Pupil Platform Pupil Platform on Neuroinformatics Database: XooNIps on Neuroinformatics Database: XooNIps Kazutsuna YAMAJI, Hiroyuki SAKAI Yoshihiro OKUMURA, Shiro USUI Neuroinformatics Lab., RIKEN Brain Science Institute 1. Development of Neuroinformatics Base Platform System: XooNIps 2. Application of XooNIps to Pupil Platform
Neuroinformatics Rapid accumulation of fragmented knowledge Narrow specialization and diversification of fields Problems in understanding the research targets (organs) as a system Solution! Neuroinformatics combines neuroscience and informatics research to develop and apply advanced tools and approaches essential for a major advancement in understanding the structure and function of the brain.
Background: Visiome Platform Neuroinformatics Research in Vision project (PI: S. Usui, 1999-2003) developed the neuroinformatics database in vision: Visiome Platform . Digital resources in Visiome Platform Model Data Tool Stimulus Simulator Presentation Reference Book URL Comment Binder Memo http://platform.visiome.org
Purpose Pioneering Variety of research levels and fields future Visiome Retina Eye Mov Auditory Platform Platform Platform Platform A customizable base database system is necessary Objective Objective 1. Develop the customizable base platform system: XooNIps 2. Apply the system to the PUPIL research
XooNIps: Basic Concept • Developed as an extended module of XOOPS • Accessible by web browser and optionally OS native application • Runs on the Linux and other POSIX based operating systems • Available as open source software http://sourceforge.jp/projects/xoonips/ Contents management system XOOPS Web browser OS native appli User I nterface NI Database Access from XOOPS General XooNI ps XooNIps Module Module Module Abstract XOOPS Layer PHP Apache MySQL RDBMS NI database Access from XOOPS W eb Application General Module
XooNIps: Submission Procedure Submission Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index No OK ? Data are … categorized according to the item type (expandable). Yes systematically stored in a tree-structure keyword index. Reviewing process
XooNIps: Submission Procedure Submission Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index No OK ? Yes Reviewing process
XooNIps: Submission Procedure Submission Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index No OK ? Yes Reviewing process
XooNIps: Submission Procedure Submission Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index No OK ? Yes Reviewing process
XooNIps: Reviewing Procedure Review Login as Moderator Certify Public Items Check by Reviewer No Accept ? Yes Open in Public Modify by Contributor Re-submission
XooNIps: Reviewing Procedure Review Login as Moderator Certify Public Items Check by Reviewer No Accept ? Yes Open in Public Modify by Contributor Re-submission
XooNIps: Other Key Features � User Authority Hierarchical relation Guest Registered User Group Moderator Moderator System Admin • Browse • Edit Account • Certify Group Member • Certify User • Registration • Edit Private Index Tree • Certify Group Item • Certify Group • Contribute New Item • Edit Group Index Tree • Certify Public Item • Edit Public Index Tree • Import item � Private, Group, Public Area � Registered users obtain a private area They can freely create and modify their own private index tree � Groups also can be created by applicants of registered users Private Group Public � Metadata Communication DB3 DB2 � The metadata from a certain database will be propagated to other XooNIps database DB1 � Each XooNIps database can harvest the metadata from the others � This allows the keyword search across the XooNIps database DB4
Pupil Platform: How to Construct 1. Create Keyword Index Tree • Not easy to develop the ontology of a certain field However • Handbook written by Dr. Loewenfeld can be used Anatomy and Physiology • The Iris • Spontaneous Pupillary… 2. Prepare Initial Set of Items • The Light Reflex • Reaction to Darkness • … • Literature Information Special Fields in Physiology • Mathematical Approaches • Mathematical Model • Psychology • Experimental Data • Pharmacology Methods • Conference Information Symptomatology Sign in Various Diseases • etc.
Pupil Platform: Literatures Utilize extensive bibliography of the handbook Easy to input Just input the PubMed ID or ISBN and press Complete button Pupil Literature database • Literature information associate with the keyword index allows users to keep track of progress in pupil research. • It provide a useful overview to students and beginners. • Not only the directory search based on index tree, but also keyword search provides a good selection.
Pupil Platform: Mathematical Models Model study serves as a framework for the comprehension of pupil control system 1957 : Stark 1967 : Dennison History of modeling 1971 : Semmlow Serial elastic component 1972 : Hansmann Viscous component 1974 : Usui 1982 : Usui Contractile Parallel 1983 : Sun component elastic component 1983 : Krenz 1985 : Krenz 1994 : Hirata 1998 : Sun Various mathematical models of the pupil have been developed
Pupil Platform: Experimental Data � Pupillary Light Reflex Range Nonlinearity � Psychophysics � Ergonomics � Clinical � Physiology & Pharmacology Length-Tension Relationship Peptide Mediated Innervations 2.5 * Sphincter Dilator Sphincter Dilator Tension [g] Amplitude [%] Total 0 0.5 1 1.5 2 2 5 1 2 1 5 100 100 * Passive 0 1 0 1 * 7 5 5 7 50 50 d ] % [ e u i l p m A t 0 5 A m p l i t u d [ % ] e 0 5 Active 5 2 5 2 0 0 0 0 Cont SRF CGRP VIP Cont SRF CGRP VIP 5 10 15 2 3 4 5 6 7 Length [mm] Length [mm] NPY GAL SP PACAP NPY GAL SP PACAP
Pupil Platform: Clinical Data (Objective Monitoring Indices) � Clinical Testing : diagnostic data � Autonomic Monitoring Monitoring Methods with Data at Micro Gravitational Experiments � Sleepiness & Awareness Open-angle glaucoma Pigmentary retinal degeneration � Pupil Perimetry Subjective Perimetry (Humphrey) Right Left Right Left Data from Yoshitomi Pupil Perimetry & Ishikawa
Pupil Platform: Information � Tools and Equipments Review by Dr. Wilhelm is very helpful � News � New Paper or Book Publication � Conference Information (with Dr. Howarth) � Forum � Clinical Forum � Physiological and Pharmacological Forum � Psychophysical Forum � Mathematical Model Forum � … � Links
Conclusions � Neuroinformatics Japan Center will set up the database server in the near future. After the initial testing � We would like to start the discussion for determining the site policy and index tree. � Prepare initial set of items. We need collaborators to develop the pupil platform Wish to show you the PUPIL Platform in Tokyo 2007 !!
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