Changes between Version 35 and Version 36 of ImplementationBootcamp

2010/02/11 21:28:59 (13 years ago)



  • ImplementationBootcamp

    v35 v36  
    4545MDW:  Can we re-phrase the question to be clear what we are asking?  :-) 
     47== Web services == 
    4749===  I have an analysis tool, how do I expose it as a semantic web resource? === 
    6870MDW:  Going back as far as 2004, when the LSID specification was being finalized, this issue was a top-priority, so there is a sub-commmunity of bioinformatics data providers who have thought about this problem for many many years! :-)  This has led to a variety of "shared names" proposals, including the Science Commons, Semantic Science, LSRN, and others.  In SADI (and now LSRN, since my lab has taken-over the LSRN project in the past 2 months) we have decided to work with the Semantic Science shared-names proposal from Michel Dumontier.  He has developed an ontology (I will provide a link to this as soon as Michel decides that the ontology is "final"... within days!!).  The ontology defines how a URI should "behave" during resolution, depending on the kind of "thing" that the URI represents - e.g. a biological/physical entity, a database record, or a particular ''representation'' of a database record in html, xml, rdf, etc.  Within the SADI project, we will be writing all of our support code to make compliance with the Semantic Science ontology as automatic as possible.  We are also in the process of doing the same for URIs resolved through the LSRN resolution system... so if you use SADI or LSRN, you should get compliance with this ontology "for free" within the next week or two!  ''In My Opinion This Is One Of The Most Important Issues We Have Addressed At This Hackathon!!''  The Semantic Web works SO much better if we are careful to pay attention to what our URIs REPRESENT: things, records, or representations of records.  It sounds tedious, but we're doing everything we can to shield the data providers from having to think deeply about the problem, and trying to encode the complexity in our respective codebases. 
     72=== How do I create a SADI service? === 
     74Links to tutorials coming soon!!! 
    7176===  What are the similarities and differences between the various shared names proposals?  === 
    97102MDW:  There was a VERY brief discussion of this issue on Thursday... the answer was "be pragmatic".  Highly granular data (like absolute expression-level changes for microarrays) might not be appropriate for conversion into RDF because it explodes the size of the dataset in a circumstance where (a) the dataset is generally going to be used as a whole anyway, and (b) there are completely adequate parsers for existing file-formats, and (c) the benefit of being able to reason over an RDF representation of the data is limited, or absent.   
    99 === How do I create a SADI service? === 
    101 Links to tutorials coming soon!!! 
    104104=== Where do I validate my RDF/XML? ===