Dear Luca,

The access to the structures (and data) is assumed to be via the OpenTox
REST web services API, not through database calls.

As it was explained at http://ambit.uni-plovdiv.bg/downloads/ambit2/  the
ambit2.war file have to be deployed to a servlet container and data accessed
via API calls.  The content of the download page is also accessible at
http://ambit.sourceforge.net/download_ambitrest.html .

For the API documentation and publications
http://opentox.org/dev/apis/api-1.2

http://www.jcheminf.com/content/2/1/7
http://www.jcheminf.com/content/3/1/18

http://ambit.sourceforge.net/api.html
http://ambit.sourceforge.net/ambit_services.html


On 7 September 2011 16:36, <luca_settimo at vrtx.com> wrote:

> Dear Opentox support and dear Vedrin
> I thank you for the answer that you gave me last month.
> We had some difficulty to get the structures from the database dump
> http://ambit.uni-plovdiv.bg/downloads/ambit2/db/ambit2-2011051401.7z
> that you sent me some time ago
> My colleague (Pat Walters) tried to load the database  into MySQL, he said
> that there are about 50 tables and we don't see any documentation.  Do
> you know if there is a description or an entity relationship diagram
> available?
>
> There's a table called "structures", that has 478,009 structures in SDF
> format and 70,646 in INC (INChI?) format.
> There's another table called "chemicals" with 118,726 SMILES
>
> The other tables contain descriptors and data, but we are not sure how it
> all fits together.
>
>

If you would like to study the database schema, a version of it could be
found in the Prototype Database deliverable (p.12), along with other
information.

http://www.opentox.org/data/documents/development/opentoxreports/opentoxreportd32


The updated document for the final database is under review by partners and
hopefully will be published soon.

Information about the schema can be found a at
https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-db/src/main/resources/ambit2/db/sql/ambit2.mwb
(MySQL workbench file) and in the book chapter [1] .


If you only would like to access structures (and.or data), and not necessary
install OpenTox web services, it might be more appropriate to use the
pre-installed service at
https://ambit.uni-plovdiv.bg:8443/ambit2/dataset<https://ambit.uni-plovdiv.bg:8443/ambit2/dataset?max=100>
and
just download the structures in the preferred format.

Best regards,
Nina Jeliazkova

[1] Jeliazkova N., Jaworska J., Worth A. (*2010*) Chapter 17. Open Source
Tools for Read-Across and Category Formation, In M. Cronin, & Madden J.
(Eds.), In Silico Toxicology : Principles and
Application<http://www.rsc.org/publishing/ebooks/2010/9781849730044.asp>(pp.
408-445). Cambridge, UK: RSC Publishing


> Please include Pat Walters in the reply if you could help thanks
>
> Thanks
> Luca
>
>
>
> From:   Vedrin Jeliazkov <vedrin.jeliazkov at gmail.com>
> To:     luca_settimo at vrtx.com
> Cc:     opentox development mailing list <development at opentox.org>
> Date:   04/08/2011 13:29
> Subject:        Re: Luca Settimo
>
>
>
> Hi Luca,
>
> > could you give me some more info on the databases that you collected for
> AMBIT?
>
> The database dump that is available at
> http://ambit.uni-plovdiv.bg/downloads/ambit2/db/ambit2-2011051401.7z
> contains the following datasets:
>
> ECHA list of pre-registered substances (143835 entries)
> ChemIDplus (structures for 80468 chemicals from the ECHA list of
> pre-registered substances)
> Chemical Identifier Resolver (structures for 72985 chemicals from the
> ECHA list of pre-registered substances)
> ChemDraw (structures for 22519 chemicals from the ECHA list of
> pre-registered substances)
> CPDBAS (1547 entries)
> DBPCAN (209 entries)
> EPAFHM (617 entries)
> FDAMDD (1216 entries)
> HPVCSI (3548 entries)
> HPVISD (1006 entries)
> IRISTR (544 entries)
> KIERBL (278 entries)
> NCTRER (232 entries)
> NTPBSI (2330 entries)
> NTPHTS (1408 entries)
> ISSCAN (1150 entries)
> ISSMIC (151 entries)
> ISSSTY (232 entries)
> TOXCST (320 entries)
> TXCST2 (960 entries)
> ECETOC Technical Report No. 66 Skin irritation and corrosion Reference
> Chemicals data base (1995) (176 entries)
> Local Lymph Node Data for the Evaluation of Skin Sensitization -
> Compilation of historical data (Dermatitis Vol 16 No 4 2005) (209
> entries)
> Local Lymph Node Data for the Evaluation of Skin Sensitization -
> Second compilation (Dermatitis Vol 21 No 1 2010) (108 entries)
> Bioconcentration factor (BCF) Gold Standard Database (1130 entries)
> Benchmark Data Set for pKa Prediction of Monoprotic Small Molecules
> the SMARTS Way (185 entries)
> Benchmark Data Set for In Silico Prediction of Ames Mutagenicity (6512
> entries)
> Bursi AMES Toxicity Dataset (4337 entries)
> EPI_AOP (818 entries)
> EPI_BCF (685 entries)
> EPI_BioHC (175 entries)
> EPI_Biowin (1263 entries)
> EPI_Boil_Pt (5890 entries)
> EPI_Henry (1829 entries)
> EPI_KM (631 entries)
> EPI_KOA (308 entries)
> EPI_Kowwin (15809 entries)
> EPI_Melt_Pt (10051 entries)
> EPI_PCKOC (788 entries)
> EPI_VP (3037 entries)
> EPI_WaterFrag (5764 entries)
> EPI_Wskowwin (2348 entries)
> TOXCST_ACEA (320 entries)
> TOXCST_Attagene (320 entries)
> TOXCST_BioSeek (320 entries)
> TOXCST_Cellumen (320 entries)
> TOXCST_CellzDirect (320 entries)
> TOXCST_Gentronix (320 entries)
> TOXCST_NCGC (320 entries)
> TOXCST_Novascreen (320 entries)
> TOXCST_Solidus (320 entries)
> TOXCST_ToxRefDB (320 entries)
> ECBPRS (structures and data for 80410 chemicals from the ECHA list of
> pre-registered substances)
> OPSIN (structures for 78458 chemicals from the ECHA list of
> pre-registered substances)
>
> You can also access all of the above mentioned datasets at
> https://ambit.uni-plovdiv.bg:8443/ambit2/dataset after you login with
> your OpenTox username and password at
> https://ambit.uni-plovdiv.bg:8443/ambit2/opentoxuser (You can register
> as an OpenTox user at http://www.opentox.org/join_form if you haven't
> already).
>
> In addition to these datasets, you could access at the same location
> the PubChem Structures + Assays dataset (473965 entries), which is not
> included in the MySQL dump that is available for download in order to
> keep it more compact.
>
> Please note that some additional datasets (not listed above, but
> available in the DB) are accessible only by OpenTox partners, due to
> specific licensing requirements and agreements.
>
> > Are you aware of this paper?
>
> [http://dx.doi.org/10.1016/j.taap.2009.08.022]
>
> > Perhaps you will find very useful Table 1 because it shows all databases
> for tox that are available in the literature. Which of these
> > do you have?
>
> As you can see from the list above, there's some degree of overlap
> between the references in Table 1 of this paper and the datasets
> included in the OpenTox DB, but both have entries that are absent in
> the other list. One major obstacle for including some of the sources
> that you mention is the lack of computer-readable bulk download for
> them. In addition, the AMBIT database is evolving continuously (even
> as I write these lines) and it can be somehow hard to tell what's
> included and what's not -- all registered users with sufficient
> privileges can add datasets at any time. In general, the OpenTox
> framework (and AMBIT as one particular implementation of the OpenTox
> API) provides the infrastructure to store and process relevant data in
> a more or less similar way as the Apache HTTP server acts for making
> available web site content. It's up to the users to upload whatever
> datasets, algorithms, models, etc..., they like to use or make
> available to others. So, in essence, the OpenTox DB is a kind of
> starting reference point, with particular emphasis on datasets that
> are relevant to the European REACH legislation, mainly due to the
> specific context of the OpenTox project. However, the OpenTox
> framework was designed in a generic way, to enable its use in other
> domains as well. It's up to the users to install, populate, run,
> maintain their own instances of OpenTox services. Furthermore, due to
> the common API, these services could be linked together and rely on
> each other for executing specific tasks (e.g. an algorithm provided by
> service A can be used to build a model by service B, using training
> dataset available at service C; the model at service B could be
> validated by service D and used to predict properties for a dataset
> hosted at service E, etc). You can have all of these running on a
> single box, or on a private cluster, or as (distributed) services that
> you offer to the public to use.
>
> > So Barry told me that you have a linux version of
> tox-create/tox-predict? Is that true?
>
> See my previous and Micha's mail for a detailed answers to these
> questions. The apps are platform independent and can run on any OS.
> ToxPredict and its dependencies are Java-based, ToxCreate and its
> dependencies are Ruby-based.
>
> As a somehow easier first step you might want to try the OpenTox
> virtual appliance, which has all of these apps pre-installed for you
> on a recent version of Linux:
>
>
> http://ambit.uni-plovdiv.bg/downloads/opentox/Opentox%20Virtual%20Appliance%20DC.ova
>
>
> Please note that this is a large file (2730474496 bytes). Its md5
> checksum which you could check to ensure that no errors have occurred
> while downloading it is: 1530bb83e88c3c646bcbac3183745bab
>
> You could import and run the appliance in VirtualBox
> (http://www.virtualbox.org/).
>
> Let us know if we can be of further assistance.
>
> Kind regards,
> Vedrin
>
>
>
>
>
>
>
> "Registered in England and Wales No: 2907620
> Registered Office: 88 Milton Park, Abingdon, Oxfordshire OX14 4RY, UK"
>
>
>
>
>
>
> "Disclaimer: The information contained in this transmission may contain
> privileged and confidential information. It is intended only for use of
> the person(s) named above. If you are not the intended recipient, you are
> hereby notified that any review, dissemination, distribution or
> duplication of this communication is strictly prohibited. If you are not
> the intended recipient, please contact the sender by reply e-mail and
> destroy all copies of the original message."
>
>
>
>
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
>