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Knowledge Fair Table D - Query & Access Toxicity Data

Posted by Jeliazkov Vedrin at Sep 13, 2010 09:15 PM |

In this workshop you will query and access toxicity data, which has been compiled from various public sources, further curated and available online in OpenTox dataset services. More advanced techniques for querying and accessing toxicity data through OpenTox APIs would be demonstrated at Table F - Techie Table: Create an OpenTox App.

Objective

Learn to handle searching facilities and data visualization through the OpenTox framework, specifically in the context of in vivo Micronucleus mutagenicity assay in rodents data. ISSMIC is a curated database, containing critically-selected information on chemical compounds tested with the in vivo Micronucleus mutagenicity assay in rodents. In Vivo mutagenicity testing is ranked three (well ahead of rodent caricnogenicity) as animal consuming experimentation. Results in Bone Marrow cells, Peripheral blood cells and Splenocytes for Male/ Female Rat/Mouse, are reported. The data are collected from publicly available databases (Toxnet, NTP), and from the Leadscope FDA CRADA Toxicity Database. ISSMIC provides both biological calls and chemical structures, and is the basis for establishing sound read-across and QSAR risk assessment.

Step 1: Inspect data from the ISSMIC dataset

⇨ Open the following URL in your web browser: http://apps.ideaconsult.net:8080/ambit2/dataset

⇨ Enter the following keyword in the search box and press the Search button: ISSMIC_v2a_151_2Apr09

⇨ Click on the returned URL and take your time to browse the information available in the ISSMIC dataset

⇨ Click on a given property value of interest to retrieve a list of chemicals with similar property values

Step 2: Retrieve data in selected formats

⇨ Download and inspect a selected subset (or the entire dataset) in SDF, CML, SMILES, URI list, XML, PDF, XLS, ARFF and/or RDF format

Step 3: Find similar structures and browse the available data for a given chemical

⇨ Select some chemical of interest and perform a search for similar compounds (e.g. Tanimoto > 0.85) in the entire OpenTox database

⇨ Select some chemical of interest and perform a search by substructure in the entire OpenTox database

⇨ Browse available data for similar compounds (use the “All available feature values” link)

Handout availabe at:

http://www.ideaconsult.net/downloads/rhodes/Rhodes_WS_QUERY_DATA.pdf

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