Black Skin Dermatology Online : Contribution to teledermatology

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Black Skin Dermatology Online :Contribution to teledermatology

Prime Minister's office Federal office for scientific, technical and cultural affairs

Multiannual information society support programme 2001-2008

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Contents

General objective and partnership Project management Feasibility study Content acquisition Platform Prototype Demo Second phase

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General objective

To establish an experimental web platform of teledermatology on black skin, multilingual and open, integrating image and voice recognition technologies.

Phase 1 Development of a prototype Build a representative corpus in dermatology on

black skin Phase 2

Development of telematics services related to the database.

Evaluation of the prototype, including its usability

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Partnership

Five partners Contents and medical expertise Definition of the functionalities of the platform Guarantee scientific reliability of the database Testing

Centre hospitalier régional de Kaolack (Sénégal) Hôpital Erasme Institut de médecine tropicale Prince Léopold Universiteit Gent Universiteit Antwerpen (UIA)

A coordinator Realize data-processing analysis and developments Plan partner ’s action in the study of the needs, the functional

analysis and the evaluation of the prototype

Université Libre de Bruxelles

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Advisory committee

Dermatologists Expert in voice technology Expert in information technology

Feedback on various issues

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Project management (1)

Successful follow-up of tasks during the project State of art (months 1-6) Study of needs (months 1-6) Feasibility study (months 6-12) Development of a prototype (months 12-24) Content acquisition and alpha-tests (months 1-

24) Project management (months 1-24)

Supervision of four activity reports Creation and regular updates of a Web site

(http://www.bib.ulb.ac.be/RDIB/Blackskin/index.htm)

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Project management (2)

Organization of twelve working meetings among partners

Organization of two advisory committee meetings

Conclusion of a subcontract with the expert in vocal recognition for a state of the art and a feasibility study

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Feasibility study

Covers: Study of needs Metadata of the images Software overview and choices

To efficiently store and retrieve the images To deliver content to the end-user

Voice recognition

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> Feasibility Study Study of needs (1)

Phase 1 : Online image database

Comprehensive description of images Image submission through Web interface,

with appropriate authentication mechanisms Interoperable Data protection mechanisms Integration of voice recognition technologies,

if feasible Content management system Free and open-source software

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> Feasibility Study Study of needs (2)

Phase 2 : Image database

Continuous development of image collections Possibility to add comments on already existing images Collection export onto self-contained CD-ROM for offline

browsing Prototype evaluation Added-value services in the CMS:

Expert’s forum « Ask a specialist » service Teaching support (didactic quizzes, integration in e-

courses, …) Technological watch Collaboration with other existing projects in

telemedecine and teledermatology

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> Feasibility Study

Metadata of the images (1)

based on other existing atlases Dermis/DOIA (Dermatology Online atlases) Dermatology image bank (“Knowledge

weavers” University of Utah) Knowledge Lumen University of Chicago Dermatlas (Johns Hopkins University) Atlas Tunisien de Dermatologie online ULB image library

MS-Access prototype to determine required fields

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> Feasibility Study

Metadata of the images (2)

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> Feasibility Study

Metadata of the images (3)

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> Feasibility Study

Metadata of the images (4)

Thesaurus Study of MESH, ICD-10, CISP-2, UMLS Based on ICD-10 (WHO’s International

Classification of the Diseases): 10th version of the nomenclature created in 1893.

Descriptive structure of pathologies in 5 levels. Contains more than 2000 terms coming from all

the chapters from the standard. Translation in NL, FR, EN and DE. Interoperability with other systems that use

PubMed classification (Dermis, Dermatlas, …) and with the CISP-2, UMLS and MESH standards.

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> Feasibility Study

Metadata of the images (5)

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> Feasibility Study

Software

Content management system Digital library software

Characteristics Open-source Interoperable Maintainable

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> Feasibility study

Content Management System (1)

Definition“A content management system (CMS) supports the creation, management, distribution, publishing, and discovery of corporate information. It covers the complete lifecycle of the pages on your site, from providing simple tools to create the content, through to publishing, and finally to archiving.It also provides the ability to manage the structure of the site, the appearance of the published pages, and the navigation provided to the users. […]”

(http://www.steptwo.com.au/papers/kmc_what/)

Lots of competitors: 350+ CMS on http://www.cmsreview.com

Requirements Open-source Localization multilingual Plug in API

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> Feasibility study Content Management System (2)

Comparison of 4 CMS: Magnolia/OpenCMS/Mambo/Typo3

Our Choice: Typo3 Rapid prototyping Hundreds of available plug-ins

Forum News management News letter Quiz

Active community (+3000 registered sites) Rich documentation

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> Feasibility study Content Management System (3)

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> Feasibility Study

Image Database (1)

Dspace Java Workflow Management Indexed fields are hard-coded

Greenstone 2.52 lots of desirable features lack of powerful communication interface for our CMS building process requires the whole collection to be rebuilt

each time Home-made solution

blackskin specific cost seriously investigated before announcement of…

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> Feasibility Study

Image Database (2)

Greenstone 3 complete redesign of Greenstone 2 structured

as a network of independent modules that communicate with XML

collections are backward compatible written in Java → servlet new incremental collection building process

quicker more flexible

SOAP interface still alpha release

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> Feasibility Study

Image Database (3)

Interoperability Major concern SOAP interface Open Archives Initiative Z39.50 Seamless integration in existing digital library systems

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> Feasibility Study

Voice Recognition (1)

Experts recommended to adopt an already existing software solution rather than a home-made one. Cost Integration problems

2 widely available software solutions were benchmarked IBM ViaVoice vs Dragon Naturally Speaking

Dragon was available in all 3 languages required (FR, NL & EN)

Dragon proved to be the clearest and the most user friendly.

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> Feasibility Study

Voice Recognition (2)

Experts’ general conclusions: Integration of voice recognition techniques

in Blackskin not as easy as it first seemed. Voice recognition is definitely not

appropriate to fill in forms such as those requested by Blackskin Much slower encoding Discouragement of users

But we wanted to confirm the experts’ conclusions by conducting empirical tests.

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> Feasibility Study

Legal aspects

No specific Belgian legal directives for image databases but: Law of 8 december 1992 with respect to “the protection

of privacy in processing data of a person”. Ordre des Médecins: «Recommandations relatives à la

tenue de bases de données médicales contenant des données nominatives ou identifiables» http://www.ordomedic.be/web-Fr/fr/a97/a097008f.htm

Blackskin does not contain any personal information of the patients (except for age and gender).

Draft of license agreement in which submitter gives away all his rights over the images to Blackskin

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Content acquisition

Scanning of existing slides 400 slides selected and scanned from which 300 are completely described and

available in the prototype

Picture acquisition in Senegal 1800 pictures from which 600 are suitable for inclusion in the

prototype 300 completely described and ready for upload

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Prototype Development

Software architecture Web site structure Typo3 plugin Greenstone3 configuration Backend

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> Prototype development

Software Architecture

Open-source components Typo3 plug-in and GSDL3 backend

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> Prototype development

Web site structure (1)

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> Prototype development

Web site structure (2)

Home Welcome message Short presentation # of pictures

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> Prototype development

Web site structure (3)

Search pages Browsing tools

ICD10 Description Body site

(Homunculus) (New Images) Site search

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> Prototype development

Web site structure (4)

Information about: Project ICD10 classification Staff Contributors Disclaimer

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> Prototype development

Web site structure (5)

Tools Submit an image Contact

maintainers Forums Newsletter

subscription Links page

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> Prototype development

Web site structure (6)

Teaching Ask a specialist Pedagogic cases

and quizzes Bibliography CD-ROM order

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> Prototype development

Web site structure (7)

Help Technical help FAQ Sitemap

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> Prototype development

Typo3 plug-in (1)

Handles communication between Typo3 and Greenstone3 through SOAP calls

Fully configurable Configuration files TypoScript

Problem Lack of documentation about available

messages and options Solution: use of tcpTunnelGui and demo

collection to analyze messages

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> Prototype development

Typo3 plug-in (2)

GSDL3 can query remote installations

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> Prototype development

Typo3 plug-in (3)

Features: Search a given index Browse hierarchical classifiers Multilingual support Look and feel can be adjusted using CSS

Flexible but could be more generic

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> Prototype development

Greenstone 3 (1)

Using latest version from CVS Problem

Lack of up-to-date documentation for installation

Alpha software Solution: Live with it!

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> Prototype development

Greenstone 3 (2)

Collection configuration One collection for each partner

Inherent to GSDL building process One supercollection Indexes for searching

For each searchable field Hierarchical classifiers

Body site Used by homunculus

Contributor Diagnostic Description ICD10

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> Prototype development

Greenstone 3 (3)

1 supercollection 1 collection / partner

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> Prototype development

Configuration files (1)

Used to populate drop down menus and to configure classifiers

Automatically generated from Excel files Easily maintainable

Depending on their nature, generated by: Java application XSLT

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> Prototype development

Configuration files (2)

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> Prototype development

Configuration files (3)

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> Prototype development

Configuration files (4)

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> Prototype development

Configuration files (5)

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> Prototype development

Backend (1)

New user-friendly GSDL3 backend J2EE servlets and JSP

Motivation 2 existing means Collector

Web-based interface Too limited

Greenstone Librarian Interface Java application Effectively allows users to upload, modify and build

collections

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> Prototype development

Backend (2)

GLI screenshot

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> Prototype development

Backend (3)

Motivation Why? Must be run on same computer

Solution: applet but... not always available No preview mechanism

need for a second application Difficult speech recognition integration Graphical layout harder to modify than

HTML

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> Prototype development

Backend (4)

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> Prototype development

Backend (5)

Features Authentication Upload Metadata Enriching Image preview Modify & delete Collection building Experimental speech recognition interface Multilingual

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> Prototype development

Backend (6)

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> Prototype development

Backend (7)

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> Prototype development

Backend (8)

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> Prototype development

Backend (9)

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> Prototype development

Backend (10)

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> Prototype development

Backend (11)

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> Prototype development

Collection building (1)

We want more than just display a picture Need to show metadata too Solution: create a folder with HTML file

Collection building process Collection preparation

Create folder for each jpg file Copy thumbnail created at upload time Use template file to generate HTML with values from

metadata file more flexibility

Then, we can use the regular GSDL building mechanisms

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> Prototype development

Collection building (2)

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> Prototype development

Voice recognition (1)

Followed expert’s advices Alternative interfaces were created

Drop down menus replaced by lists of clickable links Intermediary steps to reduce on -screen choices Results were deceiving

Similar terms Software not finely tuned for this field of application

Solution Only speak an identifying number Better recognition but still slower than keyboard and

mouse

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> Prototype development

Voice recognition (2)

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> Prototype development

Voice recognition (3)

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> Prototype development

Bulk import (1)

Motivation To not slow down dermatologists with

classification and description of pictures Excel file Use of XSLT to convert it to a metadata.xml

file no validation made at this stage erases any record metadata that could be

present in the collection Allowed import of ± 300 pictures

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> Prototype development

Bulk import (2)

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Demo

http://localhost:8080/blackskin

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Concluding remarks

Technical platform put in place, taking into account users needs for both phases of project Extensibility through Typo3 plug-ins Interoperability (OAI, Z39.50) can be easily integrated into

existing or new-to-come networks Open source and free reusability Maintainability in mind

Voice recognition : not mature enough

Deliverables OK Development of a prototype Build a representative corpus in dermatology on black skin

Robust basis for the added value services planned in the second phase

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Phase 2

Hand-over of scientific management of project head librarian of ULB medicine library

Collection development continue collection development of project partners creation of additional collections: old dermatological

atlases, medical documents (e-books),… development of partnerships : other on-line atlases,

dermatological sites, foreign institutions, individual dermatologist in African countries, …

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Phase 2

Added value services users forum to discuss clinical cases. forum for experts: discussion of complex cases front-end for submitting cases and images diagnosed by

the users medical cases didactic functions: quizzes, … collection export onto a CD-ROM with a complete search

and visualization system

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Phase 2

Interfaces Backend : testing procedure of the encoding

interfaces for the experts and search interfaces for the users in collaboration with specialists in ergonomics. A generic procedure that could be used for the evaluation of all databanks of medical images in general.

Front-end improvements thanks to users feedback.

French, German and Dutch versions of the Website, encoding interface and search pages.

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Phase 2

Technical Development of a registration office to handle the

administration of new and existing partners Security and authentication issues e.g.

watermarking solution implementation and rights. A more generic Typo3 plug-in for accessing

Greenstone collection Technical follow-up of the platform (upgrades,

potentially useful developments [e.g. the new GSDL3 collection building process])

Business plan