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
- 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:
- Transport Protocols:
- HTTP/FTP/MultiCast Sockets
- Data Encoding:
- XML - Simple Object Access Protocol
- Lookup Service:
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