- A monthly newsletter which supports information integration -

BioResource Newsletter  Vol.1  No.1

 Introduction :

 Newsletter Publication
-Our monthly newsletter has started !

 News from the Resource
    Center No.1:

 Information via the Internet

 Hot news from abroad
    No.1 No.2 :

 (1)POC in-person meeting

 (2)Visiting ZFIN at Uni. of Oregon

 Information Technology vol.1:

 What is an Access Log ?


No.1 2005/01/31  

Newsletter Publication
Our monthly newsletter has started !
  The Center for Genetic Resources Information, National Institute of Genetics is an information hub for accumulating, providing and publicizing information related to bioresource (genetic resources). Currently, the databases and information released through the internet are categorized by species. However, in an effort to provide a central location for information integration unbounded by species categorization, we have started publishing this monthly newsletter. We will be introducing current hot topics and undertakings happening in the local and international bioresource scene.
   The bioresource mentioned above is defined tentatively as genetic materials such as experimental animals and plants, microbe, cell and DNA but is not unrelated to biodiversity and environmental conservation issues. This newsletter will also be covering topics related to these issues, in hopes of playing a part to build the "human", "object" and "information" network.
Download the PDF version of this newsletter here.

News from the Resource Center
Information via the Internet
This center comprehensively researches public websites related to bioresource and provide such information to the public.
   WGR (World-wide Genetic Resources) keeps a record of over 400 URLs, enabling easy access to many bioresource related worldwide websites. WGR allows you to search for information with species names and any keyword. Moreover, WGR has an online registration system that allows users to recommend websites of their choice.
  JGR(Genetic Resources in Japan)which is a branch of the WGR, holds information to all the major bioresource related Japanese websites.
  We also construct databases for each species (Shigen Databases) and manage a website detailing the progress of the National BioResource Project (NBRP)
  We have also released a test version of an Integrated Search Site for BioResource (BioResource World : BRW). We hope to develop a system that will be fully utilized by the users.

Hot news from abroad (1)
POC in-person meeting
  A closed meeting was held during the Plant and Animal Genome XIII Conference (San Diego, Jan.15-19) and construction of the Plant Ontology(PO) and preparations for the 1st International Biocurator Meeting were discussed. I attended the meeting as a representative for Oryzabase, a database for rice. It was focused on the construction of the plant ontology. Although ontology has not yet been given much attention in Japan, databases of model organisms (FlyBase for Drosophila, WormBase for C.elegans, MGI for mouse, RGD for rat, ZFIN for Zebrafish, TAIR for Arabidopsis, Gramene for rice, MaizeGDB for maize, SGD for yeast) will play a central role in developing a common set of controlled vocabulary (ontology) terms to describe specific expression of genes and phenotype.
   The Plant Ontology Consortium (POC) will be categorizing the anatomical ontology and growth stage ontology construction into Monocot (rice, maize and wheat) and Dicot (arabidopsis, soybean, medicago, solaneceae and poplar). We will keep you updated with the details of the 1st International Biocurator Meeting as soon as possible.
(Author: Yukiko Yamazaki)

Hot News from abroad (2)
Visiting ZFIN at University of Oregon
  A 20 min drive from Eugene Airport heading south east, soon after passing down town is the University of Oregon (photo 1) on your right. On the other side of Franklin Blvd. (Route 99) are the resource center (ZIRC: photo 2) and the information center (ZFIN: photo 3) for Zebrafish. The Zebrafish Information Network (ZFIN) is housed on "Riverfront Research Park", a private building surrounded by a rich natural environment overlooking Alton Baker Park which stretches alongside Willamette River.
   The purpose for this visit is to learn about the Phenotype and Trait Ontology (PATO) implemented by ZFIN and ZFIN's database model, which will be useful when constructing the Japanese database for Medaka.
   ZFIN has a total of 17 members; half in charge of developing the database while the other half are scientific curators. Public server maintenance and network administration are carried out by the computer center which is located on the main campus. I was surprised to learn that as many as half of the team members are assigned to carry out scientific curation, which entails extracting pertinent information from literatures and adding them to the database. I credit this to be the reason that ZFIN is considered as a reliable database. ZFIN was also the first to implement PATO, conducting it through trial and error.
   The fact that ontology is a linguistic hurdle for Japanese and that it is focused mainly on western countries, has made it necessary for us to consider the manner in which Japan should tackle it. Hands-on manpower with a certain level of expertise, time and a deep understanding of the English language is necessary for ontology to be considered at the developmental stage. Although obtaining such manpower may seem to be a problem, this matter cannot be ignored. As an information center, we intend to continuously supply information concerning international activities.

Photo 1

Photo 2:ZIRC

Photo 3:ZFIN

(Author: Yukiko Yamazaki)

Information Technology        Vol. 1
"What is an Access Log?"
  As we browse through websites on the internet, we are actually leaving behind our footprints on the server every time we access the pages. The server keeps track of every visitor and stores the information in the access log. This access log is very important to us as we strive to improve the contents of our website for full utilization.
   We can derive a lot of information from this access log; for example, users tend to view pages with certain information, or users visit mostly on weekdays in the daytime and less at night, or that most users are Mac users.
   In this articles series on access log, I will begin by introducing what an access log is, followed by useful tools to analyze access logs and moving on to other related topics such as what to interpret from the analysis results and how to improve the access to your website.
Genetic Informatics Laboratory, Center for Genetic Resource Information

( translated by Sharoh Yip )

Editor's notes :  We somehow managed to publish the first volume in January (although on the last day) as planned. Being a new publication, we would deeply appreciate your comments and suggestions as they would be invaluable to help us achieve our potential as an information newsletter.

Contact : Yata 1111, Mishima, Shizuoka 411-8640, JAPAN
Center for Genetic Resources Information, National Institute of Genetics


055-981-6885 (Yamazaki)