Pupil Platform Pupil Platform on Neuroinformatics Database: XooNIps - - PowerPoint PPT Presentation

Pupil Platform

• n Neuroinformatics Database: XooNIps

Pupil Platform

• n 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. Model Data Tool Stimulus Simulator Presentation Reference Book URL Comment Binder Memo Digital resources in Visiome Platform

http://platform.visiome.org

Purpose

Pioneering Variety of research levels and fields

Visiome Platform Retina Platform Eye Mov Platform Auditory Platform future

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

MySQL XOOPS

XooNI ps Module

Web browser

XOOPS General Module

Access from XooNIps Module

RDBMS

NI database

W eb Application User I nterface

PHP Apache

Access from XOOPS General Module

Abstract Layer

OS native appli

NI Database

XooNIps: Submission Procedure

Submission

Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index OK ?

Yes No Data are … categorized according to the item type (expandable). 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 OK ?

Yes No

Reviewing process

XooNIps: Submission Procedure

Submission

Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index OK ?

Yes No

Reviewing process

XooNIps: Submission Procedure

Submission

Login Contribute New Item Select Item Type Fill Metadata Select Keyword Index OK ?

Yes No

Reviewing process

XooNIps: Reviewing Procedure

Review

Login as Moderator Certify Public Items Accept ?

Open in Public

Yes No

Check by Reviewer Modify by Contributor Re-submission

XooNIps: Reviewing Procedure

Review

Login as Moderator Certify Public Items Accept ?

Open in Public

Yes No

Re-submission Check by Reviewer Modify by Contributor

XooNIps: Other Key Features

Guest Registered User

• Browse
• Registration
• Edit Account
• Edit Private Index Tree
• Contribute New Item
• Certify Group Member
• Certify Group Item
• Edit Group Index Tree
• Certify User
• Certify Group
• Certify Public Item
• Edit Public Index Tree
• Import item

Group Moderator Moderator System Admin

Hierarchical relation 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

Metadata Communication

The metadata from a certain database will be propagated to

• ther XooNIps database

Each XooNIps database can harvest the metadata from the others This allows the keyword search across the XooNIps database

User Authority

Private Group Public DB1 DB2 DB3 DB4

Pupil Platform: How to Construct

• 1. Create Keyword Index Tree
• Not easy to develop the ontology of a certain field
• Handbook written by Dr. Loewenfeld can be used
• 2. Prepare Initial Set of Items
• Literature Information
• Mathematical Model
• Experimental Data
• Conference Information
• etc.

However

Anatomy and Physiology

• The Iris
• Spontaneous Pupillary…
• The Light Reflex
• Reaction to Darkness
• …

Special Fields in Physiology

• Mathematical Approaches
• Psychology
• Pharmacology

Methods Symptomatology Sign in Various Diseases

Pupil Platform: Literatures

Utilize extensive bibliography of the handbook Easy to input

Just input the PubMed ID or ISBN and press Complete button

• 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 Literature database

Pupil Platform: Mathematical Models

Model study serves as a framework for the comprehension of pupil control system

Various mathematical models of the pupil have been developed

1957 : Stark 1967 : Dennison 1971 : Semmlow 1972 : Hansmann 1974 : Usui 1982 : Usui 1983 : Sun 1983 : Krenz 1985 : Krenz 1994 : Hirata 1998 : Sun

History of modeling

Serial elastic component Contractile component Parallel elastic component Viscous component

Pupil Platform: Experimental Data

Pupillary Light Reflex Psychophysics Ergonomics Clinical Physiology & Pharmacology

Range Nonlinearity

5 10 15 Length [mm] 0 0.5 1 1.5 2 2.5 Tension [g] 2 3 4 5 6 7 Length [mm] Total Active Passive Sphincter Dilator

Length-Tension Relationship

*

Cont NPY SRF GAL CGRP SP VIP PACAP

Cont NPY SRF GAL CGRP SP VIP PACAP

Sphincter Dilator * * 100 Amplitude [%] 50 100 50

Peptide Mediated Innervations

Pupil Platform: Clinical Data

(Objective Monitoring Indices)

Clinical Testing : diagnostic data Autonomic Monitoring Sleepiness & Awareness Pupil Perimetry

Monitoring Methods with Data at Micro Gravitational Experiments

Open-angle glaucoma Pigmentary retinal degeneration Left Right Left Right

Subjective Perimetry (Humphrey) Pupil Perimetry

Data from Yoshitomi & 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.

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

After the initial testing

Wish to show you the PUPIL Platform in Tokyo 2007 !!