Advances in Bioinformatics

Research Article

Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

Figure 1

Computation of pfs. (A) pfs was calculated with regard to the validity of bibliographic citations as well as a description and comments section. In line 9, the FUNCTION and CATALYTIC ACTIVITY records were evaluated. In step 2, automated entries resulting from large-scale experimental approaches were detached from further analysis. (B) Section evaluation. In every section, every single sentence was evaluated independently. Lines 12–14 are required in case literature citations contain down-weighting phrases, yet conclusions regarding functional properties of a protein have eventually been made by mere resemblance at the primary sequence level (Swiss-Prot term: “BY SIMILARITY”).

(A)

Input: Swiss-Prot entry
Output: protein function score
(1) forall referance entries do
(2) if not large scale experiment paper then
(3) (referance title);
(4) ;
(5) end
(6) end
(7) ;

(8) ;
(9) ;
(10) pfs ;

(B)

Input: section/subsection text, keyword-score-table
Output: protein function score
(1) forall sentences do
(2) ;
(3) forall keyword do
(4) if keyword matches sentences then
(5) ;
(6) break;
(7) end
(8) end
(9) ;
(10) end
(11) ;

(12) if and last sentences was “BY SIMILARITY” then
(13) ;
(14) end