Interaction network of human proteins found with Nucleotide binding and ATP binding. Networks 1-11 represent the 70 protein-protein interactions found by the ontology-based search with the query of 'Nucleotide binding' from the HPRD data. Networks 7-11 represent the 31 interactions found by the ontology-based search with the query of 'ATP binding', which is a more specific term than 'Nucleotide binding'. The ID-matching search found only 5 interactions (networks 5-6) with 'Nucleotide binding' and missed all the other interactions whereas its search results with 'ATP binding' are same as those of the ontology-based search (networks 7-11). Yellow nodes represent the human proteins explicitly annotated with 'ATP binding', pink nodes represent the human protein explicitly annotated with 'Nucleotide binding', and white nodes represent the human proteins with no explicit annotation of 'ATP binding' nor 'Nucleotide binding'. The GO term IDs of the proteins found by the search methods are listed in Table 5.