1 black skin dermatology online : contribution to teledermatology prime minister's office...
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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 (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
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
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 (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
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 (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
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
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 (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 (5)
Features Authentication Upload Metadata Enriching Image preview Modify & delete Collection building Experimental speech recognition interface Multilingual
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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
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
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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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