Question: What Open Toxicology Databases Are Available?
5
gravatar for Egon Willighagen
9.9 years ago by
Maastricht
Egon Willighagen5.3k wrote:

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.

database • 11k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 9.9 years ago by Egon Willighagen5.3k
12
gravatar for Ngn
9.9 years ago by
Ngn130
BG
Ngn130 wrote:

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.

ADD COMMENTlink modified 14 months ago by RamRS30k • written 9.9 years ago by Ngn130

Well, lacking the filter for 'Open Data', but otherwise good enough for me now.

ADD REPLYlink written 9.9 years ago by Egon Willighagen5.3k
2
gravatar for Apd
9.6 years ago by
Apd20
Apd20 wrote:

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.

ADD COMMENTlink written 9.6 years ago by Apd20

Is it Open Data, according to the Open Knowledge Foundation guidelines?

ADD REPLYlink written 9.6 years ago by Egon Willighagen5.3k
1
gravatar for Egon Willighagen
9.8 years ago by
Maastricht
Egon Willighagen5.3k wrote:

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)
ADD COMMENTlink modified 14 months ago by RamRS30k • written 9.8 years ago by Egon Willighagen5.3k
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