On Wed, Sep 5, 2012 at 8:00 PM, Maciek Sykulski <macie...@gmail.com> wrote:
>
> *4. Indexing Uniprot* results with huge ammount of errors of a following
> type:
[..]
> 21:09:48,217 [Thread-3] ERROR impl.RDFDefaultErrorHandler - (line 6 column
> 82): {E211} Base URI is null, but there are relative URIs to resolve.: <#_2>
[..]I think this is because the RDF/XML file is missing the xml:base header. See http://www.w3.org/TR/2003/PR-rdf-syntax-grammar-20031215/#section-Syntax-ID-xml-base > > This is because the graph from uniprot rdf contains many self-references > like these: I added <?xml version="1.0"?> <rdf:RDF xmlns="http://default.namespace.org/namesoace"; xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; xml:base="http://base.example.com/base-uir-demo";> > > <rdf:Description rdf:about="#_5136475A5833004"> > <rdf:type rdf:resource="http://purl.uniprot.org/core/Gene"/> > <orfName>FV3-002L</orfName> > </rdf:Description> > <rdf:Description rdf:about="#_5136475A5833005"> > <rdf:type rdf:resource=" > http://purl.uniprot.org/core/Subcellular_Location_Annotation"/> > <locatedIn rdf:resource="#_5136475A5833006"/> > </rdf:Description> </rdf:RDF> and where able to import the data of this snippet without any ERROR/WARN messages > However, is there a way to index such entities? (other way than manually > replace them inside rdf with absolute URLs)? adding the correct xml:base as described about should fix this problem. best Rupert -- | Rupert Westenthaler rupert.westentha...@gmail.com | Bodenlehenstraße 11 ++43-699-11108907 | A-5500 Bischofshofen
