Data Set Information:

The data was collected from several sources, including GenProtEC ([Web link]) and SWISSPROT ([Web link]). Structure prediction was made by PROF ([Web link]). Homology search was provided by PSI-BLAST ([Web link]).

The data is in Datalog format. Missing values are not explicit, but some genes have more relationships than others.

E. coli genes (ORFs) are related to each other by the predicate ecoli_to_ecoli(EcoliNumber,E-value,Psi-blast_iteration). They are related to other (SWISSPROT) proteins by the predicate e_val(AccNo,E-value). All the data for a single gene (ORF) is enclosed between delimiters of the form:

begin(model(EcoliNumber)).
end(model(EcoliNumber)).

The gene functional classes are in a hierarchy. See [Web link] (note: the classes may have changed since original data collection).

There are two datalog files: ecoli_data.pl and ecoli_functions.pl

1. ecoli_functions.pl

Lists classes and ORF functions. Lines are of the following form:

  class(5,1,1,'Colicin-related functions').
  class(5,1,'Laterally acquirred elements').
  class(5,'Extrachromosomal').

Arguments are up to 3 numbers (describing class at up to 3 different levels), followed by a string class description. For example:

  function(ecoli210,7,0,0,'b0217','putative aminopeptidase').

Arguments are ORF number, exactly 3 class numbers, gene name (or blattner number if no gene name), ORF description.

2. ecoli_data.pl

Data for each ORF (gene) is delimited by

  begin(model(ecoliX)).
  end(model(ecoliX)).

where X is the ORF number. Other predicates are as follows (examples):
  ecoli_orf(ecoliX).    % X is ORF number
  ecoli_mol_wt(176624.1).  % float
  ecoli_theo_pI(5.81).     %float
  ecoli_atomic_comp(c,7940).   % {c,h,n,o,s} , int
  ecoli_aliphatic_index(69.57). % float
  ecoli_hydro(-0.549).          % float
  sec_struc(1,c,2).           % int (start), {a,b,c}, int (length)
  sec_struc_coil(1,2).        % int (start), int (length)
  sec_struc_beta(1,5).        % int (start), int (length)
  sec_struc_alpha(1,7).       % int (start), int (length)
  sequence_length(255).       % int
  amino_acid_ratio(a,8.9).    % amino_acid_char, float
  amino_acids(ecoli3013,a,70). % ORF_num, amino_acid_char, int
  amino_acid_pair_ratio(a,a,9.0). % amino_acid_char, amino_acid_char, float
  amino_acid_pairs(a,a,7).    % amino_acid_char, amino_acid_char, int
  ecoli_to_ecoli(1170,1.0e-105,5).  % ORF_num, double (e-value), int (iteration)
  e_val(o42893,2.0e-99).  % accession_number, double (e-value)
  psi_iter(o42893,5).     % accession_number, int (iteration)
  species(p52494,'candida_albicans__yeast_').  % accession_number, string
  mol_wt(p52494,104022). % accession_number, int
  classification(p52494,candida).  % accession_number, name
  keyword(p25195,'plasmid').   % accession_number, string