New challenges for text mining: mapping between text and manually curated pathways

<p>Abstract</p> <p>Background</p> <p>Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge.</p> <p>Results</p> <p>To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, ‘bio-inference,’ as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of ‘bio-inference’ schemes observed in the pathway corpus.</p> <p>Conclusions</p> <p>We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text.</p

Crystal Structure of Asparagine Synthetase Reveals a Close Evolutionary Relationship to Class II Aminoacyl-tRNA Synthetase (MOLECULAR BIOFUNCTION-Functional Molecular Conversion)

The crystal structure of E. coli asparagine synthetase has been determined by X-ray diffraction analysis at 2.5 A resolution. The overall structure of the enzyme is remarkably similar to that of the catalytic domain of yeast aspartyl-tRNA synthetase despite low sequence similarity. These enzymes have a common reaction mechanism that implies the formation of aminoacyl-adenylate intermediate. The active site architecture and most of the catalytic residues are also conserved in both enzymes. These enzymes have probably evolved from a common ancestor even though their sequence similarities are small

Mechanism of Benzyl Migration from Nitrogen to Carbon in Enamines

The rearrangement of (R)-N-isobutenyl-N-methyl-benzylamine-a-d was thermally effected to give (R)-2, 2-dimethyl-3-phenyl-propanal-3-d with over-all retention of configuration ofthe migrating terminus in 91 % asymmetric yield. The stereochemical outcome in the present benzyl migration unequivocally established the mechanism to be the sequential N-alkylation, retrogressive dissociation and C-alkylation, with two Walden inversions involved in the process