WOMBAT reference database

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. 

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). 

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