Re: updating SIDER LODD

Hi Paul,

Given the difference in the bare numbers of drugs in each dataset, it
is likely that the owl:sameAs relations are not all bidirectional.
That may affect the semantics of both queries, as for one you are
starting off in Sider and using its available owl:sameAs relations to
get to DrugBank, and for the other you are starting off in Drugbank
and using its owl:sameAs relations to get to Sider.

Does your endpoint infer "X owl:sameAs Y" when it sees "Y owl:sameAs X"?

You could do a simple test by comparing the results of:

?drug sider:sideEffect ?sideEffect .
?dbDrug rdf:type drugbank:drugs .
    owl:sameAs ?drug .

and

?drug sider:sideEffect ?sideEffect .
?dbDrug rdf:type drugbank:drugs .
 ?drug owl:sameAs ?dbDrug .

Cheers,

Peter

On 4 August 2011 06:36, Paul Rigor <paul.rigor@uci.edu> wrote:
> Hi all,
> As a follow up, here's some stats: There are over 4700 DrugBank drugs, 893
> SIDER drugs.
> More importantly, the equivalence mapping between SIDER and DrugBank drug
> entities are not accurate (or not current). In fact, the mapping doesn't
> seem to be symmetric. For example, if I query with a pattern where the
> subject is a SIDER drug and the predicate a DrugBank drug, only 275 overlap
> between them. On the other hand, if the graph pattern uses a DrugBank drug
> as the subject and the SIDER drug as a predicate, then resulting graph
> captures a larger overlap with 833 drugs. Please let me know if I have
> overlooked something! Thank you in advance.
> The queries used are as follow:
> (SIDER -> DrugBank)
> PREFIX owl: <http://www.w3.org/2002/07/owl#>
> PREFIX sider: <http://www4.wiwiss.fu-berlin.de/sider/resource/sider/>
> PREFIX drugbank:
> <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
>
> SELECT count distinct ?drug
> FROM <http://semanticweb.ics.uci.edu/LODD/SIDER#>
> FROM <http://semanticweb.ics.uci.edu/LODD/DrugBank#>
>
> WHERE {
> ?drug sider:sideEffect ?sideEffect .
> ?dbDrug rdf:type drugbank:drugs .
>     owl:sameAs ?drug .
> }
> (DrugBank -> SIDER)
> PREFIX owl: <http://www.w3.org/2002/07/owl#>
> PREFIX sider: <http://www4.wiwiss.fu-berlin.de/sider/resource/sider/>
> PREFIX drugbank:
> <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> SELECT count distinct ?dbDrug
> FROM <http://semanticweb.ics.uci.edu/LODD/SIDER#>
> FROM <http://semanticweb.ics.uci.edu/LODD/DrugBank#>
> WHERE {
> ?dbDrug rdf:type drugbank:drugs .
> ?drug sider:sideEffect ?sideEffect ;
>      owl:sameAs ?dbDrug .
> }
>
> --
> Paul Rigor
> http://www.ics.uci.edu/~prigor
>
>
> On Wed, Aug 3, 2011 at 10:39 AM, Paul Rigor <paul.rigor@uci.edu> wrote:
>>
>> Hi gang,
>> I was wondering whether there are plans to update the SIDER LODD and sync
>> it with the latest version of the SIDER database? It's over two years old.
>> Is there a published procedure for performing the RDFisation? I'm willing to
>> help out as well.
>> Cheers,
>> Paul
>>
>> --
>> Paul Rigor
>> http://www.ics.uci.edu/~prigor
>
>

Received on Wednesday, 3 August 2011 23:07:59 UTC