2. Chemical Toxicity and Safety Information System Shuanghui Luo Ying Li Jin Xu

3. Outline  Introduction  Goals and system functionalities  Technologies and tools  System architecture  Reference  Acknowledgement  Implementation Demo

4. Cheminfomatics Cheminformatics is an exciting and rapidly developing field, and focuses on solving problems arising from chemistry using methodology from computer science. The practice not only to leverage the accumulated knowledge in various forms but also to derive new understanding based on the available knowledge using information technologies and tools.

5. Introduction Significance: ChemInformatics system is a useful tool for different users such as scientists, students and so on to raise the awareness of chemical hazards & to improve chemical safety management.  To show the selected chemical toxicity, risky and safety information.  To compare the toxicity data, risky and safety phrases with the analogue chemicals.  To indicate the risky phrases and safety guidelines, for example, some chemicals are high toxic and need to keep away from human being and living entities.

6. Goals  Establish a distributed chemical toxicity and safety information service system using a multi-tier architecture  Follow the process of software development  Learn and apply middleware technologies (EJB and XML)  Understand component based programming approach Client Tier Browser Servlet EJB JDBC DataBase Representation Tier Business Tier Integration Tier Resource Tier

7. System Functionalities  online search application  presents users chemical toxicity, risky, and safety information and services  manages user logins for security  processes the queried data and does some analysis and returns the corresponding data table and view in graph.

8. Technology and Tools (1/3) Browser Web container Web container EJB container EJB container EIS resources HTML Servlets Enterprise Beans, JDBC (or connectors) RMI, SQL

9. Technology and Tools (2/3) EJB ( Enterprise Java Beans)  Server-side architecture for distributed, transactional components.  Framework for easily creating business objects.(e.g. transaction, naming, persistence services)  Relive developers from managing Low-level transaction and state management Multithreading and resource pooling Security Persistence and other complex APIs.  Provide standard Java component architecture. Allow combining components developed using different tools. Compatible with existing server platforms, existing Java APIs and CORBA. Write once, and run anywhere.

10. Technology and Tools (3/3) Java: programming language Servlet: web presentation XML: used to write deployment descriptor JDBC-ODBC: connection to DB MS-Access: DB Jboss-Jetty Ant - Build Tool

11. Web Browser Web Browser Database Tier 1Tier 2 Tier 3 EJB container Web container Servlet QueryBean Sesssion Bean ChemDBBean Entity Bean UserDBBean (Entity Bean) AdminBean Sesssion Bean SafeDBBean Entity Bean RiskDBBean Entity Bean LoginBean Sesssion Bean System architecture

12. EJB Beans Four Entity Beans UserDBBean: store user information for user management. ChemDBBean: store chemical toxicity, and chemical properties. RiskDBBean: store chemical information about risky phrases. SafeDBBean: store chemical information about safety phrases Three Session Beans LoginBean: handle user verification (uses UserDBBean check the user ID and password) AdminBean: for administrator to manage user accounts QueryBean: handle client request retrieve chemical information

13.  LoginServlet: User verification.  FormulaServlet: Query by chemical formula.  QueryServlet: Query for chemical information including toxicity, risky and safety phrases.  Compareservlet: Compare chemical information by category. Servlets

14. Root=/cheminfo Ant Project scripts:= /build Package com.cheminfo: =/com/cheminfo chemrisk File structure (1) safeuserqueryloginadminservlethtml

15. File structure (2)

16. Container-managed Persistence(CMP)  Container automatically manages persistence. (Developer does not write database calls.)  The CMP-field element describe a container managed field. The field element includes an optional description of the field, and the name of the field.

17. Container-managed Persistence(CMP) cont’d  Since the container is accessing the database on behalf of the bean, the container need to know: a) the fields that are to be persisted by the container b) the type of persistence, connection to database c) the table name, the mapping between table columns d) field names in the beans e) the semantics of the finder methods and so on.  This information is specified in the deployment descriptors: ejb-jar.xml; jboss-web.xml, web.xml, jaws.xml

18. ejb-jar.xml This file tells the EJB server which classes make up bean implementation, the home interface and the remote interface. Also called deployment descriptor.

19. ejb-jar.xml example - Chemical Toxicity and Safety - User database UserDBBean com.cheminfo.user.UserDBHome com.cheminfo.user.UserDB com.cheminfo.user.UserDBBean Container java.lang.String False - UserName - PassWord - Email - Address - UserName

20. jboss-web.xml file Specify servlets & beans about their setup to deploy the web application. Example: A servlet wants to call methods on a bean B B bean = home.create(pk); the servlet must declare a reference to the ejb in its deployment descriptor. This is done by an tag in the web.xml file.

21. jboss-web.xml example - ejb/Admin cheminfo/Admin - ejb/Login cheminfo/Login - ejb/Query cheminfo/Query - ejb/ChemDB cheminfo/ChemDB - ejb/RiskDB cheminfo/RiskDB - ejb/SafeDB cheminfo/SafeDB

22. jaws.xml file JAWS is the mapper used by JBoss to manage CMP entity beans.  Specify a datasource and the type-mappings to use with it  Set a bunch of options concerning jaws behavior  Specify how JAWS should build/use your tables  Define finders to access you entity beans  Define a type mapping

23. jaws.xml example ChemInfoDB MS SQLSERVER UserDBBean user false UserName PassWord PassWord Email Email Address Address name> false UserName ……..

24. EJB security  Integrate application security into the EJB.(authentication, access control, portability, ease of use).  Allow security policies to be set by the application deployer rather than hard-coded at development time.  Work with existing security system.  Fit into the overall J2EE environment.

25. Person, Work and Time PersonWork Time Shuanghui Luo In charge of system architecture and deployment, EJB entity and session beans, package the source files, and documentation 200 hours Ying LiFocus on EJB entity beans and database setup and connection, and documentation 200 hours Jin XuFocus on web server including web page interfaces and servlets and system deployment, and documentation 200 hours

26. Reference 1. http://www.genomicglossaries.com/cheminformatics_gloss.asp “ Genomics Glossaries & Taxonomies” http://www.genomicglossaries.com/cheminformatics_gloss.asp 2. http://www.borland.com/visibroker/papers/ejb/ “ Enterprise JavaBeans Simplifying Development of Distributed Multi-tier Applications” http://www.borland.com/visibroker/papers/ejb/ 3. http://macedonia.nrcps.ariadne-t.gr/ “The Information retrieval in chemistry- www server”http://macedonia.nrcps.ariadne-t.gr/ 4. http://tis.eh.doe.gov/web/chem_safety/Roadmap.html “Chemical Safety Requirements Roadmap”http://tis.eh.doe.gov/web/chem_safety/Roadmap.html 5. Budde, T., Haude, M., Hopp.H.W., Keber, S., Caspari, G., Fabbender, G., Fingerhut, M., Novopashenny, I., Berithardt, G., Erbel, R., Erdmann, E., and Wischnewsky, M.B., “A prognostic computer model to predict individual outcome in interventional cardiology”. Eur. Heart J. 18: 1611-9, 1997 6. Roman, E., Oberg, R., The Business Benefits of EJB and J2EE Technologies over COM+and Windows DNA. 1999 7. Zona research, Inc. Enterprise JavaBeans TM Technology. 1999 8. Ennerich, W. Engineering Distributed Objects. John Wiley & Sons, Ltd. 15-20, 2000 9.Will Howerry, Enterprise Application Development Using UML, Java Technology and XML, JavaOne, Sun’s 2000 Worldwide Java Developer Conference, San Francisco 10.http://www.jboss.orghttp://www.jboss.org

27. Acknowledgement Thank you!!

28. This Demo is available at: Server: http://kc-sice460-15:8080/cheminfo/ register as a new user i.e. Username: xu password: 123 Formula: C2H6O, C7H8, C3H3O, etc Implementation Demo