Content-rich biological network constructed by mining PubMed abstracts

BMC Bioinformatics

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%).

ISSN: 1471-2105