The jena warnings are another issue, on the uniprot rdf production site.
Not for you to worry about, in any case will be fixed by the next
uniprot data release on the 9th of January.
Thanks for looking into the owl:sameAs issue.
Regards,
Jerven
On 12/19/2012 02:47 PM, Barry Norton wrote:
Further, I converted to NTriples (note, Jena gives a lot of warnings -
it's probably worth duplicating this and taking note), and pulled out
only the sameAs statements:
$ apache-jena-2.7.4/bin/rdfparse citations.rdf > citations.rdf.nt
$ wc citations.rdf.nt
12693123 217642066 2491240008 citations.rdf.nt
$ grep 'sameAs' citations.rdf.nt > citations-sameAs.r.nt
$ wc citations-sameAs.rdf.nt
789525 3158100 103875838 citations-sameAs.rdf.nt
These I upload by themselves:
$ curl -X POST -H "Content-Type:text/turtle" -T citations-sameAs.rdf.nt
http://localhost:8080/openrdf-sesame/repositories/citations/statements
I received then the same results as below.
So I think we can disregard the effect of other data and concentrate
purely on what's happening to these sameAs statements. This requires
looking into the internals, so I'll leave you in Damyan's capable hands.
Barry
On 19/12/12 12:42, Barry Norton wrote:
Jerven, confirmed I can reproduce your problem thus:
$ wget
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/citations.rdf.gz
$ gunzip citations.rdf.gz
$ curl -X POST -H "Content-Type:application/rdf+xml" -T citations.rdf
http://localhost:8080/openrdf-sesame/repositories/citations/statements
And now (unlike with P68353.nt) get only:
$ curl -d "query=DESCRIBE <http://purl.uniprot.org/uniprot/P68359>"
http://localhost:8080/openrdf-sesame/repositories/citations
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sesame: <http://www.openrdf.org/schema/sesame#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix fn: <http://www.w3.org/2005/xpath-functions#> .
[no results]
And:
$ curl -H "Accept:application/sparql-results+json" -d "query=PREFIX
owl: <http://www.w3.org/2002/07/owl#> SELECT * WHERE {?s owl:sameAs
?o} LIMIT 10" http://localhost:8080/openrdf-sesame/repositories/citations
{
"head": {
"vars": [ "s", "o" ]
},
"results": {
"bindings": [
]
}
[again, nothing]
Barry
On 19/12/12 11:50, Jerven Bolleman wrote:
Hi Barry,
No there are two systems which show the same problem.
All triples with owl:sameAs as predicate are gone.
i.e.
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT * WHERE {?s owl:sameAs ?o}
returns no results. Both at linkedlifedata and at
beta.sparql.uniprot.org.
Apparently Vassil claims that linkedlifedata deletes all owl:sameAs
statements and therefore should not return results. This is silly but
ok, if you really do that then you can not replicate my problem at
that endpoint.
However, we at uniprot do not remove any owl:sameAs statement. We
load these into the store and then do not get them back in query
answering.
Basically all triples with owl:sameAs are silently deleted by the store.
A dataset that you can use for experimenting is
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/citations.rdf.gz
Which is moderate in size.
Regards,
Jerven
On 12/19/2012 11:38 AM, Barry Norton wrote:
Thanks for the clarification - I believe Vassil has answered the
question in the mean time, this is down to the way the data is loaded
and exposed in LinkedLifeData.
OWLIM does index the equivalence in the raw dataset and, under
appropriate conditions, will infer the symmetric dual.
Barry
On 19/12/12 10:24, Jerven Bolleman wrote:
Hi Barry,
The workbench is not involved its just using directly the sesame api.
e.g.
((GraphQuery) query).evaluate();
As the triple is explicit in the dataset. Which means
setIncludeInferred
true or false should not matter. Testing with the debugger it is
unaffected.
Tobe clear we load the data using ruleset=none. Which might impact the
scenario.
The query used to work its just in the latest version that I notice it
being gone.
Regards,
Jerven
On 12/19/2012 11:03 AM, Barry Norton wrote:
Jerven, using owlim-se-5.3.5689 I just executed:
$ wget http://www.uniprot.org/uniprot/P68353.nt
$ curl -X POST -H "Content-Type:text/turtle" -T P68353.nt
http://localhost:8080/openrdf-sesame/repositories/uniprot/statements
$ curl -d "query=DESCRIBE
<http://purl.uniprot.org/intact/EBI-530932>"
http://localhost:8080/openrdf-sesame/repositories/uniprot
I got:
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sesame: <http://www.openrdf.org/schema/sesame#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix fn: <http://www.w3.org/2005/xpath-functions#> .
{
<http://purl.uniprot.org/intact/EBI-530932> a
<http://purl.uniprot.org/core/Participant> ;
owl:sameAs <http://purl.uniprot.org/uniprot/P68359> ,
<http://purl.uniprot.org/intact/EBI-530932> ;
rdfs:label "CSN4" .
*<http://purl.uniprot.org/uniprot/P68359> owl:sameAs
<http://purl.uniprot.org/intact/EBI-530932> .**
****
**<http://purl.uniprot.org/intact/EBI-530932> owl:sameAs
<http://purl.uniprot.org/intact/EBI-530932> .**
*
<foo:bar#_5036383335330019>
<http://purl.uniprot.org/core/participant>
<http://purl.uniprot.org/intact/EBI-530932> .
}
Can you provide any more details that might help to reproduce your
problem?
Could it simply be your parameter _equivalent=false (I believe
there's a
checkbox in the UI), as the database clearly has triples
expressing this
equivalence?
Barry
On 19/12/12 09:52, Jerven Bolleman wrote:
Dear ontotext developers,
I am missing a lot of owl:sameAs statements in our data.
I can reproduce the problem both on the linkedlifedata.com as at
beta.sparql.uniprot.org
The version is OwlimSchemaRepository: version: 5.3, revision: 5689
An example is
*MailScanner has detected a possible fraud attempt from
"linkedlifedata.com" claiming to be*
http://linkedlifedata.com/sparql?query=DESCRIBE+%3Chttp%3A%2F%2Fpurl.uniprot.org%2Fintact%2FEBI-530927%3E&_implicit=false&implicit=true&_equivalent=false&_form=%2Fsparql
The following triple is missing
<http://purl.uniprot.org/intact/EBI-530932>
<http://www.w3.org/2002/07/owl#sameAs>
<http://purl.uniprot.org/uniprot/P68359> .
Which you can find in the source data i.e.
http://www.uniprot.org/uniprot/P68353.nt
This is messing up quite a few queries on our end could you
please look
into this as soon as possible. This also affects select and ask
queries so its not just describe.
Regards,
Jerven
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