Slide1: 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


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


General objective: 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


Partnership: Partnership Five partners Contents and medical expertise Definition of the functionalities of the platform Guarantee scietific 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


Advisory committee: Advisory committee Dermatologists Expert in voice technology Expert in information technology Feedback on various issues


Project management (1): Project management (1) Successful follow-up of tasks during the project State of art (months 1-6) Study of the 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)


Project management (2): 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


Feasibility study: Feasibility study Covers: Study of needs Metadata of the images Software overview and choice To efficiently store and retrieve the images To deliver content to the end-user Voice recognition


Feasibility Study Study of needs (1): 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


> Feasibility Study Study of needs (2): > 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


> Feasibility StudyMetadata of the images (1): > 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


> Feasibility StudyMetadata of the images (2): > Feasibility Study Metadata of the images (2)


> Feasibility StudyMetadata of the images (3): > Feasibility Study Metadata of the images (3)


> Feasibility StudyMetadata of the images (4): > 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.


> Feasibility StudyMetadata of the images (5): > Feasibility Study Metadata of the images (5)


> Feasibility StudySoftware: > Feasibility Study Software Content management system Digital library software Characteristics Open-source Interoperable Maintainable


> Feasibility studyContent Management System (1): > 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


> Feasibility study Content Management System (2): > 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 (+2000 sites) Rich documentation


> Feasibility study Content Management System (3): > Feasibility study Content Management System (3) screenshot of typo3 backend here


> Feasibility StudyImage Database (1): > Feasibility Study Image Database (1) DSpace Greenstone 2.52 Home-made solution


> Feasibility StudyImage Database (2): > Feasibility Study Image Database (2) Greenstone 3 complete redesign structured as a network of independent modules that communicate with XML backward compatible written in Java → servlet new incremental collection building process quicker more flexible SOAP connectivity still alpha release


> Feasibility StudyImage Database (3): > Feasibility Study Image Database (3) Interoperability Major concern SOAP interface Open Archives Initiative Z39.50 Seamless integration in existing digital library systems


> Feasibility StudyVoice Recognition (1): > 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.


> Feasibility StudyVoice Recognition (2): > 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 BS Much slower encoding Discouragement of users But we wanted to confirm the experts’ conclusions by conducting empirical tests.


> Feasibility Study Legal aspects : > 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


Content acquisition: 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


Prototype Development: Prototype Development Software architecture Web site structure Typo3 plugin Greenstone3 configuration Backend


> Prototype developmentSoftware Architecture: > Prototype development Software Architecture


> Prototype developmentWeb site structure (1): > Prototype development Web site structure (1)


> Prototype developmentWeb site structure (2): > Prototype development Web site structure (2) Home Welcome message Short presentation # of pictures


> Prototype developmentWeb site structure (3): > Prototype development Web site structure (3) Search pages Browsing tools ICD10 Description Body site (Homunculus) (New Images) Site search


> Prototype developmentWeb site structure (4): > Prototype development Web site structure (4) Information about: Project ICD10 classification Staff Contributors Disclaimer


> Prototype developmentWeb site structure (5): > Prototype development Web site structure (5) Tools Submit an image Contact maintainers Forums Newsletter subscription Links page


> Prototype developmentWeb site structure (6): > Prototype development Web site structure (6) Formation Ask a specialist Pedagogic cases and quizzes Bibliography CD-ROM order


> Prototype developmentWeb site structure (7): > Prototype development Web site structure (7) Help Technical help FAQ Sitemap


> Prototype developmentTypo3 plug-in (1): > 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


> Prototype developmentTypo3 plug-in (2): > Prototype development Typo3 plug-in (2) Features: Search a given index Browse hierarchical classifiers Multilingual support Look and feel can be adjusted using CSS Flexible but could be more generic


> Prototype developmentGreenstone 3 (1): > 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!


> Prototype developmentGreenstone 3 (2): > Prototype development Greenstone 3 (2) Collection configuration One collection for each partner Inherent to GSDL building process One supercollection Indexes for searching Hierarchical classifiers (for browsing) Body site Used by homunculus Contributor Diagnostic Description ICD10


> Prototype developmentConfiguration files (1): > 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


> Prototype developmentConfiguration files (2): > Prototype development Configuration files (2)


> Prototype developmentConfiguration files (3): > Prototype development Configuration files (3)


> Prototype developmentConfiguration files (4): > Prototype development Configuration files (4)


> Prototype developmentConfiguration files (5): > Prototype development Configuration files (5)


> Prototype developmentBackend (1): > 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


> Prototype developmentBackend (2): > Prototype development Backend (2) GLI screenshot


> Prototype developmentBackend (3): > 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


> Prototype developmentBackend (4): > Prototype development Backend (4)


> Prototype developmentBackend (5): > Prototype development Backend (5) Features Authentication Upload Metadata Enriching Image preview Modify & delete Collection building Experimental speech recognition interface


> Prototype developmentBackend (6): > Prototype development Backend (6)


> Prototype developmentBackend (7): > Prototype development Backend (7)


> Prototype developmentBackend (8): > Prototype development Backend (8)


> Prototype developmentBackend (9): > Prototype development Backend (9)


> Prototype developmentBackend (10): > Prototype development Backend (10)


> Prototype developmentBackend (11): > Prototype development Backend (11)


> Prototype developmentCollection building (1): > 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


> Prototype developmentCollection building (2): > Prototype development Collection building (2)


> Prototype developmentVoice recognition (1): > 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 Solution Only speak an identifying number Better recognition but still slower than keyboard and mouse


> Prototype developmentVoice recognition (2): > Prototype development Voice recognition (2)


> Prototype developmentVoice recognition (3): > Prototype development Voice recognition (3)


> Prototype developmentBulk import (1): > 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 that could be present in the collection Allowed import of ± 300 pictures


> Prototype developmentBulk import (2): > Prototype development Bulk import (2)


Demo: Demo http://localhost:8080/blackskin


Concluding remarks: 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


Phase 2: Phase 2 Hand-over of scientific management of project head librarian of medicine library of ULB 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, … 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.


Phase 2: 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.


Phase 2: 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