- Use convenient formats like CSV
- Early majority will publish data if direct benefit
- Concentrate on data integrators not just publishers
- Generic mashup engines solve architectural problems
Talk at Japan Semantic Web Conference 2014 at Keio University in Tokyo. March 7, 2014
RSVP see http://en.wikipedia.org/wiki/Rapid_serial_visual_presentation#cite_note-8
Arabidopsis thaliana is one of the most popular experimental plants. However, only 40% of its genes have at least one experimental Gene Ontology (GO) annotation assigned.
Systematic observation of mutant phenotypes is an important technique for elucidating gene functions. Indeed, several large-scale phenotypic analyses have been performed and have generated phenotypic data sets from many Arabidopsis mutant lines and overexpressing lines, which are freely available online.
Since each Arabidopsis mutant line database uses individual phenotype expression, the differences in the structured term sets used by each database make it difficult to compare data sets and make it impossible to search across databases.
Therefore, we obtained publicly available information for a total of 66,209 Arabidopsis mutant lines, including loss-of-function (RATM and TARAPPER) and gain-of-function (AtFOX and OsFOX) lines, and integrated the phenotype data by mapping the descriptions onto Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) terms. This approach made it possible to manage the four different phenotype databases as one large data set.
Here, we report a publicly accessible web-based database, the RIKEN Arabidopsis Genome Encyclopedia II (RARGE II; http://rarge-v2.psc.riken.jp/), in which all of the data described in this study are included.
Using the database, we demonstrated consistency (in terms of protein function) with a previous study and identified the presumed function of an unknown gene. We provide examples of AT1G21600, which is a subunit in the plastid-encoded RNA polymerase complex, and AT5G56980, which is related to the jasmonic acid signaling pathway.
dropped an announcement on the Linked Open Data mailing in regards to the new Linked Open Data Cloud pictorial, and more importantly, a new research paper covering how the data was crawled.
A new research paper, to be presented at the upcoming ISWC (International Semantic Web Conference) was also part of the announcement.
Naturally, you'll get more out of this with embedded Nanotations using RDF-Turtle notation.
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 http://data.dws.informatik.uni-mannheim.de/lodcloud/2014/ISWC-RDB/ -- Adoption of Linked Data Best Practices in Different Topical Domains
 http://data.dws.informatik.uni-mannheim.de/lodcloud/2014/ISWC-RDB/#toc4 -- Linked Open Data Cloud Pictorial (2014 Edition)
#LinkedData #SemanticWeb #Nanotation #ISWC2014 #ISWC #RDF #BigData #SPARQL #NewSQL #Web30 #LOD
Researchers can control diseases using epigenetics by targeting the modifying enzymes that add or ‘write’ acetyl (Ac) or methyl groups (Me) onto histones, and the molecules that read or the enzymes that reverse these chemical modifications. (Figure 2)
28 February 2014
Minoru Yoshida, Group Director
Chemical Genomics Research Group
RIKEN Center for Sustainable Resource Science
Many diseases occur due to abnormalities in patterns of gene expression caused by epigenetic changes as a result of aging, stress or other factors. To address these changes and advance the field of medicine, Minoru Yoshida is leading research into the control of epigenetics using chemical compounds. Together with colleagues at the Chemical Genetics Laboratory, he is also investigating the activation of ‘dormant genes’ in plants and microorganisms to produce useful substances and to enable the cultivation of crops on arid and high-salinity soils.
Venue: Main Auditorium, Main Office Building Hall, Yokohama campus, Contact: CSRS Plant Immunity Research Group http://www.csrs.riken.jp/en/labs/pirg/
Abstracts Posted on the Facebook site: https://www.facebook.com/ukjapanrhizosphere
9:00 open, 9:30 Opening Remarks
9:40-12:35: Session 1: Symbiotic Interactions
Giles Oldroyd, Makoto Hayashi, Uta Paszkowski, Masayoshi Kawaguchi
13:40-1720: Session 2: Parasitic Interactions
Sophien Kamoun, Ryohei Terauchi, Julie Scholes, Ken Shirasu
9:30-12:30: Session 3: Designing Roots
Ottoline Leyser, Keiko Sugimoto, Veronica Grieneisen, Toru Fujiwara
RIKEN Event Notice (Japanese): http://www.riken.jp/pr/blog/2014/140219_1/
- RIKEN Institute2011 - present2014 April - Center for Sustainable Resource Science Gene Discovery Research Group 環境資源科学研究センター 機能開発研究グループ 2011-2014 Database Integration Unit Advanced Center for Computing and Communication, (ACCC) 理化学研究所 情報基盤センター 統合データベース特別ユニット (formerly BASE: Bioinformatics And Systems Engineering division)
- Platform One - DJG JapanP.R., Marketing, 2011
- Victor Company of Japan, Ltd., JVC
- Crimson Tech
- Chedd Angier Productions
April 2014- Center for Sustainable Resource Science
International and Public Relations
The RIKEN Center for Sustainable Resource Science’s mission is to enhance the use of biomaterials based on an understanding of the diversity of both biological and chemical functions, and contributing to the society by developing production technologies that are gentle on the natural world and promote a sustainable society.
Here are posts from CSRS and related fields:
2011- March 2014 - RIKEN Integrated Database Unit/ACCC, Bioinformatics and Systems Engineering Division
Scientific research modelling including collaboration, innovation and business, including Semantic Web and Linking Open Data.
Designing Linked Open Data and collaboration maps, analysis and assessment tools.
Scientific editing and writing contribution to scientific papers for Journals including Nucleic Acids Research, and Books including Methods in Enzymology, as well as for presentations, documentation, web publications, communications, press releases and annual report.
Managing Global Marketing and Public Relations. 17 year award winning career for headquarters in Japan of electronics manufacturer JVC; prior 5 years selling to and servicing business and retail customers, plus earlier 6 year journalism editing documentary television programs for network and public TV.
- Robert Earley
The KAUST Catalysis Center: A Hub for Global Energy Research - King Abdu...
“We are trying to become a hub for global energy research,” says Dr. Jean-Marie Basset, Director of the KAUST Catalysis Center (KCC). Dr. Ba
RIKEN CSRS - Center for Sustainable Resource Science
David Gifford's insight: The RIKEN CSRS Center for Sustainable Resource Science’s mission is to enhance the use of biomaterials based on an
Integrated Analysis of Seaweed Components Toward field analysis of agric...
David Gifford's insight: Integrated Analytical Technology for Complex Systems of Organic and Inorganic Mixtures in Seaweed Toward field anal
King Abdullah University of Science and Technology
An international, graduate-level research university dedicated to inspiring a new age of scientific achievement