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Data for the initial gene synonym dictionary was collected from publicly available databases, e.g. LocusLink (Pruitt et al., 2000), FlyBase, or UniProt (Apweiler et al., 2004). In addition to primary gene symbols and names, when known, this initial dictionary also contained alternative synonyms and orthographic variants. Although genome databases, were the principal sources of primary symbols and names, manually curated resources of synonyms, e.g. the HUGO Nomenclature Committee (White et al., 1997), are also of great importance, since genes that were discovered and described by different laboratories often have various synonyms. Synonyms from this initial dictionary were then altered using an iterative process to account for orthographical variations. The heuristics for these alterations were derived manually, and besides general rules (e.g. Expanding ‘LAIR1’ to ‘LAIR-1’), also contained organism-specific rules (e.g. Converting ‘AP*’ to ‘APETALA*’ in Arabidopsis thaliana). As a result of this iterative extension, the total number of synonyms expanded drastically from half a million to 3.2 million, with the average number of synonyms per gene increasing from 3 to 19. Pre-generating the complete list of synonyms makes it possible to assess the quality (or uniqueness) of each synonym, according to the number of distinguishing characteristics, before using it in the identification process. Depending on the quality of a synonym, either its occurrence alone was sufficient to associate the corresponding gene to a text, or additional evidence was necessary (e.g. a second synonym or parts of the name). Moreover, every synonym is defined by the grade of precision and by where in a sentence it must be found (e.g. casesensitive, not at the beginning of a sentence).