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 Wednesday, 29 April 2009 09:26:37 UTC