National Bioscience database center: the activity for integration and usage promotion of life science databases in Japan
Creators: name: Yatsuzuka, Shigeru
name: Jun-Ichi Onami
name: Nobusada, Tomoe
name: Miyazaki, Atsuko
name: Hatanaka, Hideki
name: Toshihisa Takagi
Publisher: name: F1000Research
Year: 2016

description: National Bioscience Database Center (NBDC; http://biosciencedbc.jp/en/) was founded in 2011, as a core institution for the integration of life science databases in Japan. We took over our mission from Integrated Database Project (2006-2010). For integration and usage promotion of life science databases scattered among many research institutes, we have conducted the following activities:<br>- Strategic planning for database research and development<br>- Enhancement of life science databases<br>- Sharing research data<br>- International cooperation<br>And we have released, expanded and sophisticated the following services:<br><br>Integbio Database Catalog (http://integbio.jp/dbcatalog/?lang=en):<br>The catalog includes basic information of greater part of life science databases in Japan and major life science databases around the world. It consists of URL, database maintenance site, category, organism, operational status, and so on. We curate those information according to our consistent curation policy. Now we prepare to release the RDF formatted version of the catalog.<br><br>Life Science Database Cross Search (http://biosciencedbc.jp/dbsearch/index.php?lang=en):<br>Life Science Database Cross Search is a searching service across more than 160 databases which include literatures and patent publications. This system is composed of a lot of servers in 5 organizations of 4 ministries. To realize distributed search among remote organization, we adopted full text search engine, Hyper estraier. Now, we started changing this engine to "Elasticsearch" so as to resolve growing index data. Curators play an important role in adding a new database to this system. Curators investigate the crawling region in each database, predict the URIs of each entry, and classify attribute information. So, cross search curators are needed to have two backgrounds, information technology and life science. We constructed a reasonable workflow for advanced curation of cross search, and we achieved to add new database tenfold faster than before. Now, user can also search "Deep-web" data (even Google cannot find) from this cross search system. This system can be used as an infrastructure of comprehensive database search.<br><br>Life Science Database Archive (http://dbarchive.biosciencedbc.jp/index-e.html):<br>The archive collects life science databases scattered among many research institutes. We will stably keep and maintain them over the long term. To help users to understand databases, we provide detailed metadata of databases and curate them. Each metadata links to the information of researchers (ORCID, researchmap), articles (PubMed, J-GLOBAL) and funds (Life science projects in Japan, J-GLOBAL). To promote reuse, databases in the archive are published under Creative Commons Attribution-Share Alike (CC BY-SA) in principle.<br><br>Integrated Search:<br>Connecting databases organically enables users to search them with complicated conditions. To realize it:<br>- We are RDFizing Integbio Database Catalog and databases in Life Science Database Archive.<br>- We have released RDF portal (http://integbio.jp/rdf/). It collects life science data in RDF format.<br>- We are developing tools for RDF search in collaboration with Database Center for Life Science (DBCLS; http://dbcls.rois.ac.jp/en/)<br>