Re: availabilty of dailymed and diseasome

Hi Umutcan, please see inline....

On 03/19/2013 07:22 PM, Umutcan ŞİMŞEK wrote:
> Hi Richard,
>
> Thank you first of all, secondly, the links from drugbank dataset to 
> dailymed are old. I mean to old server. I don't know how to relate 
> your triples to corresponding drugbank triples.
REPLY: We have done the mapping from each active ingredient to DrugBank 
in linkedSPLs. The new mappings use bio2rdf formatted namespace (e.g., 
naproxin is <http://bio2rdf.org/drugbank:DB00788>). You can find them by 
including dailymed:subjectXref in your query. Now, if your dataset uses 
a different namespace for drugbank, you might be able to do find and 
replace like:

FIND: http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/
REPLACE WITH: http://bio2rdf.org/drugbank: 
<http://bio2rdf.org/drugbank:DB00788>

.....
> I guess linking through activeingredient would be convenient but there 
> is no uri as value of dailymed:activeIngredient available. From 
> drugbank side, for instance, Naproxen has a few brandedDrug property 
> triples, but I couldn't find any clue that can be counted as a 
> connection to current working dailymed dataset.
REPLY: I have an olde version of LODD dailymed sitting around and I 
found that the 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
predicate links the branded drug to DrugBank identifiers. When I grep 
for naproxin I recapture what appears to be the uris for exact same 
branded drugs that you got:

$ grep 00788 
/home/boycerd/DI_DIR/python/DIKB-product-label-mashup/rdf_data/dailymed_dump.nt
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/352> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/494> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/705> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/1086> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/1600> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/2630> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/3022> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/3105> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/3139> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/3240> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/4198> 
<http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/genericDrug> 
<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00788> .


>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/1086>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/1600>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/2630>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/3022>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/3105>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/3139>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/3240>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/352>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/4199>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/494>
> drugbank:brandedDrug 
> <http://wifo5-04.informatik.uni-mannheim.de/drugbank/resource/drugbank/brandedDrug> 
> 	<http://wifo5-04.informatik.uni-mannheim.de/dailymed/resource/drugs/705>
>
>
> That one above is how drugbank represents naproxen.
>
> And this is just only one of above from dailymed, which I cannot 
> figure out where it goes.
>
> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/page/structuredProductLabelMetadata/00051a01-1c2e-4abb-b04c-548401f822c6
>
> Except the case I'm missing something, is there a quick way to link 
> them appropriately? Maybe a conversion between mannheim's dailymed 
> drug codes and setid of current dailymed?
REPLY: Hopefully, i have given you some ideas. Please continue to 
provide feedback. Glad to help further.

-Rich
>
> Umutcan
>
>
>
>
> On 19-03-2013 01:47, Richard Boyce wrote:
>> Umatcan, LinkedSPls replaces LODD Dailymed which appears to be no 
>> longer maintained. Can't say whats going on with diseaseome. -R
>>
>>
>>
>> On 03/18/2013 07:48 AM, Umutcan Şimşek wrote:
>>> After movement of lodd datasets there were some availability issues. 
>>> Some of them seems resolved but dailymed and diseasome seem 
>>> unreachable. Is there another hosting of those datasets or dump files?
>>>
>>> -- 
>>> Umutcan ŞİMŞEK
>>>
>>> Ege Üniversitesi Bilgisayar Mühendisliği 4. Sınıf
>>> ARGEFAR İlaç Geliştirme ve Farmakokinetik Araştırma - Uygulama Merkezi
>>> Bilgi Sistemi Koordinatörlüğü Ekip Sorumlusu
>>>
>>> ****
>>>
>>> Ege University Computer Engineering 4
>>> ARGEFAR Drug Development and Pharmacokinetic Research - Application 
>>> Center
>>> IT Team Supervisor
>>>
>>
>>
>


-- 
Richard D Boyce, PhD
Assistant Professor of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training Program
Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
rdb20@pitt.edu
Office: 412-648-9219
Twitter: @bhaapgh