Changes between Version 9 and Version 10 of OpenBio*

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Timestamp:
2008/02/12 11:24:13 (11 years ago)
Author:
markjschreiber
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  • OpenBio*

    v9 v10  
    33One of the goals of BioSQL was to provide an interchange platform for the Bio* objects. This has not yet succeeded due to differences in the way the Bio* projects interpret an individual sequence record and how they persist it to the database. 
    44 
     5Common sequence semantics and object/ format handling would probably be of great benefit to many other WS providers and consumers. If Bio* can agree on semantics it would be a good reference for many other projects. 
     6 
    57 
    68= Possible Tasks = 
    7  
     9* Choose some 'reference' sequences to see how the Bio* projects 'round-trip' them. Where are the differences and why are there differences? 
     10* Find out where each Bio* project persists it's data into BioSQL during ORM. Why are there differences? 
     11* Establish guidelines for where things should go in BioSQL, eg given a Genbank file, what bits should go where. 
     12* Define an interchange format for the Bio* projects. Probably XML, probably borrow something already existing (XEMBL etc). 
     13* Decide on a restricted vocab for annotations and feature types. Probably use SO. 
    814 
    915 
     
    3238= Task achieved = 
    3339== Tuesday == 
     40 * Initial planning. 
    3441 * Approved a BioSQL logo. 
    3542