Re: drug side effects

I have also started to convert SIDER into aTags, but our two conversions 
will be complementary. What I am doing is mapping the information to the OBO 
disease ontology and to DBpedia (for drug names), and reusing OBO and 
DBpedia URIs directly. The conversion will be lossy when no matches are 
found in these resources, but it will be bound more tightly to OBO and 
DBpedia.

The STITCH ids for chemicals seem to be equivalent to Pubchem in all cases I 
checked. Are there deviations?

By the way, some time back I also found two other datasets about drug side 
effects / pharmacovigilance data that could be used for conversions.

Maximum Recommended Therapeutic Dose (MRTD) Database
http://www.fda.gov/Cder/Offices/OPS_IO/MRTD.htm

Adverse Event Reporting System (AERS) Statistics
http://www.fda.gov/cder/aers/extract.htm

I will try to analyze those to see if they are worthwhile candidates for 
conversion. The AERS data is a bit complicated, and converting only some of 
the data might suffice.

Adverse events seem to be generally identified with terms from the MedDra 
dictionary (http://www.meddramsso.com), which is proprietary. I find this a 
bit irritating -- the entry barriers for institutions to create reports 
about adverse events should be as low as possible, which is not really 
helped by locking away the standard dictionary for codifying adverse 
events...

Cheers,
Matthias Samwald

DERI Galway, Ireland
http://deri.ie/

Konrad Lorenz Institute for Evolution & Cognition Research, Austria
http://kli.ac.at/


--------------------------------------------------
From: "Peter Ansell" <ansell.peter@gmail.com>
Sent: Tuesday, April 28, 2009 11:43 PM
To: "Matthias Samwald" <samwald@gmx.at>
Cc: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Subject: Re: drug side effects

> 2009/4/29 Matthias Samwald <samwald@gmx.at>:
>> We have metadata! The download page 
>> (http://sideeffects.embl.de/download/)
>> contains Creative Commons licensing HTML, which in turn contains RDFa.
>> We can extract the RDF from the page with a web service:
>>
>> http://srv.buzzword.org.uk/turtle,strict=aegu/sideeffects.embl.de/download/
>> (The swignition service adds additional metadata for some reason)
>>
>> Of course, metadata associated with the HTML does not help much with
>> automated data processing further down the road -- just attaching 
>> metadata
>> does not solve the whole problem, of course.
>
> I have been rdfising the sideeffects database for Bio2RDF over the
> last week. It is linked pretty well to stitch so there is value in
> having the actual information in RDF. When it is complete the scripts
> will be available for others to also use to perform the rdfisation
> themselves.
>
> I haven't been focusing on the license metadata but as they aren't
> using the same license for all of their files it would be good to go
> back and encode which license each piece of information is released
> under.
>
> Cheers,
>
> Peter

Received on Wednesday, 29 April 2009 07:17:05 UTC