Table 2

Failure to detect known DIP relationships

Reason

Undetected relationships (%)


member of protein family (name generalization)

30.8

incomplete synonym list

26.5

no reference at abstract level

22.1

other

20.6


Chilibot was used to retrieve information about 770 pairs of known protein interactions obtained from the Database of Interacting Proteins (DIP). A total of 702 relationships were found (recall = 91.2%). Relationships were undetectable (n = 68) for the following reasons: 21 (30.8%) occurred when a specific member of the protein family (e.g. cdc25a) was recorded in DIP, yet only the general family name (e.g. cdc25) appeared in abstracts; 18 (26.5%) were due to synonyms present in abstracts and not in Chilibot's dictionary of nomenclature; 15 (22.1%) were caused by lack of documentation of the relationships in PubMed abstracts. Miscellaneous reasons accounted for the remainder (20.6%).

Chen and Sharp BMC Bioinformatics 2004 5:147   doi:10.1186/1471-2105-5-147

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