Changes between Version 61 and Version 62 of ImplementationBootcamp

Show
Ignore:
Timestamp:
2010/02/12 10:47:34 (13 years ago)
Author:
jerven
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • ImplementationBootcamp

    v61 v62  
    207207http://www.w3.org/RDF/Validator/ 
    208208 
    209 == How should I build the URI's of my resources == 
    210   * see Data_Provider_Session 
    211   * for the unknown/non-existing URI's (link a resource that was not described before ) it was suggested to use '''urn:void:mydatabase:id'''. For example '''urn:void:mylab:table0980:row1:col10'''. 
    212  
    213209== SPARQL == 
    214210 
     
    240236 
    241237=== What is reasoning? === 
     238 
     239Reasoning can be used in a few ways. It can be used to infer data that was not hard coded into the database. 
     240e.g. Triples are added in the store that you did not encode. 
     241 
     242an example. 
     243 
     244ProteinA :interactsWith ProteinB 
     245 
     246without reasoning when you ask 
     247{{{ 
     248sparql  ?with where (ProteinB :interactsWith ?with) 
     249}}} 
     250will return no results. When the owl statement is added 
     251 
     252:interactsWith owl:inverseOf :interactsWith 
     253 
     254Then the same query will return proteinA as ?with. 
     255 
     256You can also introduce classes as shown by the SADI example. To make more readable queries. 
     257For example give me all human proteins known to be a kinase. 
     258e.g.  
     259{{{ 
     260select ?p where {?p a :Protein . 
     261?p :classifiedWith <http://purl.uniprot.org/keywords/418> . 
     262?p :organism <http://purl.uniprot.org/taxonomy/9606> .) 
     263}}} 
     264While 
     265{{{ 
     266select ?p where (?p a :HumanKinase) 
     267}}} 
     268is much more readable to a human/biologist. This :HumanKinase type can be generated on the fly using owl inference. 
     269 
     270 
     271It can also be used to do quality control. 
     272e.g. when assigning the keyword complete proteome to an uniprot entry a chromosomal location must be known. When an entry is found for a with the keyword complete proteome but no chromosomal location. A contradiction is raised. i.e. and error. This allows us to notify a curator and fix this oversight.  
    242273 
    243274=== What reasoners are available? ===