part_of pathogen host host-Brucella interaction To establish logical reasoning for a virulence factor, we developed five description rules as defined below. In the formulation of these rules, o denotes an organism O, g and g’ denote genetic materials, e denotes a molecular entity, p denotes a process, i denotes a host-pathogen interaction process, and mo denotes a mutant of O. (IR3) If o has_part g, ∩ g encodes e, then o has_part e IR3 means that if a molecular entity (i.e., gene product such as protein) is encoded by a gene from an organism, then this molecular entity is part of an organism. (IR4) If mo has_part g’, ∩ g’ derives_from g, ∩ ( g’ lacks_part part of g ∪ g lacks_part part of g’) ∩ genome of o has_part g, then genome of mo lacks_part g IR4 means that if a mutant of an organism has an artificially altered gene sequence g’ that is derived from g, either by an insertion or partial deletion, then the genome of the mutant has no intact g as its part. When the g is fully deleted from mutant mo (i.e., g gene knock-out), the above rule won’t apply. In this case, we simply assert that genome of mo lacks_part g (see below). (IR5) If genome of mo lacks_part g, then mo lacks_part g If the genome of mutant has no intact gene g as its part, the mutant has no g as its part. (IR6) If genome of mo lacks_part g, ∩ g encodes e, then mo lacks_part e IR6 means that if the mutant has no intact gene g as its part, and the gene g encodes the molecular entity e in the unmutated organism, then the mutant has no intact e as its part. IR7 was given as a final definition of virulence factor: (IR7) If (mo has disposition at some time attenuated disposition ∩ attenuated disposition realized in i) ∩ (mo lacks_part e ∪ mo lacks_part g), ∩ (mo agent_in_compromised_process p ∩ p part_of i), then e is_a virulence factor For example, as shown in Figure 5, (B. abortus eryC mutant lacks_part eryC ) AND (B. abortus eryC mutant agent_in_compromised_process intracellular replication in macrophage) AND (intracellular replication in macrophage part_of macrophage-Brucella interaction) means that EryC is_a Brucella virulence factor. We can therefore to identify the biological process important to the virulence during the host-Brucella interaction. For example, (EryC participate_in Brucella erythritol catabolic process) AND (EryC mutant of B. abortus agent_in_compromised_process intracellular replication in macrophage), which means that the Brucella erythritol catabolic process is crucial to the intracellular replication in macrophage. YL ‘host-Brucella interaction’ is ‘a process that Brucella and its host (host organism or host cell) have effects upon each other during the course of Brucella’s establishing the infection and the host’s responses in order to fight the infection’. All those processes fall into two categories: Brucella infect host process or host anit-Brucella process. host-pathogen interaction host cell Brucella