Refactoring BioMoby

1
Upgrading
Central
Dennis Wang Wilkinson Lab
2
Moby-Services Branch

• System through which a client interacts with
  multiple sources of biological data
• Components include
• Moby-Central
• Moby-Services
• Moby-Clients

      Ensembl
Local BLAST
3
Database
MOBY Central
4
What is Moby Central?

• A central repository for knowledge
• Knowledge about the web services available (eg.
  EMBL, RepeatMasker)
• Knowledge about input and output data
• Provides tools for adding knowledge
• MOBY Central lives at the iCAPTURE but open
  source
• Server address mobycentral.icapture.ubc.ca

5
0.85 Application Programming Interface (API)

• find/retrieve functions
• services names, types, providers, instances
• Blast2seq, ExPASy, NCBI, etc
• namespaces
• Swissprot/accession, GenBank/gi,
  'MRL_CardioDB_Image' etc.
• data-objects names, definition, XML Schema,
  relationships
• actual sequence, PHASE, gi numbers, etc
• register/deregister functions
• object, service types, namespace, service
  instances

6
Purpose of Upgrade

• Allow Moby Central to be independent of database
• Offer greater compatibility with other
  bioinformatic servers/tools
• Share knowledge with other repositories

7
Renovating the BackEnd

• Adaptor module to reduce coupling with
  database
• A new query API language to communicate with
  various database management systems (DBMS)
• An implementation of query API for mySQL
• Removal of all explicit SQL calls from Moby
  Central
• Use Lsids to identify services, objects,
  namespaces instead of DBids

8
Query API Design
Central.pm
mySQL DBMS
authority.pm
oracle.pm?
........
.
9
What is Refactoring?
Definition Refactoring is a disciplined
technique for restructuring an existing body of
code, altering its internal structure without
changing its external behavior.

• Refactoring helps understanding code
• programs that are hard to read
• programs that have duplicate logic
• programs that require additional behaviour that
  requires you to change running code
• programs with complex conditional logic

10
Refactoring Example
11
Affects to other Moby-S Components

• Ahab front end
• Code Generator
• XML Schema Generation

12
Future Endeavors

• More implementations of query API for Oracle,
  SQLServer, RDF, etc.
• Incorporate Moby objects into myGrid XML
  repository
• Reduce manual curation of new ontologies within
  repository
• Automation of data integration input and output
  data-objects

13
In Summary

• Moby Central is the back-end application of the
  Moby-Services branch
• Moby Central should be portable and compatible
  with other bioinformatic systems
• Incorporation of other systems with Moby Central
  increases its robustness, hence, more users
• Database Adaptor is just the first step!

14
Acknowledgements

• Dr. Mark Wilkinson
• Lab Members
• Eddie Kawas
• Benjamin Good
• Clarence Kwan
• Michael Ng
• Peter Pichlak
• Lixin Shen

15
Contact
http//www.biomoby.org http//bioinfo.icapture.ub
c.ca/dwang