Chemical Toxicity and Safety Information System

1
Chemical Toxicity and Safety Information System

• Shuanghui Luo Ying Li
• Jin Xu

2
Outline

• Introduction
• Goals and system functionalities
• Technologies and tools
• System architecture
• Illustration of the implementation

3
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.

4
Introduction

• Significance
• Our designed system is to provide a useful
  on-line resource for different users such as
  scientists, students and so on.
• 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.

5
Metadatabase
Metadata Data that describes data Structured
data about data.

• ? Precise Enables the creation of customized
  virtual collections--pulling objects
  together seamlessly from any digital space to
  meet exact information requirements.
• ? Flexible Supports any search engine, search
  strategy, transport or display option
• ? Efficient Provides immediate access to the most
  appropriate asset for the searcher.
• ? Durable independent of changes to hardware,
  software and network infrastructure
• ? Interoperable Can be seamlessly shared across
  the web with disparate hardware, software,
  network infrastructure and search engines

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 distributed meta-database service

Browser
Client Tier
Servlet
Representation Tier
EJB
Business Tier
Integration Tier
meta-data layer
DB2
Resource Tier
DB1
DB3
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System Functionalities

• Online search application
• Presents users chemical toxicity, risky, and
  safety information and services
• Manages user logins for security
• The meta data layer will integrate data from
  distributed sources and does some analysis and
  returns the corresponding data table and view in
  graph.

8
Technology and Tools (1/3)
Browser
EIS resources
Web container
EJB container
Meta Data Layer
HTML
Servlets
Enterprise Beans
Entity Bean
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
• Jboss-Jetty
• Ant - Build Tool
• MS-Access DB1
• SQL-Server DB2
• Oracle DB3

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System architecture
Tier 1
Tier 2
Tier 3
EJB container
UserDBBean (Entity Bean)
ChemDBBean Entity Bean
SafeDBBean Entity Bean
RiskDBBean Entity Bean
Database
AdminBean Sesssion Bean
QueryBean Sesssion Bean
LoginBean Sesssion Bean
Web Browser
Servlet
Web container
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Proposed System architecture
Web Browser
Web container
Servlet
EJB Container
LoginBean Sesssion Bean
AdminBean Sesssion Bean
QueryBean Sesssion Bean
UserDBBean (Entity Bean)
Knowledge Database
Entity Bean
Meta Data Layer
ChemDBBean Entity Bean1
ChemDBBean Entity Bean3
ChemDBBean Entity Bean2
DB3
DB2
DB1
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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

14
Servlets

• 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.

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File structure (1)
Root/cheminfo
Ant Project scripts /build
Package com.cheminfo /com/cheminfo
chem
risk
safe
user
query
login
admin
servlet
html
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File structure (2)
17
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.

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Container-managed Persistence(CMP) contd

• 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

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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.

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ejb-jar.xml example

• lt?xml version"1.0" ?gt  
• lt!DOCTYPE ejb-jar (View Source for full
  doctype...)gt
• ltejb-jargt  ltdisplay-namegtChemical Toxicity and
  Safetylt/display-namegt
• - ltenterprise-beansgt
• - ltentitygt 
• ltdescriptiongtUser databaselt/descriptiongt  
• ltejb-namegtUserDBBeanlt/ejbnamegt  
• lthomegtcom.cheminfo.user.UserDBHomelt/homegt
   
• ltremotegtcom.cheminfo.user.UserDBlt/remotegt
   
• ltejb-classgtcom.cheminfo.user.UserDBBeanlt/e
  jb-classgt  
• ltpersistence-typegtContainerlt/persistence-t
  ypegt  
• ltprim-key-classgtjava.lang.Stringlt/prim-ke
  yclassgt  
• ltreentrantgtFalselt/reentrantgt
• -ltcmp-fieldgt  ltfield-namegtUserNamelt/field-name
  gt lt/cmp-fieldgt
• - ltcmp-fieldgt  ltfield-namegtPassWordlt/field-nam
  egt   lt/cmp-fieldgt
• - ltcmp-fieldgt  ltfield-namegtEmaillt/field-namegt
    lt/cmp-fieldgt
• -ltcmp-fieldgt  ltfield-namegtAddresslt/field-namegt
    lt/cmp-fieldgt 
• -ltprimkey-fieldgtUserNamelt/primkey-fieldgt  
• lt/entitygt

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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 ltejb-refgt tag in the
  web.xml file.

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jboss-web.xml example

• lt?xml version"1.0" encoding"UTF-8" ?gt
• - ltjboss-webgt
• - ltejb-refgt
• ltejb-ref-namegtejb/Adminlt/ejb-ref-namegt
• ltjndi-namegtcheminfo/Adminlt/jndi-namegt
• lt/ejb-refgt
• - ltejb-refgt
• ltejb-ref-namegtejb/Loginlt/ejb-ref-namegt
• ltjndi-namegtcheminfo/Loginlt/jndi-namegt
• lt/ejb-refgt
• - ltejb-refgt
• ltejb-ref-namegtejb/Querylt/ejb-ref-namegt
• ltjndi-namegtcheminfo/Querylt/jndi-namegt
• lt/ejb-refgt

- ltejb-refgt ltejb-ref-namegtejb/ChemDBlt/ejb-ref
-namegt ltjndi-namegtcheminfo/ChemDBlt/jndi-name
gt lt/ejb-refgt - ltejb-refgt
ltejb-ref-namegtejb/RiskDBlt/ejb-ref-namegt
ltjndi-namegtcheminfo/RiskDBlt/jndi-namegt
lt/ejb-refgt - ltejb-refgt ltejb-ref-namegtejb/Safe
DBlt/ejb-ref-namegt ltjndi-namegtcheminfo/SafeDB
lt/jndi-namegt lt/ejb-refgt lt/jboss-webgt
23
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

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jaws.xml example

• ltjawsgt
• ltdatasourcegtChemInfoDBlt/datasourcegt
• lttype-mappinggtMS SQLSERVERlt/type-mappinggt
• ltenterprise-beansgt
• ltentitygt
• ltejb-namegtUserDBBeanlt/ejb-namegt
• lttable-namegtuserlt/table-namegt
• ltcreate-tablegtfalselt/create-tablegt
• ltcmp-fieldgtltfield-namegtUserNamelt/field-namegt
• ltcolumn-namegtUserNamelt/column-namegtlt/cmp-fieldgt
• ltcmp-fieldgtltfield-namegtPassWordlt/field-namegtlt
  column-namegtPassWordlt/column-namegtlt/cmp-fieldgt
• ltcmp-fieldgtltfield-namegtEmaillt/field-namegtltcolu
  mn-namegtEmaillt/column-namegtlt/cmp-fieldgt
• ltcmp-fieldgtltfield-namegtAddresslt/field-namegtltco
  lumn-namegtAddresslt/column-namegtlt/cmp-fieldgt
• lt/entitygtnamegt  
• ltcreate-tablegtfalselt/create-tablegt
• ltcmp-fieldgt ltfield-namegtUserNamelt/field-namegt
   
• ltcolumn-namegtUserNamelt/column-namegt  
  lt/cmp-fieldgt
• ..

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Administrator
Change users information
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User
New User register
New User registered successfully
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Query a chemical
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Query page
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Safety, risky, toxicity result page
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Toxicity comparison result page