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Session "Data sharing in life sciences" in JOSS2018 on Jun. 19, 2018

NBDC will organize the session "Data sharing in life sciences" in Japan Open Science Summit 2018.

  • Date: Jun. 19 (Tue), 2018, 11:15 to 12:45
  • Venue: National Center of Sciences (Chiyoda-ku, Tokyo)

Website: https://events.biosciencedbc.jp/sympo/joss2018
(Japanese text only.)

【Hands-on seminar on NGS】 Release of the seminar report

NBDC has held the “hands-on seminar on NGS” from Aug. 28th to Sep 1st, 2017 at the Univ. of Tokyo, and its report has been released as below.

https://biosciencedbc.jp/gadget/human/h29_ngs_report.pdf
*only in Japanese

Seminar materials and videos are available at the following webpage.
2017 hands-on seminar on NGS
https://biosciencedbc.jp/human/human-resources/workshop/h29
*only in Japanese

【Event】"International Proteogenome Workshop 2018" May 19th, 2018(Kyoto)

"International Proteogenome Workshop 2018" will be held at Fujita Memorial Hall, Kyoto University, Kyoto.
In this workshop, current status of cancer proteogenomics research and bioinformatics for proteogenomics in Asia and Oceania regions will be discussed with members from ProteomeXchange, an international consortium to which jPOST joins and from International Cancer Proteogenome Consortium.
This workshop is a satellite event of Mass Spectrometry and Proteomics 2018 (MSP2018).

Date: May 19th, 2018
Venue: Fujita Memorial Hall, Kyoto University
Registration fee: Free (pre-registration required)

Detail & Registration: http://seizai.pharm.kyoto-u.ac.jp/ipgw2018/

Schedule (tentative):
 9:50-10:00 Opening
10:00-12:30 Current status of Cancer Protegenomics in Asia Oceania regions
14:00-16:00 Current status of Bioinformatics for Proteogenomics
16:00-17:00 Discussion

Organizer: Mass Spectrometry and Proteomics 2018 (MSP2018)
Co-organizer: Kyoto University (SPIRITS), JST-NBDC, EMBL-EBI and JPrOS


Related Projects
Database Integration Coordination Program
"Development of functional and interactive database for proteomics"
Prof. Yasushi Ishihama, Graduate School of Pharmaceutical Sciences, Kyoto University

[LSDB Cross Search] 2 databases have been added to Life Science Database Cross Search

Following 2 databases have been added to the search index of Life Science Database Cross Search.
  • [Mouse Basement Membrane Bodymap[Archive]]:The Mouse Basement Membrane Bodymap is a visual database of extracellular protein localization. The database consists of high-resolution images of hundreds of mouse embryos showing the localization of dozens of extracellular matrix and basement membrane proteins. Images were obtained by IHC and users can zoom and display images using the built-in Bodymap applet.
  • [Oligonucleic Acid Drug Database[Archive]]:Oligonucleic Acid Drug Database is focused on nucleic acid drugs known as biopharmaceuticals and displayed approval drugs and information on three phases of clinical trial stage. It contains clinical information of nucleic acid drugs which based from pharmaceutical companies and clinical information sites (https://clinicaltrials.gov/, https://www.clinicaltrialsregister.eu/). This database also provides information on nucleic acid drugs that are being considered for future practical use (such as target diseases and related protein information).

"AJACS training seminar for TogoDatabase" in FY2018 : Site & Schedule has been decided.

Site and Schedule of AJACS is as follows:

  • Niigata University (Jun. 26-27th 2018)
  • National Institute for Materials Science (NIMS) (Jul. 10th 2018)
  • Japan Science and Technology Agency (JST) (Aug. 29th 2018)
  • Sapporo Medical University (Nov. 9th 2018)
  • Aichi Cancer Center Research Institute (Dec. 5th 2018)
  • Kyowa Hakko Kirin Co., Ltd. (Dec. 14th 2018)
  • Japan Science and Technology Agency (JST) (Jan. 28th 2019)
  • *Training seminar will be performed in Japanese.

    [LSDB Cross Search] 2 databases have been added to Life Science Database Cross Search

    Following 2 databases have been added to the search index of Life Science Database Cross Search.
    • [JASPAR]:JASPAR is a database of transcription factor binding sites. The database contains experimentally verified promoter and other gene expression regulation sites represented as sequence logos indicating critical nucleotides for recognition and binding by a given factor. Dozens of species are represented, and users can search by protein, motif, species, or protein structure family.
    • jPOST repository metadata:This is a proteomic database named jPOST to integrate proteome information including post-translational modifications and absolute protein abundance, acquired by multiple projects and institutions. Currently, only the jPOST repository part is open for researchers to deposit their proteome datasets (May, 2016).

    The report about LSDB Archive has posted in Research Data at Springer Nature.

    The report about Life Science Database Archive (LSDB Archive) , "What is involved in archiving life science datasets?" written by Shigeru Yatsuzuka, an NBDC researcher has posted in Research Data at Springer Nature.

    [LSDB Cross Search] 6 databases have been added to Life Science Database Cross Search

    Following 6 databases have been added to the search index of Life Science Database Cross Search.
    • [Pt_spiderBASE]: Pt_spiderBASE is a database for ESTs of the spider Parasteatoda tepidariorum, a model arthropod to study developmental biology, comparative embryology and evolutionary development.
    • [FAIRsharing.org]: This site for FAIRsharing.org is a registry site intended to promote data-sharing in the sciences, such as life, environmental, and biomedical sciences. It consists of "Standards", "Databases", "Policies", and "Collections" sections that catalog both in-house and crowd-sourced curated descriptions. The Biosharing.org (https: //biosharing.org) has been developed into the FAIRsharing.org in July, 2017.
    • [NBDC RDF Portal]: This is a portal site that integrates life science databases in RDF format. The portal was jointly developed by the JST National Bioscience Database Center (NBDC) and the Database Center for Life Science (DBCLS), Research Organization of Information and Systems. The DBCLS formulated guidelines for the construction of high quality RDF data (http://wiki.lifesciencedb.jp/mw/RDFizingDatabaseGuideline), and publishes only those data that meet a minimum level of quality for a highly reliable database. Users can browse the summaries of the data for the various databases. Data downloads and SPARQL (standard query language for RDF format data) searches are also possible.
    • [GlyTouCan]: GlyTouCan is an international repository of glycan structures. This database contains uncurated glycan structures ranging in resolution from monosaccharide composition to fully defined structures, as long as there are no inconsistencies in the structure. The database allows users to search by text, graphic input or motif, and browse using motif-list or glycan-list.

    [LSDB Cross Search] 3 databases have been added to Life Science Database Cross Search

    Following 3 databases have been added to the search index of Life Science Database Cross Search.
    • PHDB(timeseriesdb, morphologydb, PHML Model Database)
    • PHDB is an integrated database for human physiome and systems biology researches. It contains three databases:
      1) PHML Model Database, which stores a number of modules representing biological/physiological functions which are formulated by mathematical equations to describe dynamic changes of states. The models in the database are written in an XML format called "Physiological Hierachy ML (PHML)"
      2) Morphology Database, which provides datasets representing morphometric models of biological organs.
      3)Timeseries database, which includes dynamic data obtained from physiological and numerical experiments.

    Exhibition at Science Agora 2017(Nov. 25-26 at Telecom Center Building,Odaiba Tokyo).

    NBDC will exhibit the booth at the Science Agora 2017. We will introduce the activities, services and tools of NBDC. Please come and visit our booth.

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