I am composing a list of Open databases with information related to toxicology. Of course, databases with assay data are a good start, including PubChem (partly Public Domain) and ChEMBL (a CC license). But I am interested too in databases with data on, for example, CYP metabolism. The exact nature of the data I am impartial too, and OpenTox servers are of interest too.
Important is that the database must be Open Data, or close to it. Any data available according to the Panton Principles is perfect, and anything under a Creative Commons license acceptable. Explicit statements on license or waiver must be provided by the database.
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written
by
Egon Willighagen
Here are some links (non exhaustive list). These offer publicly available data, but in most of the cases there is no explicit license.
Within software packages
Web services:
OpenTox REST web services (these include some of the datasets listed above as well as others, and new datasets could be uploaded):
Example search
EU projects:
There is a recent book "In Silico Toxicology, ed. M.Cronin, J.Madden, RSC Publishing,2010" with relevant chapters.
Well, lacking the filter for 'Open Data', but otherwise good enough for me now.
The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org/) is a free resource that manually curates the peer-reviewed literature to describe chemical-gene-disease interactions. It also integrates GO and pathway annotations to produce over 5 million toxicogenomic relationships. You can search CTD via your favorite chemical, gene, disease, GO term, or Pathway annotation. It also provides multiple analytical and visual tools.
Is it Open Data, according to the Open Knowledge Foundation guidelines?
It turns out the ChEMBL (CC-SA 3.0 unported) has a decent amount of toxicology data. This SPARQL data exposes the amount for release 02 (live query):
SELECT DISTINCT ?type count(?activity) as ?activities
WHERE {
?activity chembl:type ?type
FILTER regex(?type, "tox", "i")
}
ORDER BY DESC(?activities)
•
written
by
Egon Willighagen
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