WOMBAT database structure

Structure - chemical structure in both formats MOL SMILES 

Keywords - structure keywords (chirality, salt information) 

Range - confidence range for the activity value, in log units 

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WOMBAT is a dynamic database, which evolves as new data types are included. The database structure is, however, preserved as much as possible from one release to the next. Each root record (or WOMBAT entry) is identified by a unique number (SMDLID), and is defined by the combination of one chemical structure and one or more associated biological activities as entered in one publication (Fig. 13.2-3). One field, series identifier (SID), links all the root records indexed from one reference (article). There are 6801 SID values in WOMBAT 2006.1 (see also Fig. 13.2-7). At the root level, information about the bibliographic reference (unique SID) from which the entry originated the entry is recorded together with various properties (illustrated in Fig. 13.2-6). 

In an effort to understand if HAMs are, in any way, different from LAMs (low activity molecules), we extended this survey to compounds published between 1991 and 2002, as indexed in WOMBAT [26]. This database [27] contains 4927 unique structures with at least one measured activity better than 1 nM (HAMs), and 34028 unique structures with at least one activity less than 1 XM (LAMs). Between HAMs and LAMs, 1080 molecules are common, that is, they have at least one activity above 1 nM and at least one activity below 1 XM. This is not uncommon for, for example, highly selective molecules. We did not exclude these from either set since we monitor trends, not exact figures. We studied these trends using 2-D-(two-dimensional) descriptors, that is, descriptors that do not use information related to the three-dimensional characteristics of model compounds. These descriptors can be classified as follows ... 

Each substance in the database has its unique ID number. With every structure, there are two associated functions similar and related. Similar searches WOMBAT and related searches all Cabinet databases. Some series involve an enzyme with an EC number listed and can be searched by selecting the related by EC button. 

When the related button above the structure is selected, a list of similar structures in other databases is shown. Empath, Planet, TCM and WOMBAT are found. In Planet, the closest structure is IHWK. Selecting it brings up the Planet version of the PDB... 

Because the internal dissemination of this database within AstraZeneca R D (a company with 11 R D sites across four continents) was not deemed a success, AstraZeneca decided to discontinue the project as of May 2002. Backed by private funding, the database, renamed WOrld of Molecular BioAc-Tivity (WOMBAT) in 2003, continued to evolve [13] as discussed for WOMBAT 2006.1, below. Recognizing the paucity of chemical databases that capture clinical pharmacokinetics data in a searchable manner, we further developed the WOMBAT-PK (WOMBAT-Pharmacokinetics), to index such data from literature [14]. This chapter summarizes the contents of WOMBAT and WOMBAT-PK [15], some of the problems encountered in appropriately indexing biological activities and correct chemical structures (with focus on machine-readable contents for data mining), and provides some examples of data mining with WOMBAT. Other bioactivity databases [16], focused mostly on patent literature, are shown in Table 13.2-1 together with the on-line references. 

The coverage of the published biological activity space described above results in a substantial number of SAR data points Eidogen-Sertanty s KKB database contains more than 350,000 SAR points (for more than 475,000 molecules), WOMBAT contains around 417,000 SAR points (for approx. 178,000 unique structures), the StARLlTe database contains around 1.7 million SAR points (for approx. 400,000 unique molecules), the AurScope databases contain around 1.9 million SAR points (for approx. 471,000 molecules), the GhemBioBase databases contain 2.8 million SAR points (for approx. 2 million molecules), and GVK Biosciences GOSTAR contains around 5 million SAR points (for approx. 2.1 million unique molecules). 

Chen J, Swamidass SJ, Dou Y, Bruand J, Baldi P (2005) ChemBD a public database of small molecules and related chemoinformatics resources. Bioinformatics 21 4133-4139 DrugBank http //www.drugbank.ca. Accessed 1 Feb 2014 WOMBAT http //www.sunsetmolecular.com/. Accessed 1 Feb 2014 MDDR http //accelrys.com/products/databases/bioactivity/mddr.html. Accessed 1 Feb 2014 Scior JT, Bernard P, Medina-Franco JL, Maggiora GM (2007) Large compound databases for structure-activity relationships studies in drug discovery. Mini Rev Med Chem 7 851-860 Leach AR, Gillet VJ (2003) An introduction to chemoinformatics. Kluwer Academic, Dordrecht... 

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