Most information extraction (IE) approaches have considered only static text corpora, over which we apply IE only once. Many real-world text corpora however are dynamic. They evolve over time, and so to keep extracted information up to date we often must apply IE repeatedly, to consecutive corpus snapshots. Applying IE from scratch to each snapshot can take a lot of time. To avoid doing this, we have recently developed Cyclex, a system that recycles previous IE results to speed up IE over subsequent corpus snapshots. Cyclex clearly demonstrated the promise of the recycling idea. The work itself however is limited in that it considers only IE programs that contain a single IE ``blackbox.'' In practice, many IE programs are far more complex, containing multiple IE blackboxes connected in a compositional ``workflow.''

Most current information extraction (IE) approaches have considered only static text corpora, over which we typically have to apply IE only once. Many real-world text corpora however are dynamic. They evolve over time, and to keep extracted information up to date, we often must apply IE repeatedly, to consecutive corpus snapshots. We describe Cyclex, an approach that efficiently executes such repeated IE, by recycling previous IE efforts. Specifically, given a current corpus snapshot U, Cyclex identifies text portions of U that also appear in the previous corpus snapshot V. Since Cyclex has already executed IE over V, it can now recycle the IE results of these parts, by combining these results with the results of executing IE over the remaining parts of U, to produce the complete IE results for U. Realizing Cyclex raises many challenges, including modeling information extractors, exploring the trade-off between runtime and completeness in identifying overlapping text, and making informed, cost-based decisions between redoing IE from scratch and recycling previous IE results. We describe initial solutions to these challenges, and experiments over two real-world data sets that demonstrate the utility of our approach.

MOTIVATION: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization. RESULTS: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size. AVAILABILITY: Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. CONTACT: [email protected], [email protected] SUPPLEMENTARY INFORMATION: http://www.psort.org/psortb/supplementaryinfo.html.

A number of medically important disease-causing bacteria (collectively called Gram-negative bacteria) are noted for the extra "outer" membrane that surrounds their cell. Proteins resident in this membrane (outer membrane proteins, or OMPs) are of primary research interest for antibiotic and vaccine drug design as they are on the surface of the bacteria and so are the most accessible targets to develop new drugs against. With the development of genome sequencing technology and bioinformatics, biologists can now deduce all the proteins that are likely produced in a given bacteria and have attempted to classify where proteins are located in a bacterial cell. However such protein localization programs are currently least accurate when predicting OMPs, and so there is a current need for the development of a better OMP classifier. Data mining research suggests that the use of frequent patterns has good performance in aiding the development of accurate and efficient classification algorithms. In this paper, we present two methods to identify OMPs based on frequent subsequences and test them on all Gram-negative bacterial proteins whose localizations have been determined by biological experiments. One classifier follows an association rule approach, while the other is based on support vector machines (SVMs). We compare the proposed methods with the state-of-the-art methods in the biological domain. The results demonstrate that our methods are better both in terms of accurately identifying OMPs and providing biological insights that increase our understanding of the structures and functions of these important proteins.