CORBA and Life Sciences

CORBA and Life Sciences

Ulf Leser

Table of Content

• CORBA in a nutshell

• The Life Science Research Domain Task Force

• The Genome Maps Standard

CORBA

• Common Object Request Broker Architecture

- A reference architecture, not an implementation

- Developed in a community process through OMG

- Object-oriented middleware

• Target

- Easier, more flexible RPCs

- Interoperability of applications over networks

- Language- and platform independent

- Free

specification of interfaces

• Main elements

Similar techniques

• RPC, RFC

- Calling a procuedre/function on a remote machine

- Very old

• Enterprise Java Beans

- Also interface-centric

- Also object-oriented

- Pure JAVA

• DCOM

- Also interface-centric

- Somewhat object-oriented

- Pure Microsoft

Object Management Goup (OMG)

• Over 800 member organizations - world’s

largest software consortium

• Founded April 1989

• Small staff (30 full time); no internal

development

• Dedicated to creating and popularizing

object-oriented standards for application

integration based on existing technology

Object Management Architecture

Object Request Broker

Application Objects

Domain Objects

Object Services

Common Facilities

CORBA Object

Legacy Application

Wrapper

Implementation with CORBA

Interface Definition

Client stub generation

Bind stubs to (existing)

application

Bind ORB to application

Server skeleton generation

Implementation of methods

Start ORB

Bind stubs to implement.

Code generation

OMG IDL

specification

OMG IDL

specification

IDL Compiler

IDL Compiler

Client

code

Client

code

Server

code

Server

code

Stub

code

Skeleton

code

Client

ready to request

Client

ready to request

ready to serve

Server

Server

ready to serve

ORB

Library

ORB

Library

Language

mapping

Your parts

RPCs in CORBA

Application

Stub

ORB

ORB

Stub

Server

Database

IIOP

Client:

- Obtain CORBA reference

- Transparent method invocation

Server:

- Manage CORBA objects

- Receive and execute RPCs

Request

Result

ORB:

- Server localisation

- Request propagation

Interface Definition Language

• Defining an

interface

, not an implementation

• Object-oriented language

- Strongly typed

- Multiple inheritance

- Structs

• Language independent

• Mapped to programming languages:

- JAVA

- C++

- App. 20 more

Example: HelloWorld.idl

module Tutorial1 {

interface HelloWorld {

string get_text();

};

};

module Tutorial1 {

interface HelloWorld {

string get_text();

};

};

module defines a naming

context:

names from this module

used outside this module

must be referenced as (for

example):

Tutorial1::HelloWorld

interface defines a CORBA object

(class):

these objects are available for

clients and are implemented by a

server

an available method:

methods are called by

clients to fulfill their

requests

CORBA Services

• CORBA Services support development and

deployment:

-

Naming service

: object localization by name

-

Trading service

: service localization by properties

-

Transaction service

: ‘2-phase commit protocol’ management

-

Query service

-

Event service

-

Relationship service

The Life Science Research

Domain Task Force

Domain Services: LSR

• OMG is organized in “domain services”

- Financial

- Automotive

- Life Science

- Etc.

• L

ife

S

cience

R

esearch Task Force since 1997

(www.omg.org/homepages/lsr)

• Task forces have working groups

• Task forces supervise

definition and adoption

of specifications

(I.e., documents)

LSR working groups

• Biomolecular Sequence Analysis (adopted)

• Genomic Maps (adopted)

• Bibliographic Query Service (adopted)

• Macromolecular Structure

• Laboratory Equipment Control Interfaces

• Gene Expression

• Chemical Structure Access and

Representation

Standardisation Process

RfI

RfP

LoI

Proposals

Standard

• Time-consuming

process

• OMG Architectural board committed to:

- Orthogonality

- Cutting-edge technology

• Participation: relatively open

• Submitters must commit themselves to

provide implementations

Genomic Maps

• Differences:

- Co-ordinate system

- Ordering

- Object types

• Different species,

chromosomes,

regions

Scope of “Genome Maps”

•

Maps

- no sequences

•

Access

- no calculation or comparison

•

Retrieval

- no writing

• An

interface

– not a data model:

- Easy to implement for providers

- Powerful enough for clients

- Covering most types of maps

First Proposal

MapObje ct database name id Mappable species chromosome type getMaps() Se g m e nt length unit Po int Clo ne Bin Ma rke r Ma p getNrOfElements() getAllElements() getRangeBetweenObjects() getElementsInSegment() Cyto g e ne ticEle m e nt rank Line a rMap maxCoordinate minCoordinate 1..1 MapEle m e nt positionPrecision

Inte rva lPo s itio n Po intPo s itio n Ra ng e Po s itio n

leftEnd

rightEnd frameWorkElementposition leftFlankingObjrightFlankingObj 1..* onMap 1..1 1..1 crossReferences 0..* mappedObj 1..1

Mappable Objects

Mappable species chromosome type getMaps() MapObje ct database name id Se g m e nt length unit Po int

•

Mappable

are all objects which can be placed on a

map

• Cross-linked to

equal objects

in other databases

•

Segments

have extent: clones, bands, maps, ...

•

Points

are points: marker, EST, STS, ...

Maps

•

Maps

are segments

• Maps can be placed on

maps

• Two types:

-

Linear maps

have a co-ordinate

system:

• physical maps

• genetic maps

-

Bin maps

have only ranges:

• Radiation-hybrid maps

Bin Map getNrOfElements() getAllElements() getRangeBetweenObjects() getElementsInSegment() Line a rMa p maxCoordinate minCoordinate getScalarRange() getAround() Se g m e nt length unit 1

MapElement

•

MapElement

is the assignment of a

Mappable

to a

Map

with a

Position

in a

Co-ordinate

system

• n:m relationship between Map and Mappable

• Map, MapElement and Mappable could be on

different servers

Vag ue Po s itio n Orde re dPo s itio n

MapEle m e nt

rank

positionPrecision

Inte rvalPo s itio n Po intPo s itio n Ra ng e Po s itio n

leftEnd

First Proposal

MapObje ct database name id Mappable species chromosome type getMaps() Se g m e nt length unit Po int Clo ne Bin Ma rke r Ma p getNrOfElements() getAllElements() getRangeBetweenObjects() getElementsInSegment() Cyto g e ne ticEle m e nt rank Line a rMap maxCoordinate minCoordinate 1..1 MapEle m e nt positionPrecision

Inte rva lPo s itio n Po intPo s itio n Ra ng e Po s itio n

leftEnd

rightEnd frameWorkElementposition leftFlankingObjrightFlankingObj 1..* onMap 1..1 crossReferences 0..* mappedObj 1..1 1..1

Implementation: Wrapping IXDB

• Integrated database: > 30 data sources

• Many different maps available

Experiences - Semantic

• Different semantics:

- Relational database, object-oriented MapIDL

- IXDB.Locus does not exists in MapIDL

- Genes with or without extent

- Cardinalities: IXDB stores many values

- Synonyms

• Not all information in IXDB is representable in

MapIDL

Experiences - Technical

• Transient versus persistent references

• Consistency

- Between client and server

- Between CORBA server and database

• Memory management

- Releasing objects

- Multi-copy objects

• Multi-threaded programming

⇒

First shot easy, but “good” implementation

difficult

Interoperability

GDB

RHdb

• Maps are stored in many

data sources ...

- GDB

- RHdb

- CEPH

- Hugemap

- IXDB

- XACE

- ....

• Difficult to get an

integrated view

on all

available data

If Standards were used ...

GDB _MGD RHdb

ORB

Map Comparison

Application

CEPH

Choose source:

GDB

MGD

RHdb

CEPH

Choose source:

GDB

MGD

RHdb

CEPH

.getMaps(‘X’)

.getMaps(‘X’)

User

Two Approaches to Interoperability

D ata S ou rc e S ou rc eD ata D ata S ou rc e O R B ID L H T M L H T M L H T M L M e d ia to r JD B C

• Someone builds an

integrating system

:

- Typically laborious

- Req. understanding of source data

- Schema and interface evolution

Data

Source SourceData

Data Source

ORB

IDL 1 IDL 1

Mediator

IDL 1

• Sources provide a

standard access

method:

- Fixed structure and semantic

- Most problems are shifted from

Integration Obstacles Removed ?

• Semantic & structure

- Documentation, MapIDL

• Data model

- CORBA (IDL->language mapping)

• Access mechanism

- CORBA (IIOP)

• Query capabilities

Obstacles Removed, cont’d

• Data conflicts

- Not resolved

• Data source autonomy

- Source implements and maintains server

• Fuzzy concepts

- Documentation

• Object identification

Conclusions and Open

Questions

General Design Problem

• Clients:

- Typed access: no

impedance mismatch, no

parsing

- Homogeneous structure

and semantic

- “Standard” canned queries

• Server:

- Install CORBA (ORB ...)

- Adopt standard semantic

- Implement interface

Make it

powerful !

Make it

simple !

Questions

• Designing a good interface is non-trivial

- Performance:

• Objects versus structs

• Navigation versus queries

- Complexity

• Do we need 5 different position types ?

• Hierarchies ?

- What are the specific needs of potential applications ?

• Map comparison

• Map integration

• Map visualisation

Questions cont’d

• Using CORBA services

- Availability ? For all clients at low cost ?

- Maturity ?

Object-by-Value, MOF, POA ?

• Personal opinion

-

Naming service

: useful

-

Query service

: useless

-

Collection service

: too expensive

-

Relationship service

: too expensive

-

Trading service

: unclear

-

Object-by-Value

: wonderful

-

POA

: essential

Questions cont’d

• Ad-hoc queries ? Against what schema ...

- the IDL ?

• Not possible - IDL is not a data model, no query language

- the schema of the source ? “execQuery( in string query)”

• schema is possibly unknown

• varies from source to source

• sources might not have a schema at all

• sources may change schema

• What is the result ?

- Must be a programming language construct described in IDL

Conclusions

• Trade-off: Comprehensiveness versus ease

- Standard as least common denominator ?

- Sufficient power for all applications ?

• Trade-off: Performance, comfort, usability

- Sufficient performance requires caching and structs / OBV

- Caching affects consistency

- Structs are less elegant

- OBV not yet commonly implemented

• Success ?

- Hype has gone: few implementations available

- Performance !

Literature

• L. Wang, P. Rodriguez-Tome, N. Redaschi, P. McNeil, A. Robinson and P.

Lijnzaad. Accessing and distributing EMBL data using CORBA (common

object request broker architecture). Genome Biology, 1 (5): 2000.

- G. Vossen. The CORBA Specification for Cooperation in Heterogeneous

Information Systems. 1st Workshop on Cooperative Information Systems;

LNCS 1202, Kiel, Germany, 1997.

- S. Baker. CORBA and Databases - Do you really need both ? Object Expert,

May: 1996.

• Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim

Jungfer, Fridiric Guyon, Guy Vaysseix, Carsten Helgesen and Patricia

Rodriguez-Tome: "A Proposal for a Standard CORBA Interface for Genome

Maps", Bioinformatics, 15(2), pp. 157-169.

• http://www.omg.org/lsr/

• http://corba.ebi.ac.uk/