482-848", "creator_jglobal_jgpn": "200901100393125406", "creator_is_representative": false }, { "creator_name": "Takayuki Amemiya", "creator_affiliation": "Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)", "creator_jglobal_id": "201301008288078388", "creator_researchmap_id": "7000006267", "creator_orcid": "", "creator_jglobal_jgpn": "201550000116922145", "creator_is_representative": false }, { "creator_name": "Hiroshi Kouno", "creator_affiliation": "Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST) \/ Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Nucleic Acid Drug" ], "organisms": [], "organism_free_style": "", "description": "DB is focused on nucleic acid drugs known as biopharmaceuticals and displayed approval drugs and information on three phases of clinical trial stage.", "features": "Clinical information of nucleic acid drugs is based from pharmaceutical companies and clinical information sites (https:\/\/clinicaltrials.gov\/, https: \/\/www.clinicaltrialsregister.eu\/) . DB provides information on nucleic acid drugs that are being considered for future practical use (such as target diseases and related protein information).", "fundings": [], "funding_free_style": "Collaborative graduate school system", "references": [], "maintenance_site": "Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)", "original_sites": [ "https:\/\/medals.jp\/druginfo.html" ], "operation_start_date": "2018-03-16", "last_updated_date": "2020-01-21", "upper_level_site": "https:\/\/medals.jp\/", "whole_data_download": "", "referenced_site": "DrugBank, UniProt, PDB", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/open-tggates\/desc.html", "name": "Open TG-GATEs", "alias": "", "dbcat_id": [ "nbdc00954" ], "doi": "10.18908\/lsdba.nbdc00954-01-000", "creators": [ { "creator_name": "Toxicogenomics Project \/ Toxicogenomics Informatics Project", "creator_affiliation": "National Institute of Biomedical Innovation, National Institute of Health Sciences, and 15 pharmaceutical companies", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Toxicogenomics Database" ], "organisms": [ { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 }, { "organism_name": "Homo sapiens", "taxonomy_id": 9606 } ], "organism_free_style": "", "description": "Toxicogenomics Project (TGP) is a government-private companies collaborative project started by the National Institute of Biomedical, the National Institute of Health Sciences, and 15 pharmaceutical companies in 2002. After 5 years of the project, 150 chemicals were administered to rats or exposed to rat and human primary cultured hepatocytes, and the gene expression profiles in the liver and kidney of the animal or in the cultured cells were comprehensively analyzed by microarray. As a result, a high-quality large-scale toxicogenomics database with the systems to analyze the gene expression data and predict the safety of candidate chemicals has been developed (TG-GATEs: Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system）.\r\n\r\nToxicogenomics Informatics Project (TGP2) is TGP's succeeding project, started by the National Institute of Biomedical, the National Institute of Health Sciences, and 13 pharmaceutical companies in 2007. After 5 years of the project, more than 30 safety biomarkers were develped by using TG-GATEs. In addition, data acquired to test biomarkers and analyse their mechanisms are included in TG-GATEs.\r\n\r\nOpen TG-GATEs is a toxicogenomics database open to the public for researchers to utilize research results of TGP and TGP2, and releases the data of 170 compounds stored in TG-GATEs. In Open TG-GATEs, it is possible to search toxicogenomics data by compound name or pathological finding. It is also possible to download gene expression data associated with phenotype data such as pathological findings as a CEL file.\r\n\r\nCEL is one of the file formats that expresses gene expression data (raw data) generated from Affymetrix GeneChip®.", "features": "Searching toxicogenomics data by compound name or pathological finding.\r\nDownloading gene expression data associated with phenotype data such as pathological findings as a CEL file.", "fundings": [ { "funding_name": "- Health and Labour Sciences Research Grant (H14-Toxico-001 and H19-Toxico-001)\r\n- Collaborative research funds from participating companies.", "funding_jglobal_id": "200909096803808303", "funding_lsdb_project_id": 7 } ], "funding_free_style": "", "references": [], "maintenance_site": "Toxicogenomics Informatics Project, National Institute of Biomedical Innovation", "original_sites": [ "http:\/\/toxico.nibiohn.go.jp\/" ], "operation_start_date": "2011-02-25", "last_updated_date": "2012-01-18", "upper_level_site": "http:\/\/wwwtgp.nibiohn.go.jp\/", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/open-tggates-pathological-images\/desc.html", "name": "Open TG-GATEs Pathological Image Database", "alias": "", "dbcat_id": [ "nbdc00954" ], "doi": "10.18908\/lsdba.nbdc00954-02-000", "creators": [ { "creator_name": "Toxicogenomics Project／Toxicogenomics Informatics Project", "creator_affiliation": "National Institute of Biomedical Innovation, National Institute of Health Sciences, and 15 pharmaceutical companies", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [], "categories_free_style": [ "Toxicogenomics Database" ], "organisms": [ { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "On the pathological image database, over 53,000 high-resolution whole slide digital pathological images of liver and kidney pathological specimens are open to the public. The specimens were obtained through animal tests using 160 compounds registered on Open TG-GATEs database. Therefore, you can look into the pathological findings registered on Open TG-GATEs database, with the pathological images.\r\nFor further information on Open TG-GATEs database, please visit the LSDB archive website at http:\/\/dbarchive.biosciencedbc.jp\/en\/open-tggates\/desc.html.", "features": "The pathological images can be viewed as zoomable digital slides.", "fundings": [ { "funding_name": "- Health and Labour Sciences Research Grant (H14-Toxico-001 and H19-Toxico-001)\r\n- Collaborative research funds from participating companies.", "funding_jglobal_id": "200909096803808303", "funding_lsdb_project_id": 7 } ], "funding_free_style": "", "references": [], "maintenance_site": "Toxicogenomics Informatics Project, National Institute of Biomedical Innovation", "original_sites": [ "http:\/\/virtualslide.nibiohn.go.jp\/Authenticate2.php" ], "operation_start_date": "2012-03-30", "last_updated_date": "2012-03-30", "upper_level_site": "http:\/\/wwwtgp.nibiohn.go.jp\/", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/pgdbj-ortholog-db\/desc.html", "name": "PGDBj - Ortholog DB", "alias": "Plant Genome Database Japan - Ortholog Database", "dbcat_id": [ "nbdc01194" ], "doi": "10.18908\/lsdba.nbdc01194-02-000.V002", "creators": [ { "creator_name": "Akihiro Nakaya", "creator_affiliation": "Osaka University", "creator_jglobal_id": "201101032925418574", "creator_researchmap_id": "nakaya_akihiro", "creator_orcid": "", "creator_jglobal_jgpn": "201550000299995022", "creator_is_representative": true }, { "creator_name": "Hisako Ichihara", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "201550000157748931", "creator_is_representative": false }, { "creator_name": "Erika Asamizu", "creator_affiliation": "Ryukoku University", "creator_jglobal_id": "200901002859396764", "creator_researchmap_id": "read0141555", "creator_orcid": "", "creator_jglobal_jgpn": "200901100462838746", "creator_is_representative": false }, { "creator_name": "Hideki Hirakawa", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "201501081279250007", "creator_researchmap_id": "kh15", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Yasukazu Nakamura", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "201001025273786718", "creator_researchmap_id": "yaskaz", "creator_orcid": "", "creator_jglobal_jgpn": "200901100313069420", "creator_is_representative": false }, { "creator_name": "Satoshi Tabata", "creator_affiliation": "Kazusa DNA Research Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "200901100362040461", "creator_is_representative": false } ], "categories": [ "Protein sequence databases - Protein domain databases; protein classification" ], "categories_free_style": [], "organisms": [ { "organism_name": "Viridiplantae", "taxonomy_id": 33090 }, { "organism_name": "Cyanobacteria", "taxonomy_id": 1117 } ], "organism_free_style": "", "description": "Orthology is a homologous relationship among genes derived from a common ancestor by speciation. Genes in such a relationship are referred to as orthologs or orthologous genes and provide important clues to clarify the process of genome evolution and to predict the divergence of gene function based on syntenic relationships among species. PGDBj Ortholog DB is a database that provides orthologous relationships of genes that are computationally determined according to similarities between amino acid sequences, and currently consists of 40 species of Viridiplantae (green plants) and 213 species of Cyanobacteria (blue-green algae).", "features": "PGDBj Ortholog DB is hierarchically organized to reflect evolutionary relationships among species and taxa. By connecting entries of multiple plant genome databases to this database, PGDBj Ortholog DB can work as a hub database and provide a way to gather and organize the relevant data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users can obtain the list of the links to the relevant entries of the plant genome databases in relation to the functions and characteristics of genes across various species and taxa including both model plants and crop plants. Following the links obtained, users can retrieve the actual entries from the databases.", "fundings": [ { "funding_name": "This work has been supported by National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST): Database Integration Coordination Program (FY2011-FY2013).\r\nhttps:\/\/biosciencedbc.jp\/en\/tec-dev-prog\/rdprog-over\/rdprog-over-integ#005", "funding_jglobal_id": "201304098487795099", "funding_lsdb_project_id": null }, { "funding_name": "This work has been supported by National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST): Plant Genome DataBase Japan (PGDBj) for integration of plant genome-related resources and information(FY2014-FY2016).\r\nhttps:\/\/biosciencedbc.jp\/en\/tec-dev-prog\/research-issue-in-progress\/rdprog-over-integ-h24-26#005", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases", "reference_authors": "Erika Asamizu, Hisako Ichihara, Akihiro Nakaya, Yasukazu Nakamura, Hideki Hirakawa, Takahiro Ishii, Takuro Tamura, Kaoru Fukami-Kobayashi, Yukari Nakajima and Satoshi Tabata", "journal": "Plant Cell Physiol (2014) 55 (1): e8.", "reference_pubmed_id": 24363285, "reference_jglobal_id": "" }, { "reference_title": "Plant Genome DataBase Japan (PGDBj).", "reference_authors": "Akihiro Nakaya, Hisako Ichihara, Erika Asamizu, Shirasawa Sachiko, Yasukazu Nakamura, Satoshi Tabata and Hideki Hirakawa", "journal": "Methods Mol Biol (2017) 1533: 45-77.", "reference_pubmed_id": 27987164, "reference_jglobal_id": "" } ], "maintenance_site": "Kazusa DNA Research Institute", "original_sites": [ "http:\/\/pgdbj.jp\/pages\/index.html?dir=&page=od&ln=en" ], "operation_start_date": "2012", "last_updated_date": "2016", "upper_level_site": "http:\/\/pgdbj.jp\/index.html?ln=en", "whole_data_download": "http:\/\/pgdbj.jp\/od2\/download_33090.html", "referenced_site": "NCBI RefSeq, NCBI Taxonomy\r\nEucalyptus camaldulensis Genome Database\r\nJatropha Genome Database\r\nLotus japonicus Genome Sequencing Project\r\nTomato SBM Database\r\nTrifolium pratense EST Index\r\nChlamydomonas reinhardtii EST Index\r\nLotus japonicus EST Index\r\nArabidopsis thaliana EST Index\r\nPorphyra yezoensis EST Index\r\nMiBASE Micro-Tom Database\r\nThe Rice Annotation Project Database (RAP-DB)\r\nRice TOGO Browser\r\nThe Rice Expression Profile Database (RiceXPro)\r\nSALAD Database\r\nThe Arabidopsis Information Resource (TAIR)\r\nRIKEN Arabidopsis Genome Encyclopedia (RARGE)\r\nRIKEN Populus Database (RPOPDB)\r\nTriticeae Full-Length CDS Database (TriFLDB)\r\nKEGG\/GENES\r\nPHYSCObase", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/plabrain-db\/desc.html", "name": "Plabrain DB", "alias": "Planarian Brain Database", "dbcat_id": [ "nbdc01108" ], "doi": "10.18908\/lsdba.nbdc01108-000", "creators": [ { "creator_name": "Kiyokazu Agata", "creator_affiliation": "Kyoto University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "Kaneyasu Nishimura", "creator_affiliation": "Kyoto University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Osamu Nishimura", "creator_affiliation": "Kyoto University", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Tetsutaro Hayashi", "creator_affiliation": "RIKEN Center for Developmental Biology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Hiroshi Tarui", "creator_affiliation": "RIKEN Center for Developmental Biology", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Microarray Data and other Gene Expression Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Dugesia japonica", "taxonomy_id": 6161 } ], "organism_free_style": "", "description": "Plabrain DB is a database for planarian nervous system analysis, including results of the gene expression profiling of single cells, the gene expression analysis by whole-mount in situ hybridization and the analysis by Immunohistochemical staining. This is the first case to release the result of gene expression analysis at the single-cell resolution by semi-quantitative single-cell RT-PCR (FBSC-PCR) method using FACS (Fluorescence Activated Cell Sorting) .", "features": "Plabrain DB is featured by the unique method which combines the semi-quantitative single-cell RT-PCR with FACS to analyze gene expression in single neurons.\r\nAn article \"Planaria nervous system\" in Scholarpedia also provides information about this database.\r\nSome planarian whole-mount in situ hybridization images related to this database are available at a website of JT Biohitory Research Hall (Japanese version only).", "fundings": [], "funding_free_style": "The method of gene expression profiling of single cells was developed by Dr. Kiyokazu Agata at RIKEN Center for Developmental Biology. \r\nNeural-specific gene analysis was supported by a Grant-in-Aid for Creative Scientific Research (Research Project Number: 17GS0318, Project Year: 2005-2009).", "references": [ { "reference_title": "Single-cell gene profiling utilizing FACS and its “index sorting” function for stem cell research", "reference_authors": "Tetsutaro Hayashi, Norito Shibata, Ryo Okumura, Tomomi Kudome, Osamu Nishimura, Hiroshi Tarui and Kiyokazu Agata", "journal": "Dev Growth Differ., 52, 131-144 (2010)", "reference_pubmed_id": 20078655, "reference_jglobal_id": "" }, { "reference_title": "Analysis of motor function modulated by cholinergic neurons in planarian Dugesia japonica", "reference_authors": "Kaneyasu Nishimura, Yoshihisa Kitamura, Takashi Taniguchi and Kiyokazu Agata", "journal": "Neuroscience, 168, 18-30 (2010)", "reference_pubmed_id": 20338223, "reference_jglobal_id": "201102252506930285" }, { "reference_title": "Planarians change their body size by maintaining a constant ratio of different cell types using stem cell system", "reference_authors": "Hiroyuki Takeda, Kaneyasu Nishimura and Kiyokazu Agata", "journal": "Zoolog. Sci., 26, 805-813.", "reference_pubmed_id": 19968467, "reference_jglobal_id": "201002221648417593" }, { "reference_title": "Characterization of tyramine beta-hydroxylase in planarian Dugesia japonica: Cloning and expression", "reference_authors": "Kaneyasu Nishimura, Yoshihisa Kitamura, Takeshi Inoue, Yoshihiko Umesono, Kanji Yoshimoto, Takashi Taniguchi and Kiyokazu Agata", "journal": "Dev Growth Differ., 52, 131-144 (2010)", "reference_pubmed_id": 20078655, "reference_jglobal_id": "201302233642258728" }, { "reference_title": "Identification and distribution of tryptophan hydroxylase (TPH)-positive neurons in the planarian Dugesia japonica", "reference_authors": "Kaneyasu Nishimura, Yoshihisa Kitamura, Takeshi Inoue, Yoshihiko Umesono, Kanji Yoshimoto, Kosei Takeuchi, Takashi Taniguchi and Kiyokazu Agata", "journal": "Neurosci. Res., 59, 101-106 (2007)", "reference_pubmed_id": 17624455, "reference_jglobal_id": "200902251750412020" }, { "reference_title": "Reconstruction of dopaminergic neural network and recovery of behavioral function in planarian regenerates", "reference_authors": "Kaneyasu Nishimura, Yoshihisa Kitamura, Takeshi Inoue, Yoshihiko Umesono, Shozo Sano, Kanji Yoshimoto, Masatoshi Inden, Kazuyuki Takata, Takashi Taniguchi, Shun Shimohama and Kiyokazu Agata", "journal": "Dev. Neurobiol., 67, 1059-1078 (2007)", "reference_pubmed_id": 17565705, "reference_jglobal_id": "201102241288440066" } ], "maintenance_site": "Laboratory for Molecular Developmental Biology Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University", "original_sites": [], "operation_start_date": "", "last_updated_date": "", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": false, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/place\/desc.html", "name": "PLACE", "alias": "A Database of Plant Cis-acting Regulatory DNA Elements", "dbcat_id": [ "nbdc00168" ], "doi": "10.18908\/lsdba.nbdc00168-000", "creators": [ { "creator_name": "Kenichi Higo", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Plant databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Tracheophyta", "taxonomy_id": 58023 } ], "organism_free_style": "", "description": "PLACE is a database of motifs found in plant cis-acting regulatory DNA elements based on previously published reports on vascular plants including the variations that have been identified in these motifs in other genes or in other plant species in later publications. The database also contains brief descriptions of individual motifs, literatures with PubMed links, and the corresponding accession numbers in the DDBJ\/EMBL\/GenBank.", "features": "Background and objectives\r\n\r\nA database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements (cis-elements) with tools for homology searches will be helpful in estimating the mode of gene regulation, regions involved in such regulation, and other pertinent regions in the DNA sequence. In order to provide a compilation of all reported cis-elements of higher plants, we constructed the PLACE database.\r\n\r\nFeatures and manner\r\n\r\n1. The cis-elements in this database including motif sequences, descriptions of major features, and references have been compiled by extensive survey of original literatures. Review articles on the regulatory regions of some plant genes were also used to obtain information on specific groups of motifs.\r\n2. The documents of individual motifs can be accessed by keyword search using a browser.\r\n3. The query sequence is searched by the Signal Scan program. The search can be initiated by copy and paste of the query sequence and the results are shown in a few seconds. The Signal Scan output is shown in one of three options: a list of motifs in alphabetical order, a sequence map, and a list of motifs beginning at the 5' end of the query sequence.\r\n4. The document contains information on the PubMed ID and the GenBank accession number with corresponding links.\r\n\r\nUsefulness\r\n\r\nExperimental evidence for each motif is described in the ‘Reference Criteria’ (RC) field. Users of this database must be aware that the motifs compiled here were not strictly examined on this premise. Therefore users are advised to refer to the original reports of individual motifs before using any of the results obtained for publication.", "fundings": [ { "funding_name": "Development of Advanced Bio-Technology [Next generation recombinant], 1998 (1996-1998)", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "PLACE: A database on plant cis-acting regulatory DNA elements (A preliminary report)", "reference_authors": "Kenichi Higo*, Yoshihiro Ugawa and Masao Iwamoto", "journal": "5th International Society for Plant Molecular Biology, 1997, Abst. #891", "reference_pubmed_id": null, "reference_jglobal_id": "" }, { "reference_title": "PLACE: a database of plant cis-acting regulatory DNA elements", "reference_authors": "Kenichi Higo*, Yoshihiro Ugawa, Masao Iwamoto and Hiromi Higo", "journal": "Nucleic Acids Research, 1998, Vol.26, No.1 :358-359", "reference_pubmed_id": 9399873, "reference_jglobal_id": "200902180323508143" }, { "reference_title": "Plant cis-acting regulatory DNA elements (PLACE) database: 1999", "reference_authors": "Kenichi Higo*, Yoshihiro Ugawa, Masao Iwamoto and Tomoko Korenaga", "journal": "Nucleic Acids Research, 1999, Vol.27, No.1 :297-300", "reference_pubmed_id": 9847208, "reference_jglobal_id": "200902107129219646" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/www.dna.affrc.go.jp\/PLACE\/" ], "operation_start_date": "1997-03-31", "last_updated_date": "2007-01-08", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/cgi-bin\/sogo.cgi?class=719&lang=en", "whole_data_download": "", "referenced_site": "PubMed\r\nGenBank", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/possum\/desc.html", "name": "PoSSuM", "alias": "Pocket Similarity Search using Multiple-Sketches", "dbcat_id": [ "nbdc01144" ], "doi": "10.18908\/lsdba.nbdc01144-000", "creators": [ { "creator_name": "Kentaro Tomii", "creator_affiliation": "Tokyo Waterfront, the National Institute of Advanced Industrial Science and Technology (AIST)", "creator_jglobal_id": "200901021923630070", "creator_researchmap_id": "read0205789", "creator_orcid": "", "creator_jglobal_jgpn": "201550000300179005", "creator_is_representative": true } ], "categories": [ "Structure Databases - Small molecules" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "PoSSuM is a database for detecting similar small-molecule binding sites on proteins. We have provided a service named PoSSuM drug search, in which we selected 194 approved drug compounds retrieved from ChEMBL, and detected their known binding pockets and pockets that are similar to them.", "features": "", "fundings": [], "funding_free_style": "Japan Society for the Promotion of Science (JSPS) [KAKENHI 23500374]; Grants-in-Aid for Scientific Research [25430186 and 25293079]; Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology, Japan; Grants-in-Aid for Scientific Research from the Ministry of Health, Labour and Welfare", "references": [ { "reference_title": "PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.", "reference_authors": "Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K.", "journal": "Nucleic Acids Res. DB issue 2015;43:D392-8.", "reference_pubmed_id": 25404129, "reference_jglobal_id": "" }, { "reference_title": "PoSSuM: a database of similar protein-ligand binding and putative pockets.", "reference_authors": "Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K.", "journal": "Nucleic Acids Res. DB issue 2012;40:D541-8.", "reference_pubmed_id": 22135290, "reference_jglobal_id": "" }, { "reference_title": "PDB-Scale analysis of known and putative ligand binding sites with structural sketches.", "reference_authors": "Ito J, Tabei Y, Shimizu K, Tomii K, Tsuda K.", "journal": "Proteins 2011;80:747-63.", "reference_pubmed_id": 22113700, "reference_jglobal_id": "" }, { "reference_title": "Single Versus Multiple Sorting for All Pairs Similarity Search.", "reference_authors": "Tabei Y, Uno T, Sugiyama M, Tsuda K.", "journal": "The 2nd Asian Conference on Machine Learning (ACML2010) 2010.", "reference_pubmed_id": 0, "reference_jglobal_id": "" } ], "maintenance_site": "Artificial Intelligence Research Center (AIRC), The National Institute of Advanced Industrial Science and Technology (AIST) (https:\/\/www.aist.go.jp\/index_en.html)", "original_sites": [ "http:\/\/possum.cbrc.jp\/PoSSuM\/index.html" ], "operation_start_date": "2011-11-01", "last_updated_date": "2014-10-15", "upper_level_site": "", "whole_data_download": "", "referenced_site": "PDB, UniProt, ChEMBL, EC, CATH, SCOPe, GO", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/pscdb\/desc.html", "name": "PSCDB", "alias": "Protein Structural Change DataBase", "dbcat_id": [ "nbdc01636" ], "doi": "10.18908\/lsdba.nbdc01636-000", "creators": [ { "creator_name": "Amemiya Takayuki", "creator_affiliation": "The Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)", "creator_jglobal_id": "201301008288078388", "creator_researchmap_id": "7000006267", "creator_orcid": "", "creator_jglobal_jgpn": "201550000116922145", "creator_is_representative": false }, { "creator_name": "Motonori Ota", "creator_affiliation": "Nagoya University", "creator_jglobal_id": "200901037264166160", "creator_researchmap_id": "read0102070", "creator_orcid": "", "creator_jglobal_jgpn": "201550000256508462", "creator_is_representative": false }, { "creator_name": "Kidera Akinori", "creator_affiliation": "Yokohama City University", "creator_jglobal_id": "200901093514214138", "creator_researchmap_id": "read0046933", "creator_orcid": "", "creator_jglobal_jgpn": "200901100461423933", "creator_is_representative": false } ], "categories": [ "Structure Databases - Protein structure" ], "categories_free_style": [], "organisms": [], "organism_free_style": "", "description": "The purpose of this database is to represent the relationship between protein structural change and ligand binding. We classified protein structural changes into 7 classes, in terms of the ligand binding sites and the location where the dominant motion occurs.", "features": "", "fundings": [], "funding_free_style": "", "references": [ { "reference_title": "PSCDB: a database for protein structural change upon ligand binding.", "reference_authors": "T. Amemiya, R. Koike, A. Kidera, and M. Ota.", "journal": "2012, Nucleic Acids Res., 40, D554-D558.", "reference_pubmed_id": 22080505, "reference_jglobal_id": "201102245216943042" } ], "maintenance_site": "Graduate School of Information Science Nagoya University", "original_sites": [ "http:\/\/idp1.force.cs.is.nagoya-u.ac.jp\/pscdb\/" ], "operation_start_date": "2011-11-13", "last_updated_date": "2012-03-15", "upper_level_site": "", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/qtaro\/desc.html", "name": "Q-TARO", "alias": "QTL Annotation Rice Online database", "dbcat_id": [ "nbdc01234" ], "doi": "10.18908\/lsdba.nbdc01234-000", "creators": [ { "creator_name": "Junichi Yonemaru", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Nucleotide Sequence Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "This is a database of Rice QTL information extracted from published research papers.\r\nFrom 1214 reports, we selected 5096 QTLs. The positions of these QTLs were estimated from the physical positions of either two flanking markers (the genomic positions of the distal ends of the two markers) or a co-segregated single marker (between the start and end positions on the genome). If the QTLs were isolated by map-based cloning, the position of the BAC\/PAC clone or gene locus was used. By screening for redundancy of traits at the same physical positions, as of March 31 of 2008, we selected 1051 QTLs extracted from 463 reports as representative QTLs. To arrange QTL information, we constructed QTL database (QTL Annotation Rice Online database; Q-TARO, http:\/\/qtaro.abr.affrc.go.jp\/) consists of two web interfaces. One interface is a table containing information on the mapping of each QTL and its genetic parameters. The other interface is a genome viewer for viewing genomic locations of the QTLs. Currently, update of QTL information is not continued.", "features": "Over the past two decades, genetic dissection of complex phenotypes of economic and biological interest has revealed the chromosomal locations of many quantitative trait loci (QTLs) in rice and their contributions to phenotypic variation. Mapping resolution has varied considerably among QTL studies, owing to differences in population size and number of DNA markers used. Additionally, the same QTLs have often been reported with different locus designations. This situation has made it difficult to determine allelic relationships among QTLs and to compare their positions. To facilitate reliable comparisons of rice QTLs, we extracted QTL information from published research papers and constructed a database of 1051 representative QTLs, which we classified into 21 trait categories. Q-TARO clearly displays the co-localization of QTLs and distribution of QTL clusters on the rice genome.", "fundings": [ { "funding_name": "Integrated Research Project for Plant, Insect and Animal using Genome Technology, QT-1006", "funding_jglobal_id": "200902278543564818", "funding_lsdb_project_id": null }, { "funding_name": "Genomics for Agricultural Innovation, GIR-1003", "funding_jglobal_id": "201402275902165283", "funding_lsdb_project_id": null } ], "funding_free_style": "This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated Research Project for Plant, Insect and Animal using Genome Technology, QT-1006, and Genomics for Agricultural Innovation, GIR-1003).", "references": [ { "reference_title": "Q-TARO: QTL Annotation Rice Online Database", "reference_authors": "Jun-ichi Yonemaru, Toshio Yamamoto, Shuichi Fukuoka, Yusaku Uga, Kiyosumi Hori, Masahiro Yano", "journal": "Rice, September 2010, Volume 3, Issue 2-3, pp 194-203", "reference_pubmed_id": null, "reference_jglobal_id": "201302271335420479" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/qtaro.abr.affrc.go.jp\/" ], "operation_start_date": "2009-11-15", "last_updated_date": "2010-06-01", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/cgi-bin\/sogo.cgi?class=719&lang=en", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/redii-inaho\/desc.html", "name": "RED II INAHO", "alias": "Rice Expression Database II INAHO", "dbcat_id": [ "nbdc01557" ], "doi": "10.18908\/lsdba.nbdc01557-000", "creators": [ { "creator_name": "Shoshi Kikuchi", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "200901036690986909", "creator_researchmap_id": "read0006027", "creator_orcid": "", "creator_jglobal_jgpn": "200901100360463187", "creator_is_representative": false } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Microarray, Gene Expression" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "The Rice Expression Database II INAHO (RED II INAHO) is a database that analyzed the gene expression of rice using a 60-mer oligonucleotide microarray to examine transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice.", "features": "You can get the experimental data from the redii_inaho_experiment table. Also, you can find the Accession number for a particular gene from the redii_inaho_probe table. Then, you will then get expression profiles under various experimental conditions against results of Array-BLAST.\r\n \r\nReferences:\r\nYazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A, Shimbo K, Shimatani Z, Kojima K, Suzuki K, Yamamoto M, Honda S, Endo A, Yoshida Y, Sato Y, Takeuchi K, Toyoshima K, Miyamoto C, Wu J, Sasaki T, Sakata K, Yamamoto K, Iba K, Oda T, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S.\r\nGenomics approach to abscisic acid- and gibberellin-responsive genes in rice.\r\nDNA Res. 2003 Dec 31;10(6):249-61.\r\nPMID: 15029956\r\n \r\nYazaki J, Shimatani Z, Hashimoto A, Nagata Y, Fujii F, Kojima K, Suzuki K, Taya T, Tonouchi M, Nelson C, Nakagawa A, Otomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S.\r\nTranscriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.\r\nPhysiol Genomics. 2004 Apr 13;17(2):87-100.\r\nPMID: 14982972", "fundings": [ { "funding_name": "Phase 2 of Rice Genome Research Project (1998-2004)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/red.dna.affrc.go.jp\/INAHO\/" ], "operation_start_date": "2009-04-01", "last_updated_date": "2009-04-01", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/", "whole_data_download": "", "referenced_site": "DDBJ", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/refex\/desc.html", "name": "RefEx", "alias": "Reference Expression Dataset", "dbcat_id": [ "nbdc01099" ], "doi": "", "creators": [ { "creator_name": "Ono, Hiromasa", "creator_affiliation": "Database Center for Life Science", "creator_jglobal_id": "201201055707420599", "creator_researchmap_id": "", "creator_orcid": "0000-0001-8675-963X", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "Bono, Hidemasa", "creator_affiliation": "Database Center for Life Science", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Ikeda, Shuya", "creator_affiliation": "Database Center for Life Science", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-1357-5159", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Microarray Data and other Gene Expression Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "RefEx (Reference Expression dataset; https:\/\/refex.dbcls.jp) is a web tool for browsing reference gene expression, which provides access to curated data from several other public databases, with expression levels in forty tissues measured by four well-established gene-expression quantification technologies. The web interface allows users to browse the expression profiles by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology, and to compare expression profiles by different methods at a glance.\r\n\r\nRefEx provides suitable datasets as a reference for gene expression data from 40 normal human, mouse, and rat tissues and cells. Forty tissues were selected based on the experience gained while constructing the bodymap database. The 40 tissues are classified into 10 groups (i.e., brain, blood, connective, reproductive, muscular, alimentary, liver, lung, urinary, and endo\/exocrine). These groupings are mainly used for the abstraction of the gene expression profiles in the summary view and the inference of gene functions by the gene expression profiles. The following four different measurement strategies were used in our collected gene expression data: ESTs, Affymetrix GeneChip, CAGE, and RNA-Seq. These four types of data were linked based on the NCBI gene IDs in the dataset in RefEx.", "features": "・Reference of gene expression in normal organs throughout the body\r\nBy showing in parallel with gene expression dataset in normal 40 organs (10 major groups) was obtained by four different experimental methods, you can make an intuitive comparison among gene expression values but also the methods. Users can examine the expression profiles of unfamiliar genes in normal tissues of the body, cells, and cell lines, from actual measurement data, rather than only from a description in a journal article. Recently, we incorporated CAGE data from the FANTOM5 project into RefEx. The FANTOM5 project is a broad atlas of gene expression for human and mouse. It is now possible to search against more than five hundred human samples, encompassing cell lines, primary cells, and adult and fetal tissues.\r\n・Simple search interface for clear purposes\r\nRefEx provides incremental search for gene name or gene symbol of your interests. Data in RefEx are also organized that can search for the group of genes belonging to a particular category such as \"transcription factor\" and \"G-protein-coupled receptor\". In addition, RefEx contains unique lists of genes with prominent expression patterns in a specific tissue relative to those in other tissues. The genes with tissue-specific expression patterns are calculated for all tissues using the ROKU method. Clicking on the tissue icons on the topof the RefEx page easily retrieves genes with tissue-specific expression patterns.\r\n・Intuitive visualization for new knowledge discovery\r\nThe relative gene expression values are shown in RefEx as choropleth maps on 3D human body images from BodyParts3D. This type of visualization can help users to understand the differences in gene expression patterns among tissues more intuitively. In addition, users can add up to three genes to their list and compare these genes simultaneously. Users can compare all the detailed information about the genes in that list, including the expression data. This parallel comparison enables users to easily identify the differences among the genes. Therefore, RefEx is also useful as a tool for investigating the relationships of unknown genes found in gene expression analyses.\r\n・A practical example of useful and reusable public data\r\nThe data in RefEx were manually collected by RefEx curators from public databases. Raw data from the public databases were re-organized and compared with and against each other. RefEx is freely available, not only for academic users, but also for for-profit users under a Creative Commons Attribution 4.0 International License). Under this unforced license, some users might prefer to download the data and analyze them locally with other softwares. To accomplish this, a user can download a concaten+E6ated version of all the data at the downloads page. The availability of such a reference dataset will be beneficial to biologists that wish to reuse this type of data for their own research.", "fundings": [ { "funding_name": "MEXT Integrated Database Project Life Science Database Integration Project \"Development of fundamental technologies related to integration of databases\"", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 81 } ], "funding_free_style": "MEXT Integrated Database Project Life Science Database Integration Project \"Development of fundamental technologies related to integration of databases\"", "references": [ { "reference_title": "RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes", "reference_authors": "Ono H, Ogasawara O, Okubo K, Bono H", "journal": "Scientific data\/Aug 2017\/vol. 4 170105", "reference_pubmed_id": 28850115, "reference_jglobal_id": "" } ], "maintenance_site": "Database Center for Life Science", "original_sites": [ "https:\/\/refex.dbcls.jp\/index.php?lang=en" ], "operation_start_date": "2014-04-01", "last_updated_date": "2018-04-05", "upper_level_site": "", "whole_data_download": "https:\/\/refex.dbcls.jp\/download.php?lang=en", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "http:\/\/togodb.biosciencedbc.jp\/togodb\/data_relationship_matrix#en", "user_registration": false }, { "path": "en\/refexxxeq6cse\/desc.html", "name": "RefEx", "alias": "Reference Expression Dataset", "dbcat_id": [ "nbdc01099" ], "doi": "", "creators": [ { "creator_name": "小野浩雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "201201055707420599", "creator_researchmap_id": "", "creator_orcid": "0000-0001-8675-963X", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "坊農秀雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "池田 秀也", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-1357-5159", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "マイクロアレイデータ、その他の発現データのデータベース" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "DNAマイクロアレイの開発によりゲノム規模での遺伝子の発現量の測定が可能となって以来、遺伝子発現データはさまざまな研究グループにより異なる測定手法を用いて産生され、公共データベースに蓄積しつづけています。これらのデータは、仮説の構築、研究計画の立案、実験データの解釈など、さまざまな状況において幅広い分野の研究者に利用される汎用的なデータですが、その膨大さや多様さのため、それらを自らの研究に利用することは困難な場合があります。\r\nRefEx (Reference Expression dataset) は、遺伝子発現解析の基準となる正常な組織や細胞などの大規模測定データを集め、並列に比較できるよう整理し、それらを快適に閲覧できるウェブツールです。", "features": "・正常組織・細胞等の遺伝子発現データを ひと目で\r\n複数の遺伝子発現計測手法によって得られた哺乳類の正常組織、細胞等における遺伝子発現データを収集し並列に表現することによって、各組織における遺伝子発現状況を計測手法間の差異とともに直感的に比較できることが特長です。RefExを利用することで、研究者は研究対象とする遺伝子が平常時にどの組織、細胞でどの程度発現しているのかについて、自ら実験をすることなく確認することができます。また、研究者がしばしば遭遇する馴染みのない遺伝子について、一般的には個別の研究論文における実験データや記述などからそれらの生物学的特徴を類推したりしますが、RefExでは実験デザインに左右されない大規模かつ網羅的な測定データから研究者自身の目でそれらを簡単に確認することができます。さらに、研究者の用意した複数の遺伝子IDについて一括で検索できる機能を備えているほか、リスト機能を用いて遺伝子の詳細データを並列に比較することができるため、遺伝子発現解析などで見出された遺伝子群の関係性を知るためのツールとしても有用です。\r\n・調べたい遺伝子を より探しやすく より分かりやすく\r\nもっとも基本的なキーワード·遺伝子名検索では文字を入力する度に検索語の候補が提示されるので、それらから選択することで容易にキーワード入力を行うことができます。また、 「転写因子」や「Gタンパク質共役受容体」、「2番染色体」などのように、ある分類に属する遺伝子群についてまとめて検索·比較できるよう整理されています。さらに、さまざまな実験における比較対照などに用いられる『組織特異的遺伝子』を測定データから独自に算出し、組織ごとに一覧することができます。Advanced searchでは、複雑な検索条件を一度に指定することが可能であり、あらかじめID情報などが手元にある場合には、目的とするデータに簡単に行き着くことができます。\r\n・直感的な可視化で 新たな知識発見・仮説構築を\r\n検索結果一覧および個別の遺伝子の詳細情報ページでは、 組織間の比較と測定手法間（EST、GeneChip、CAGE、RNA-seq）の比較を両立させた相対発現量が棒グラフで示されるとともに人体の3DモデルであるBodyParts3D\/Anatomographyに発現量を反映させたヒートマップが表示されます。またリスト機能を使えば、検索結果の個別の遺伝子について一時的に保存しておくことができます。リストに追加した遺伝子は、最大でその3つについて、40分類の組織·臓器における発現データを比較しながら、遺伝子に付与された機能に関する注釈情報（Gene Ontology他） を見比べることができます。これらの機能は、新たな知識発見あるいは仮説の構築をサポートします。詳細情報ページに記載された種々のIDには、それぞれRefExの内部リンクやオリジナルのデータベースサイトへの外部リンクが貼られており、同じ分類に属する遺伝子を再検索したり、RefEx自体を遺伝子検索の起点とすることもできます。\r\n・再利用可能で有用なパブリックデータの活用例\r\nRefExが提供するすべてのデータは、クリエイティブ·コモンズライセンスのもとで、オープンデータとして自由にダウンロードおよび再利用することができます。検索結果一覧や詳細情報ページのデータはいずれもダウンロードすることが可能で、研究者自身のデータと参照することも、それらを使った再解析も自由に行うことができます。 また、外部の研究データレポジトリ「figshare」にも全てのデータがDOI付きで公開されています（https:\/\/doi.org\/10.6084\/m9.figshare.c.3812815）。さらに、ソフトウェア開発プロジェクトのための共有ウェブサービス「GitHub」上にも、公開データの再解析に用いたプログラムやドキュメントを整理しており、RefExで提供する再解析データについてある一定の評価品質および再現性を担保しています（https:\/\/github.com\/dbcls\/RefEx）。RefExは生命科学データの共有および再利用の活用例のひとつであり、データ駆動型研究のためのデータセット、ウェブツールとしてだれでも自由に使うことができます。", "fundings": [ { "funding_name": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 81 } ], "funding_free_style": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "references": [ { "reference_title": "RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes", "reference_authors": "Ono H, Ogasawara O, Okubo K, Bono H", "journal": "Scientific data\/Aug 2017\/vol. 4 170105", "reference_pubmed_id": 28850115, "reference_jglobal_id": "" } ], "maintenance_site": "ライフサイエンス統合データベースセンター", "original_sites": [ "https:\/\/refex.dbcls.jp\/index.php?lang=ja" ], "operation_start_date": "2014-04-01", "last_updated_date": "2018-04-05", "upper_level_site": "", "whole_data_download": "https:\/\/refex.dbcls.jp\/download.php?lang=ja", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/refexxxeu850a\/desc.html", "name": "RefEx", "alias": "Reference Expression Dataset", "dbcat_id": [ "nbdc01099" ], "doi": "", "creators": [ { "creator_name": "小野浩雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "201201055707420599", "creator_researchmap_id": "", "creator_orcid": "0000-0001-8675-963X", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "坊農秀雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "池田 秀也", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-1357-5159", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "マイクロアレイデータ、その他の発現データのデータベース" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "DNAマイクロアレイの開発によりゲノム規模での遺伝子の発現量の測定が可能となって以来、遺伝子発現データはさまざまな研究グループにより異なる測定手法を用いて産生され、公共データベースに蓄積しつづけています。これらのデータは、仮説の構築、研究計画の立案、実験データの解釈など、さまざまな状況において幅広い分野の研究者に利用される汎用的なデータですが、その膨大さや多様さのため、それらを自らの研究に利用することは困難な場合があります。\r\nRefEx (Reference Expression dataset) は、遺伝子発現解析の基準となる正常な組織や細胞などの大規模測定データを集め、並列に比較できるよう整理し、それらを快適に閲覧できるウェブツールです。", "features": "・正常組織・細胞等の遺伝子発現データを ひと目で\r\n複数の遺伝子発現計測手法によって得られた哺乳類の正常組織、細胞等における遺伝子発現データを収集し並列に表現することによって、各組織における遺伝子発現状況を計測手法間の差異とともに直感的に比較できることが特長です。RefExを利用することで、研究者は研究対象とする遺伝子が平常時にどの組織、細胞でどの程度発現しているのかについて、自ら実験をすることなく確認することができます。また、研究者がしばしば遭遇する馴染みのない遺伝子について、一般的には個別の研究論文における実験データや記述などからそれらの生物学的特徴を類推したりしますが、RefExでは実験デザインに左右されない大規模かつ網羅的な測定データから研究者自身の目でそれらを簡単に確認することができます。さらに、研究者の用意した複数の遺伝子IDについて一括で検索できる機能を備えているほか、リスト機能を用いて遺伝子の詳細データを並列に比較することができるため、遺伝子発現解析などで見出された遺伝子群の関係性を知るためのツールとしても有用です。\r\n・調べたい遺伝子を より探しやすく より分かりやすく\r\nもっとも基本的なキーワード·遺伝子名検索では文字を入力する度に検索語の候補が提示されるので、それらから選択することで容易にキーワード入力を行うことができます。また、 「転写因子」や「Gタンパク質共役受容体」、「2番染色体」などのように、ある分類に属する遺伝子群についてまとめて検索·比較できるよう整理されています。さらに、さまざまな実験における比較対照などに用いられる『組織特異的遺伝子』を測定データから独自に算出し、組織ごとに一覧することができます。Advanced searchでは、複雑な検索条件を一度に指定することが可能であり、あらかじめID情報などが手元にある場合には、目的とするデータに簡単に行き着くことができます。\r\n・直感的な可視化で 新たな知識発見・仮説構築を\r\n検索結果一覧および個別の遺伝子の詳細情報ページでは、 組織間の比較と測定手法間（EST、GeneChip、CAGE、RNA-seq）の比較を両立させた相対発現量が棒グラフで示されるとともに人体の3DモデルであるBodyParts3D\/Anatomographyに発現量を反映させたヒートマップが表示されます。またリスト機能を使えば、検索結果の個別の遺伝子について一時的に保存しておくことができます。リストに追加した遺伝子は、最大でその3つについて、40分類の組織·臓器における発現データを比較しながら、遺伝子に付与された機能に関する注釈情報（Gene Ontology他） を見比べることができます。これらの機能は、新たな知識発見あるいは仮説の構築をサポートします。詳細情報ページに記載された種々のIDには、それぞれRefExの内部リンクやオリジナルのデータベースサイトへの外部リンクが貼られており、同じ分類に属する遺伝子を再検索したり、RefEx自体を遺伝子検索の起点とすることもできます。\r\n・再利用可能で有用なパブリックデータの活用例\r\nRefExが提供するすべてのデータは、クリエイティブ·コモンズライセンスのもとで、オープンデータとして自由にダウンロードおよび再利用することができます。検索結果一覧や詳細情報ページのデータはいずれもダウンロードすることが可能で、研究者自身のデータと参照することも、それらを使った再解析も自由に行うことができます。 また、外部の研究データレポジトリ「figshare」にも全てのデータがDOI付きで公開されています（https:\/\/doi.org\/10.6084\/m9.figshare.c.3812815）。さらに、ソフトウェア開発プロジェクトのための共有ウェブサービス「GitHub」上にも、公開データの再解析に用いたプログラムやドキュメントを整理しており、RefExで提供する再解析データについてある一定の評価品質および再現性を担保しています（https:\/\/github.com\/dbcls\/RefEx）。RefExは生命科学データの共有および再利用の活用例のひとつであり、データ駆動型研究のためのデータセット、ウェブツールとしてだれでも自由に使うことができます。", "fundings": [ { "funding_name": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 81 } ], "funding_free_style": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "references": [ { "reference_title": "RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes", "reference_authors": "Ono H, Ogasawara O, Okubo K, Bono H", "journal": "Scientific data\/Aug 2017\/vol. 4 170105", "reference_pubmed_id": 28850115, "reference_jglobal_id": "" } ], "maintenance_site": "ライフサイエンス統合データベースセンター", "original_sites": [ "https:\/\/refex.dbcls.jp\/index.php?lang=ja" ], "operation_start_date": "2014-04-01", "last_updated_date": "2018-04-05", "upper_level_site": "", "whole_data_download": "https:\/\/refex.dbcls.jp\/download.php?lang=ja", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/refexxxeirk4p\/desc.html", "name": "RefEx", "alias": "Reference Expression Dataset", "dbcat_id": [ "nbdc01099" ], "doi": "", "creators": [ { "creator_name": "小野浩雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "201201055707420599", "creator_researchmap_id": "", "creator_orcid": "0000-0001-8675-963X", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "坊農秀雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "池田 秀也", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-1357-5159", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "マイクロアレイデータ、その他の発現データのデータベース" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "DNAマイクロアレイの開発によりゲノム規模での遺伝子の発現量の測定が可能となって以来、遺伝子発現データはさまざまな研究グループにより異なる測定手法を用いて産生され、公共データベースに蓄積しつづけています。これらのデータは、仮説の構築、研究計画の立案、実験データの解釈など、さまざまな状況において幅広い分野の研究者に利用される汎用的なデータですが、その膨大さや多様さのため、それらを自らの研究に利用することは困難な場合があります。\r\nRefEx (Reference Expression dataset) は、遺伝子発現解析の基準となる正常な組織や細胞などの大規模測定データを集め、並列に比較できるよう整理し、それらを快適に閲覧できるウェブツールです。", "features": "・正常組織・細胞等の遺伝子発現データを ひと目で\r\n複数の遺伝子発現計測手法によって得られた哺乳類の正常組織、細胞等における遺伝子発現データを収集し並列に表現することによって、各組織における遺伝子発現状況を計測手法間の差異とともに直感的に比較できることが特長です。RefExを利用することで、研究者は研究対象とする遺伝子が平常時にどの組織、細胞でどの程度発現しているのかについて、自ら実験をすることなく確認することができます。また、研究者がしばしば遭遇する馴染みのない遺伝子について、一般的には個別の研究論文における実験データや記述などからそれらの生物学的特徴を類推したりしますが、RefExでは実験デザインに左右されない大規模かつ網羅的な測定データから研究者自身の目でそれらを簡単に確認することができます。さらに、研究者の用意した複数の遺伝子IDについて一括で検索できる機能を備えているほか、リスト機能を用いて遺伝子の詳細データを並列に比較することができるため、遺伝子発現解析などで見出された遺伝子群の関係性を知るためのツールとしても有用です。\r\n・調べたい遺伝子を より探しやすく より分かりやすく\r\nもっとも基本的なキーワード·遺伝子名検索では文字を入力する度に検索語の候補が提示されるので、それらから選択することで容易にキーワード入力を行うことができます。また、 「転写因子」や「Gタンパク質共役受容体」、「2番染色体」などのように、ある分類に属する遺伝子群についてまとめて検索·比較できるよう整理されています。さらに、さまざまな実験における比較対照などに用いられる『組織特異的遺伝子』を測定データから独自に算出し、組織ごとに一覧することができます。Advanced searchでは、複雑な検索条件を一度に指定することが可能であり、あらかじめID情報などが手元にある場合には、目的とするデータに簡単に行き着くことができます。\r\n・直感的な可視化で 新たな知識発見・仮説構築を\r\n検索結果一覧および個別の遺伝子の詳細情報ページでは、 組織間の比較と測定手法間（EST、GeneChip、CAGE、RNA-seq）の比較を両立させた相対発現量が棒グラフで示されるとともに人体の3DモデルであるBodyParts3D\/Anatomographyに発現量を反映させたヒートマップが表示されます。またリスト機能を使えば、検索結果の個別の遺伝子について一時的に保存しておくことができます。リストに追加した遺伝子は、最大でその3つについて、40分類の組織·臓器における発現データを比較しながら、遺伝子に付与された機能に関する注釈情報（Gene Ontology他） を見比べることができます。これらの機能は、新たな知識発見あるいは仮説の構築をサポートします。詳細情報ページに記載された種々のIDには、それぞれRefExの内部リンクやオリジナルのデータベースサイトへの外部リンクが貼られており、同じ分類に属する遺伝子を再検索したり、RefEx自体を遺伝子検索の起点とすることもできます。\r\n・再利用可能で有用なパブリックデータの活用例\r\nRefExが提供するすべてのデータは、クリエイティブ·コモンズライセンスのもとで、オープンデータとして自由にダウンロードおよび再利用することができます。検索結果一覧や詳細情報ページのデータはいずれもダウンロードすることが可能で、研究者自身のデータと参照することも、それらを使った再解析も自由に行うことができます。 また、外部の研究データレポジトリ「figshare」にも全てのデータがDOI付きで公開されています（https:\/\/doi.org\/10.6084\/m9.figshare.c.3812815）。さらに、ソフトウェア開発プロジェクトのための共有ウェブサービス「GitHub」上にも、公開データの再解析に用いたプログラムやドキュメントを整理しており、RefExで提供する再解析データについてある一定の評価品質および再現性を担保しています（https:\/\/github.com\/dbcls\/RefEx）。RefExは生命科学データの共有および再利用の活用例のひとつであり、データ駆動型研究のためのデータセット、ウェブツールとしてだれでも自由に使うことができます。", "fundings": [ { "funding_name": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 81 } ], "funding_free_style": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "references": [ { "reference_title": "RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes", "reference_authors": "Ono H, Ogasawara O, Okubo K, Bono H", "journal": "Scientific data\/Aug 2017\/vol. 4 170105", "reference_pubmed_id": 28850115, "reference_jglobal_id": "" } ], "maintenance_site": "ライフサイエンス統合データベースセンター", "original_sites": [ "https:\/\/refex.dbcls.jp\/index.php?lang=ja" ], "operation_start_date": "2014-04-01", "last_updated_date": "2018-04-05", "upper_level_site": "", "whole_data_download": "https:\/\/refex.dbcls.jp\/download.php?lang=ja", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/refexxeesxe6o2\/desc.html", "name": "RefEx", "alias": "Reference Expression Dataset", "dbcat_id": [ "nbdc01099" ], "doi": "", "creators": [ { "creator_name": "小野浩雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "201201055707420599", "creator_researchmap_id": "", "creator_orcid": "0000-0001-8675-963X", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "坊農秀雅", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "200901083788745339", "creator_researchmap_id": "", "creator_orcid": "0000-0003-4413-0651", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "池田 秀也", "creator_affiliation": "ライフサイエンス統合データベースセンター", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "0000-0002-1357-5159", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "マイクロアレイデータ、その他の発現データのデータベース" ], "categories_free_style": [], "organisms": [ { "organism_name": "Homo sapiens", "taxonomy_id": 9606 }, { "organism_name": "Mus musculus", "taxonomy_id": 10090 }, { "organism_name": "Rattus norvegicus", "taxonomy_id": 10116 } ], "organism_free_style": "", "description": "DNAマイクロアレイの開発によりゲノム規模での遺伝子の発現量の測定が可能となって以来、遺伝子発現データはさまざまな研究グループにより異なる測定手法を用いて産生され、公共データベースに蓄積しつづけています。これらのデータは、仮説の構築、研究計画の立案、実験データの解釈など、さまざまな状況において幅広い分野の研究者に利用される汎用的なデータですが、その膨大さや多様さのため、それらを自らの研究に利用することは困難な場合があります。\r\nRefEx (Reference Expression dataset) は、遺伝子発現解析の基準となる正常な組織や細胞などの大規模測定データを集め、並列に比較できるよう整理し、それらを快適に閲覧できるウェブツールです。", "features": "・正常組織・細胞等の遺伝子発現データを ひと目で\r\n複数の遺伝子発現計測手法によって得られた哺乳類の正常組織、細胞等における遺伝子発現データを収集し並列に表現することによって、各組織における遺伝子発現状況を計測手法間の差異とともに直感的に比較できることが特長です。RefExを利用することで、研究者は研究対象とする遺伝子が平常時にどの組織、細胞でどの程度発現しているのかについて、自ら実験をすることなく確認することができます。また、研究者がしばしば遭遇する馴染みのない遺伝子について、一般的には個別の研究論文における実験データや記述などからそれらの生物学的特徴を類推したりしますが、RefExでは実験デザインに左右されない大規模かつ網羅的な測定データから研究者自身の目でそれらを簡単に確認することができます。さらに、研究者の用意した複数の遺伝子IDについて一括で検索できる機能を備えているほか、リスト機能を用いて遺伝子の詳細データを並列に比較することができるため、遺伝子発現解析などで見出された遺伝子群の関係性を知るためのツールとしても有用です。\r\n・調べたい遺伝子を より探しやすく より分かりやすく\r\nもっとも基本的なキーワード·遺伝子名検索では文字を入力する度に検索語の候補が提示されるので、それらから選択することで容易にキーワード入力を行うことができます。また、 「転写因子」や「Gタンパク質共役受容体」、「2番染色体」などのように、ある分類に属する遺伝子群についてまとめて検索·比較できるよう整理されています。さらに、さまざまな実験における比較対照などに用いられる『組織特異的遺伝子』を測定データから独自に算出し、組織ごとに一覧することができます。Advanced searchでは、複雑な検索条件を一度に指定することが可能であり、あらかじめID情報などが手元にある場合には、目的とするデータに簡単に行き着くことができます。\r\n・直感的な可視化で 新たな知識発見・仮説構築を\r\n検索結果一覧および個別の遺伝子の詳細情報ページでは、 組織間の比較と測定手法間（EST、GeneChip、CAGE、RNA-seq）の比較を両立させた相対発現量が棒グラフで示されるとともに人体の3DモデルであるBodyParts3D\/Anatomographyに発現量を反映させたヒートマップが表示されます。またリスト機能を使えば、検索結果の個別の遺伝子について一時的に保存しておくことができます。リストに追加した遺伝子は、最大でその3つについて、40分類の組織·臓器における発現データを比較しながら、遺伝子に付与された機能に関する注釈情報（Gene Ontology他） を見比べることができます。これらの機能は、新たな知識発見あるいは仮説の構築をサポートします。詳細情報ページに記載された種々のIDには、それぞれRefExの内部リンクやオリジナルのデータベースサイトへの外部リンクが貼られており、同じ分類に属する遺伝子を再検索したり、RefEx自体を遺伝子検索の起点とすることもできます。\r\n・再利用可能で有用なパブリックデータの活用例\r\nRefExが提供するすべてのデータは、クリエイティブ·コモンズライセンスのもとで、オープンデータとして自由にダウンロードおよび再利用することができます。検索結果一覧や詳細情報ページのデータはいずれもダウンロードすることが可能で、研究者自身のデータと参照することも、それらを使った再解析も自由に行うことができます。 また、外部の研究データレポジトリ「figshare」にも全てのデータがDOI付きで公開されています（https:\/\/doi.org\/10.6084\/m9.figshare.c.3812815）。さらに、ソフトウェア開発プロジェクトのための共有ウェブサービス「GitHub」上にも、公開データの再解析に用いたプログラムやドキュメントを整理しており、RefExで提供する再解析データについてある一定の評価品質および再現性を担保しています（https:\/\/github.com\/dbcls\/RefEx）。RefExは生命科学データの共有および再利用の活用例のひとつであり、データ駆動型研究のためのデータセット、ウェブツールとしてだれでも自由に使うことができます。", "fundings": [ { "funding_name": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "funding_jglobal_id": "201304036502222259", "funding_lsdb_project_id": 81 } ], "funding_free_style": "文部科学省「ライフサイエンス統合データベース」プロジェクト ライフサイエンスデータベース統合推進事業「データベース統合に関わる基盤技術開発」", "references": [ { "reference_title": "RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes", "reference_authors": "Ono H, Ogasawara O, Okubo K, Bono H", "journal": "Scientific data\/Aug 2017\/vol. 4 170105", "reference_pubmed_id": 28850115, "reference_jglobal_id": "" } ], "maintenance_site": "ライフサイエンス統合データベースセンター", "original_sites": [ "https:\/\/refex.dbcls.jp\/index.php?lang=ja" ], "operation_start_date": "2014-04-01", "last_updated_date": "2018-04-05", "upper_level_site": "", "whole_data_download": "https:\/\/refex.dbcls.jp\/download.php?lang=ja", "referenced_site": "", "list_search": false, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rgp-caps\/desc.html", "name": "RGP caps", "alias": "RGP: 332 PCR-based genetic markers on rice chromosomes", "dbcat_id": [ "nbdc00318" ], "doi": "10.18908\/lsdba.nbdc00318-05-000", "creators": [ { "creator_name": "Kimiko Yamamoto", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Jianzhong Wu", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuji Sasaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Sequence", "PCR-based marker" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "We have developed 332 PCR-based genetic markers including 161 sequence tagged site (STS) markers and 171 cleaved amplified polymorphic sequence (CAPS) markers.This site shows all information for these markers.", "features": "The table (chr 1 to chr 12) summarizes all information for STS and CAPS markers, such as chromosomal location, primer sequences, size of amplified fragment (Nipponbare), restriction enzyme, etc. These markers have been developed to detect polymorphism between Nipponbare (japonica) and Kasalath (indica). Although detection of polymorphism of these markers will depend on the combination of varieties or lines, they may be used for the analysis of other combinations.\r\nBecause this archive has been created based on the following data of the last update date, it may not match the data in the current situation.", "fundings": [ { "funding_name": "Phase 2 of Rice Genome Research Project (1998-2004)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rgp.dna.affrc.go.jp\/E\/publicdata\/caps\/index.html" ], "operation_start_date": "2002-02-10", "last_updated_date": "2002-02-10", "upper_level_site": "http:\/\/rgp.dna.affrc.go.jp\/E\/", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rgp-estmap2001\/desc.html", "name": "RGP estmap2001", "alias": "RGP : A YAC-Based Rice Transcript Map Containing 6591 EST Sites", "dbcat_id": [ "nbdc00318" ], "doi": "10.18908\/lsdba.nbdc00318-04-000", "creators": [ { "creator_name": "Jianzhong Wu", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takashi Matsumoto", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuji Sasaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Genome", "Sequence" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "This database provides the information about the YAC-based rice transcript map (Wu et al, Plant Cell 14, 2002), containing 6591 EST sites that was used for the map construction.", "features": "We provide the detailed contents of the YAC-based rice transcript map with the following tables and figures (together Microsoft Excel format and pdf format for your download). Tables contain the detailed results of PCR-based YAC screening with the clone-specific EST primers. Figures contain the rice genetic and YAC physical maps with the assigned EST sites.\r\nBecause this archive has been created based on the following data of the last update date, it may not match the data in the current situation.", "fundings": [ { "funding_name": "Phase 2 of Rice Genome Research Project (1998-2004)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [ { "reference_title": "A comprehensive rice transcript map containing 6591 expressed sequence tag sites.", "reference_authors": "Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T.", "journal": "The Plant Cell \/ 2002 Mar \/ 14(3):525-535", "reference_pubmed_id": 11910001, "reference_jglobal_id": "200902141547705232" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rgp.dna.affrc.go.jp\/E\/publicdata\/estmap2001\/index.html" ], "operation_start_date": "2002-02-16", "last_updated_date": "2002-02-16", "upper_level_site": "http:\/\/rgp.dna.affrc.go.jp\/E\/", "whole_data_download": "", "referenced_site": "MAFF_Rice cDNA Clone\r\nDDBJ", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rgp-gmap\/desc.html", "name": "RGP gmap", "alias": "RGP : RICE GENETIC MAP IN NATURE GENETICS", "dbcat_id": [ "nbdc00318" ], "doi": "10.18908\/lsdba.nbdc00318-01-000", "creators": [ { "creator_name": "Yuzo Minobe", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true }, { "creator_name": "Nori Kurata", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Yoshiaki Nagamura", "creator_affiliation": "STAFF Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Masahiro Yano", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuji Sasaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Sequence, Gene Expression" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "RICE GENETIC MAP IN NATURE GENETICS is a database of 1381 DNA markers that were used to create the rice genetic map. The rice genetic map is published in the Nature Genetics volume 8, 365-372, December 1994.", "features": "The rice genetic map consists of 1381 RFLP markers (1993 version) mapped on a Nipponbare (japonica) and a Kasalath (indica) F2 intercross.\r\nBecause this archive has been created based on the following data of the last update date, it may not match the data in the current situation.", "fundings": [ { "funding_name": "Phase 1 of Rice Genome Research Project (1991-1997)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [ { "reference_title": "A 300 kilobase interval genetic map of rice including 883 expressed sequences", "reference_authors": "N. Kurata, Y. Nagamura, K. Yamamoto, Y. Harushima, N. Sue, J. Wu, B.A. Antonio, A. Shomura, T. Shimizu, S-Y. Lin, T. Inoue, A. Fukuda, T. Shimano, Y. Kuboki, T. Toyama, Y. Miyamoto, T. Kirihara, K. Hayasaka, A. Miyao, L. Monna, H.S. Zhong, Y. Tamura, Z-X. Wang, T. Momma, Y. Umehara, M. Yano, T. Sasaki, Y. Minobe", "journal": "Nature Genetics, 8: 365-372 (1994)", "reference_pubmed_id": 7894488, "reference_jglobal_id": "200902160772912713" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rgp.dna.affrc.go.jp\/E\/publicdata\/naturegenetics\/ricegmap.html" ], "operation_start_date": "1994-08-08", "last_updated_date": "1995-09-26", "upper_level_site": "http:\/\/rgp.dna.affrc.go.jp\/E\/", "whole_data_download": "http:\/\/rgp.dna.affrc.go.jp\/pub\/gmap\/naturegenetics\/", "referenced_site": "DDBJ", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rgp-gmap2000\/desc.html", "name": "RGP gmap2000", "alias": "RGP: The Latest High-Density Rice Genetic Map, Including 3267 Markers", "dbcat_id": [ "nbdc00318" ], "doi": "10.18908\/lsdba.nbdc00318-03-000", "creators": [ { "creator_name": "Yoshiaki Harushima", "creator_affiliation": "STAFF Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Nori Kurata", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Yoshiaki Nagamura", "creator_affiliation": "STAFF Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Masahiro Yano", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuji Sasaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Genome", "Sequence" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "We provide here the 2000 version of linkage map, which consists of 3267 RFLP marker information including nearly 1000 new RFLP markers which was produced after our high-density RFLP linkage map publication of 1998.", "features": "The data are shown in a table for each of the 12 chromosomes. The tables include the map position from the telomeric end of the short arm of each chromosome (genetic distance in cM), the marker name, and (where available) DDBJ accession numbers of the sequences of both the 5' and 3' ends of insert fragments of the probes used in the RFLP analysis.\r\nBecause this archive has been created based on the following data of the last update date, it may not match the data in the current situation.", "fundings": [ { "funding_name": "Phase 2 of Rice Genome Research Project (1998-2004)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rgp.dna.affrc.go.jp\/E\/publicdata\/geneticmap2000\/index.html" ], "operation_start_date": "2000-11-30", "last_updated_date": "2000-11-30", "upper_level_site": "http:\/\/rgp.dna.affrc.go.jp\/E\/", "whole_data_download": "", "referenced_site": "MAFF_Rice cDNA Clone\r\nDDBJ", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rgp-gmap98\/desc.html", "name": "RGP gmap98", "alias": "RGP: A HIGH-DENSITY RICE GENETIC MAP", "dbcat_id": [ "nbdc00318" ], "doi": "10.18908\/lsdba.nbdc00318-02-000", "creators": [ { "creator_name": "Yoshiaki Harushima", "creator_affiliation": "STAFF Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Nori Kurata", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Yoshiaki Nagamura", "creator_affiliation": "STAFF Institute", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Masahiro Yano", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuji Sasaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Genome", "Sequence" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "According to the publication of our high-density RFLP linkage map in the journal \"Genetics\" (January 1998), we provide here a large amount of relevant data that can not be published in the form of a printed paper.", "features": "The rice genetic map consists of 2275 RFLP markers mapped on a Nipponbare (japonica) and a Kasalath (indica) F2 intercross. The data includes isozyme loci and a table linked with parental Southern images of each probe and Nucleotide sequence, and other related clone information. The table also includes the results of similarity search of mapped clones. Because this archive has been created based on the following data of the last update date, it may not match the data in the current situation.", "fundings": [ { "funding_name": "Phase 1 of Rice Genome Research Project (1991-1997)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 }, { "funding_name": "Phase 2 of Rice Genome Research Project (1998-2004)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [ { "reference_title": "A High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population", "reference_authors": "Y Harushima, M Yano, A Shomura, M Sato, T Shimano, Y Kuboki, T Yamamoto, S Y Lin, B A Antonio, A Parco, H Kajiya, N Huang, K Yamamoto, Y Nagamura, N Kurata, G S Khush, and T Sasaki", "journal": "Genetics January 1, 1998 vol.148 no.1 479-494", "reference_pubmed_id": 9475757, "reference_jglobal_id": "200902197633285071" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rgp.dna.affrc.go.jp\/E\/publicdata\/geneticmap98\/geneticmap98.html" ], "operation_start_date": "1998-01-17", "last_updated_date": "1998-01-17", "upper_level_site": "http:\/\/rgp.dna.affrc.go.jp\/E\/", "whole_data_download": "http:\/\/rgp.dna.affrc.go.jp\/pub\/geneticmap98\/", "referenced_site": "DDBJ", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rgp-physicalmap\/desc.html", "name": "RGP physicalmap", "alias": "Rice Genome Mapping and Sequencing Data from RGP, STAFF\/NIAR, Japan", "dbcat_id": [ "nbdc00318" ], "doi": "10.18908\/lsdba.nbdc00318-06-000", "creators": [ { "creator_name": "Yosuke Umehara", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Nori Kurata", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false }, { "creator_name": "Takuji Sasaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": true } ], "categories": [ "Plant databases - Rice" ], "categories_free_style": [ "Sequence", "Physical map" ], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "This site contains a physical map information of rice using yeast artificial chromosome (YAC) clones selected with the Rice Genome Research Program (RGP) DNA markers from 1994 through 1997 version. A rice YAC library of RGP was constructed from cultured cells of Oryza sativa L. cv. Nipponbare and contains 6934 clones with 350 kb average insert length.", "features": "You can see the data files of yeast artificial chromosome (YAC) clones by figures and tables, which clones were selected with DNA markers in the Rice Genome Research Program (RGP) for each chromosome. In the tables, YAC clones selected with RGP DNA markers for each chromosome are shown along with the markers and the genetic distances. In the figures, the YAC physical maps of each divided region on the chromosomes are shown.\r\nBecause this archive has been created based on the following data of the last update date, it may not match the data in the current situation.", "fundings": [ { "funding_name": "Phase 1 of Rice Genome Research Project (1991-1997)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [ { "reference_title": "Construction and characterization of a rice YAC library for physical mapping", "reference_authors": "Yosuke Umehara, Akiko Inagaki, Hiroshi Tanoue, Yuji Yasukochi, Yoshiaki Nagamura, Shoko Saji, Yoshiaki Otsuki, Tatsuhito Fujimura, Nori Kurata, Yuzo Minobe", "journal": "Molecular Breeding (1995) 1(1): 79-89.", "reference_pubmed_id": null, "reference_jglobal_id": "201102160412318215" }, { "reference_title": "A 300 kilobase interval genetic map of rice including 883 expressed sequences", "reference_authors": "N. Kurata, Y. Nagamura, K. Yamamoto, Y. Harushima, N. Sue, J. Wu, B.A. Antonio, A. Shomura, T. Shimizu, S-Y. Lin, T. Inoue, A. Fukuda, T. Shimano, Y. Kuboki, T. Toyama, Y. Miyamoto, T. Kirihara, K. Hayasaka, A. Miyao, L. Monna, H.S. Zhong, Y. Tamura, Z-X, Wang, T. Momma, Y. Umehara, M. Yano, T. Sasaki and Y. Minobe", "journal": "Nature Genetics (1994) 8: 365-372.", "reference_pubmed_id": 7894488, "reference_jglobal_id": "200902160772912713" }, { "reference_title": "Physical Mapping of Rice Chromosome 1 with Yeast Artificial Chromosomes (YACs)", "reference_authors": "Zi-Xuan Wang, Atsuko Idonuma, Yosuke Umehara, Wim Van Houten, Ikuo Ashikawa, Yuzo Minobe, Nori Kurata and Takuji Sasaki", "journal": "DNA Research (1996) 3(5): 291-296.", "reference_pubmed_id": 9039498, "reference_jglobal_id": "200902157484906589" }, { "reference_title": "Yeast Artificial Chromosome Clones of Rice Chromosome 2 Ordered Using DNA Markers", "reference_authors": "Yosuke Umehara, Nori Kurata, Ikuo Ashikawa and Takuji Sasaki", "journal": "DNA Research (1997) 4(2): 127-131.", "reference_pubmed_id": 9205839, "reference_jglobal_id": "200902176636764127" }, { "reference_title": "Ordered YAC Clone Contigs Assigned to Rice Chromosomes 3 and 11", "reference_authors": "Hiroshi Tanoue, Takanori Shimokawa, Jianzhong Wu, Norio Sue, Yosuke Umehara, Ikuo Ashikawa, Nori Kurata and Takuji Sasaki", "journal": "DNA Research (1997) 4(2): 133-140.", "reference_pubmed_id": 9205840, "reference_jglobal_id": "200902147422655711" }, { "reference_title": "Physical Mapping of Rice Chromosomes 4 and 7 Using YAC Clones", "reference_authors": "Kazuhiro Koike, Katsuhiko Yoshino, Norio Sue, Yosuke Umehara, Ikuo Ashikawa, Nori Kurata and Takuji Sasaki", "journal": "DNA Research (1997) 4(1): 27-33.", "reference_pubmed_id": 9179493, "reference_jglobal_id": "200902152416086563" }, { "reference_title": "Construction of YAC Contigs on Rice Chromosome 5", "reference_authors": "Shoko Saji, Yosuke Umehara, Nori Kurata, Ikuo Ashikawa and Takuji Sasaki", "journal": "DNA Research (1996) 3(5): 297-302.", "reference_pubmed_id": 9039499, "reference_jglobal_id": "200902133976765070" }, { "reference_title": "An ordered yeast artificial chromosome library covering over half of rice chromosome 6", "reference_authors": "Y Umehara, H Tanoue, N Kurata, I Ashikawa, Y Minobe, and T Sasaki", "journal": "Genome Research (1996) 6(10): 935-942.", "reference_pubmed_id": 8908512, "reference_jglobal_id": "200902114514925426" }, { "reference_title": "Physical mapping of rice chromosomes 8 and 9 with YAC clones", "reference_authors": "Baltazar A. Antonio, Makiko Emoto, Jianzhong Wu, Ikuo Ashikawa, Yosuke Umehara, Nori Kurata and Takuji Sasaki", "journal": "DNA Research (1996) 3(6): 393-400.", "reference_pubmed_id": 9097041, "reference_jglobal_id": "200902132773353811" }, { "reference_title": "Assignment of YAC Clones Spanning Rice Chromosomes 10 and 12", "reference_authors": "Takanori Shimokawa, Nori Kurata, Jianzhong Wu, Yosuke Umehara, Ikuo Ashikawa and Takuji Sasaki", "journal": "DNA Research (1996) 3(6): 401-406.", "reference_pubmed_id": 9097042, "reference_jglobal_id": "200902132373997140" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rgp.dna.affrc.go.jp\/E\/publicdata\/physicalmap\/physicalmap.html" ], "operation_start_date": "1997-07-09", "last_updated_date": "1998-08-24", "upper_level_site": "http:\/\/rgp.dna.affrc.go.jp\/E\/", "whole_data_download": "", "referenced_site": "DDBJ", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rmg\/desc.html", "name": "RMG", "alias": "Rice Mitochondrial Genome", "dbcat_id": [ "nbdc00193" ], "doi": "10.18908\/lsdba.nbdc00193-000", "creators": [ { "creator_name": "Kouichi Kadowaki", "creator_affiliation": "National Agriculture and Food Research Organization", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Nucleotide Sequence Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa Japonica Group", "taxonomy_id": 39947 } ], "organism_free_style": "", "description": "This database contains information on the rice mitochondrial genome. You can refer entire sequence of rice mitochondrial genome and information on the analysis results.", "features": "The mitochondrial genome information can be used as standard for analysis of the mitochondria of major cereal crops such as corn and wheat as well as other monocotyledonous plants.", "fundings": [ { "funding_name": "\"Pioneer Research Project\" (2001-2003) of the National Institute of Agrobiological Sciences", "funding_jglobal_id": "", "funding_lsdb_project_id": null }, { "funding_name": "\"Grant-in-Aid for Scientific Research\" (2001-2003) of the University of Tokyo", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "This database was constructed using the research results of the National Institute of Agrobiological Sciences and the University of Tokyo.", "references": [ { "reference_title": "The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.", "reference_authors": "Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K.", "journal": "Mol Genet Genomics (2002) 268: 434–445", "reference_pubmed_id": 12471441, "reference_jglobal_id": "200902106776080041" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/rmg.rice.dna.affrc.go.jp\/" ], "operation_start_date": "2002-09-25", "last_updated_date": "2002-09-25", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/cgi-bin\/sogo.cgi?class=719&lang=en", "whole_data_download": "", "referenced_site": "", "list_search": true, "query_search": false, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rmos\/desc.html", "name": "RMOS", "alias": "Rice Microarray Opening Site", "dbcat_id": [ "nbdc00194" ], "doi": "10.18908\/lsdba.nbdc00194-000", "creators": [ { "creator_name": "Shoshi Kikuchi", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Plant databases - Rice", "Microarray Data and other Gene Expression Databases" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "The Rice Microarray Opening Site is a database of comprehensive information for Rice Microarray Project (April 1999 - March 2003). Microarray is the powerful tool for understanding comprehensive gene expression at genome-wide level (for details, refer to the Technical Background Section). By using this system, it has become possible to isolate the genes quickly that confer resistances or are responsive to cold temperature, drought, unsuitable soil condition, insect pest and disease, etc. It has become possible by using this system to begin to quickly isolate the genes that confer such resistance. Also it has become possible to isolate which genes are expressed in particular tissues and organs.", "features": "You can refer to the information of the general background for Microarray techniques and the research data related to the custom microarray we developed.", "fundings": [ { "funding_name": "Analysis of gene functions in the rice genome by using the gene expression monitoring technique (commonly called as \"the Microarray project\") (1999-2003)", "funding_jglobal_id": "", "funding_lsdb_project_id": 5 } ], "funding_free_style": "", "references": [ { "reference_title": "Chapter 2 Comprehensive Analysis of Rice Gene Expression Using the Microarray System: What We have Learned from the Microarray Project", "reference_authors": "S.Kikuchi J. Yazaki N. Kishimoto M. ishikawa D. Endo", "journal": "Rice Improvement in the Genomics Era, edited by Swapan K. Datta, CRC Press NY, 2009, pp.15-58, ISBN 978-1-56022-952-0", "reference_pubmed_id": null, "reference_jglobal_id": "" } ], "maintenance_site": "National Institute of Agrobiological Sciences\r\n*The original website was terminated.", "original_sites": [], "operation_start_date": "2001-01-12", "last_updated_date": "2004-03-16", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/cgi-bin\/sogo.cgi?class=719&lang=en", "whole_data_download": "", "referenced_site": "Rice Expression Database (RED)\r\nRice full-length cDNA Database (KOME)\r\nRice Genome Integrated Map Database (INE)\r\nRice Mutant Panel Database (Tos17)\r\nRice Genome Annotation Database (RiceGAAS)\r\nPlant Cis-Element motif search Database (PLACE)\r\nRice Proteome Database (RPD)\r\nNIAS DNA Bank", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rpd\/desc.html", "name": "RPD", "alias": "Rice Proteome Database", "dbcat_id": [ "nbdc00191" ], "doi": "10.18908\/lsdba.nbdc00191-000", "creators": [ { "creator_name": "Setsuko Komatsu", "creator_affiliation": "National Institute of Crop Science, National Agriculture and Food Research Organization", "creator_jglobal_id": "200901069795436691", "creator_researchmap_id": "read0004407", "creator_orcid": "", "creator_jglobal_jgpn": "200901100492668861", "creator_is_representative": false } ], "categories": [ "Proteomics Resources", "Plant databases - Rice" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 } ], "organism_free_style": "", "description": "Rice Proteome Database contains information on proteins identified from several organs and organelles on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) reference maps.", "features": "Proteins extracted from organs and subcellular compartments in rice on various growing stages were separated by 2D-PAGE. Based on 23 reference maps of 2D-PAGE, each of the proteins was purified and sequenced by gas-phase protein sequencer or mass spectrometry.\r\n14724 identified proteins were mapped by 2D-PAGE. The information on 6011 proteins (e.g. Mw, pI, expression, the amino acid sequence and the result of homology searches) was cataloged and entered in the Rice Proteome Database.\r\nThe database is searchable by keyword, accession number, protein name, pI, Mw and amino acid sequence, or by selection of a spot on one of the 2D-PAGE maps. Cross-references are provided to tools for proteomics and to other databases.", "fundings": [ { "funding_name": "Analysis and database construction for tissue-specific and subcellular-localized proteins from rice.", "funding_jglobal_id": "", "funding_lsdb_project_id": null } ], "funding_free_style": "", "references": [ { "reference_title": "Rice proteome database: a step toward functional analysis of the rice genome.", "reference_authors": "Komatsu S.", "journal": "Plant Mol Biol. 2005 Sep;59(1):179-90.", "reference_pubmed_id": 16217611, "reference_jglobal_id": "200902229284654322" }, { "reference_title": "Rice proteomics: a step toward functional analysis of the rice genome.", "reference_authors": "Komatsu S, Konishi H, Shen S, Yang G.", "journal": "Mol Cell Proteomics. 2003 Jan;2(1):2-10.", "reference_pubmed_id": 12601077, "reference_jglobal_id": "" }, { "reference_title": "Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.", "reference_authors": "Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K.", "journal": "Nucleic Acids Res. 2004 Jan 1;32(Database issue):D388-92.", "reference_pubmed_id": 14681440, "reference_jglobal_id": "200902281698589729" }, { "reference_title": "Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments.", "reference_authors": "Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, Kawamura Y, Mitsui T, Mikami S, Tozawa Y, Yoshinaga T, Komatsu S.", "journal": "Mol Genet Genomics. 2004 Jun;271(5):566-76. Epub 2004 Apr 7.", "reference_pubmed_id": 15069638, "reference_jglobal_id": "200902274762902596" }, { "reference_title": "Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins.", "reference_authors": "Tanaka N, Konishi H, Khan MM, Komatsu S.", "journal": "Mol Genet Genomics. 2004 Jan;270(6):485-96. Epub 2003 Nov 21.", "reference_pubmed_id": 14634867, "reference_jglobal_id": "200902249762505010" }, { "reference_title": "Update and challenges on proteomics in rice.", "reference_authors": "Komatsu S, Yano H.", "journal": "Proteomics. 2006 Jul;6(14):4057-68.", "reference_pubmed_id": 16786487, "reference_jglobal_id": "201102204445147847" } ], "maintenance_site": "National Institute of Agrobiological Sciences", "original_sites": [ "http:\/\/gene64.dna.affrc.go.jp\/RPD\/" ], "operation_start_date": "2003-01-07", "last_updated_date": "2004-04-01", "upper_level_site": "http:\/\/agrid.dna.affrc.go.jp\/", "whole_data_download": "", "referenced_site": "KOME, NCBI", "list_search": true, "query_search": true, "web_services": false, "webservice_url": "", "user_registration": false }, { "path": "en\/rpsd\/desc.html", "name": "RPSD", "alias": "Rice Protein Structure Database", "dbcat_id": [], "doi": "10.18908\/lsdba.nbdc00749-000", "creators": [ { "creator_name": "Toshimasa Yamazaki", "creator_affiliation": "National Institute of Agrobiological Sciences", "creator_jglobal_id": "", "creator_researchmap_id": "", "creator_orcid": "", "creator_jglobal_jgpn": "", "creator_is_representative": false } ], "categories": [ "Structure Databases - Protein structure" ], "categories_free_style": [], "organisms": [ { "organism_name": "Oryza sativa", "taxonomy_id": 4530 }, { "organism_name": "Sorghum bicolor", "taxonomy_id": 4558 }, { "organism_name": "Zea mays", "taxonomy_id": 4577 }, { "organism_name": "Hordeum vulgare", "taxonomy_id": 4513 }, { "organism_name": "Triticum aestivum", "taxonomy_id": 4565 }, { "organism_name": "Arabidopsis thaliana", "taxonomy_id": 3702 }, { "organism_name": "Glycine max", "taxonomy_id": 3847 } ], "organism_free_style": "", "description": "We have determined the three-dimensional structures of the protein of seven kinds of plants such as rice, and have put together the result and related informations. 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