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Re: drug side effects

From: Matthias Samwald <samwald@gmx.at>
Date: Thu, 30 Apr 2009 15:43:24 +0200
Message-ID: <9A9065FC53AB4B6A9410C92C7D2A9802@ms>
To: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Here is a small excerpt of the outcome of my SIDER conversion:

http://hcls.deri.org/atag/data/SIDER_atags_excerpt.html

Of course, listing aTags on a page in this manner is not very 
human-friendly, they should rather be embedded in a website with better 
navigation, split into several web pages. Note that you could just 
copy&paste some of the aTags to another HTML area, mix it with other RDFa, 
and the data would be carried with it ('client-side mashup'). I also encoded 
basic copyright and authorship information in RDFa.

Triples in this page, extracted with Triplr.org:
http://triplr.org/html/hcls.deri.org/atag/data/SIDER_atags_excerpt.html

(or shorter: http://tinyurl.com/cerwpp)

This is just a small excerpt, the entire file is several megabytes large. I 
still need to fix some issues with XML Literals in RDFa, and will then add 
the resulting triples of the full document to the HCLS KB.

Cheers,
Matthias


--------------------------------------------------
From: "Peter Ansell" <ansell.peter@gmail.com>
Sent: Wednesday, April 29, 2009 11:26 AM
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>:
>> 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.
>
> I will have to investigate how aTags works more deeply. I developed my
> own tagging vocabulary [1] but it hasn't seen many uses so far. From a
> rough view, the terms:hasEvidence URI seems to map well to aTags
> although it might be a bit specialised. Is [2] the only place aTags
> are described?
>
>> The STITCH ids for chemicals seem to be equivalent to Pubchem in all 
>> cases I
>> checked. Are there deviations?
>
> The STITCH and SIDER notes seem to indicate that they have reused the
> pubchem identifiers, so owl:sameAs should be appropriate to
> http://bio2rdf.org/pubchem:STITCHID.
>
>> 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.
>
> Partial rdfisations are still useful. If you release the script you
> used to do it someone else can improve the coverage in the future if
> needed.
>
>> 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...
>
> It would be interesting to see what relationships are possible between
> drugbank and these datasets, as drugbank is linked directly into a
> large number of Bio2RDF datasets so the bridge from that point is
> made.
>
> Cheers,
>
> Peter
>
> [1] http://bio2rdf.mquter.qut.edu.au/ns/terms
> [2] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags 
Received on Thursday, 30 April 2009 13:44:04 UTC

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