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OmniGene2 is Divided Into Two Layers:

  • Frameworks:
    • Reusable Components in the OmniGene code base
  • Services
    • Code implemented using our frameworks

Overview of OmniGene

In a perfect world biological data would be represented in a single acknowledged standard machine readable format such that relationships within this data could be auto-discovered, analyses could be automatically performed on the users behalf, annotations were stored for the user as they wrote them, and this all happened within an intuitive and well known user interface. Today's story is vastly different than the one told above, and here's why:

  • Biological Data is represented in multiple human readable formats
    • fasta, agp,gff etc.
  • There is no standard nomanclature for genomic, proteomic, chemi-informatics, publication, and other biological data
    • Ontology groups (GO) are working on this problem
  • No standard protocol exists to interrogate biological data stores
  • No standard data format(s) exist to exchange biological data
  • No standard data model exists for biological data

OmniGene2 is a 2+ year old open source project initiated at the Whitehead Institute. Its goal is to produced middleware which allows transparent access to disparate data repositories (nodes in the web services cloud). It provides a "federated" view of all these services by adhering to a web services model.

OmniGene is implemented as a stack of service layers using the Java programming language and XML.

OmniGene is implemented using the following technologies:

  • Database Access
    • Enterprise Java Beans
  • Transport protocols
    • HTTP/FTP/MultiCast Sockets
  • Data Encoding:
    • XML - Simple Object Access Protocol
  • Lookup Service:

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