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Table 1 Background knowledge predicates

From: Predicting virus mutations through statistical relational learning

Background knowledge predicates  
position(AA,Pos) Indicates an amino acid in the wild type sequence
mut(MutID,AA,Pos,AA1) Indicates a mutation: mutation or mutant identifier, position and amino acids involved, before and after the substitution
res_against(MutID,Drug) Indicates whether a mutation or mutant is resistant to a certain drug
color(Color,AA) Indicates the coloring group of a natural amino acid
typeaa(T,AA) Indicates the type (e.g. aliphafatic, charged, aromatic, polar) of a natural amino acid
same_color_type(AA1,AA2) Indicates whether two amino acids belong to the same coloring group
same_typeaa(AA1,AA2,T) Indicates whether two amino acids are of the same type T
same_color_type_mut(MutID, Pos) Indicates a mutation to an amino acid of the same coloring group
different_color_type_mut(MutID, Pos) Indicates a mutation changing the coloring group of the amino acid
same_type_mut_t(MutID, Pos, T) Indicates a mutation to an amino acid of the same type T
different_type_mut_t(MutID, Pos) Indicates a mutation changing the type of the amino acid
aamutations(Pos,AA1,AA2,Num) Indicates whether a given mutation requires at least a single, double, or triple nucleotide substitution
close_to_site(Pos) Indicates whether a specific position is close to a binding or active site if any
location(L,Pos) Indicates in which fragment of the primary sequence the amino acid is located
conservation(Pos,ConsClass) Indicates whether a position is highly conserved or not
in_ss(SS,N,Pos) Indicates whether a mutation occurs within the Nth secondary structure element of a given type
in_motif(Pos,Motif) Indicates whether a mutation occurs within a known sequence motif
catalytic_propensity(AA,CP) Indicates whether an amino acid has a high, medium or low catalytic propensity
mutated_residue_cp(Rw,Pos,Rm,CPold,CPnew) Indicates how, in a mutated position, the catalytic propensity has changed (e.g. from low to high)
  1. Summary of the background knowledge facts and rules. MutID is a mutation or a mutant identifier depending on the type of the learning problem.