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Re: updating SIDER LODD

From: Paul Rigor <paul.rigor@uci.edu>
Date: Wed, 3 Aug 2011 13:36:44 -0700
Message-ID: <CAKEyXb-YairrpRTvvwN=Jn6-WdsH00FKXthkqPWXonFi59XL+g@mail.gmail.com>
To: HCLS <public-semweb-lifesci@w3.org>
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 20:37:31 UTC

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