Algorithms for effective querying of compound graph-based pathway databases

<p>Abstract</p> <p>Background</p> <p>Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate them using the well-understood concepts of graph theory in order to predict their structural and dynamic properties. An extension of this graph representation, namely hierarchically structured or compound graphs, in which a member of a biological network may recursively contain a sub-network of a somehow logically similar group of biological objects, provides many additional benefits for analysis of biological pathways, including reduction of complexity by decomposition into distinct components or modules. In this regard, it is essential to effectively query such integrated large compound networks to extract the sub-networks of interest with the help of efficient algorithms and software tools.</p> <p>Results</p> <p>Towards this goal, we developed a querying framework, along with a number of graph-theoretic algorithms from simple neighborhood queries to shortest paths to feedback loops, that is applicable to all sorts of graph-based pathway databases, from PPIs (protein-protein interactions) to metabolic and signaling pathways. The framework is unique in that it can account for compound or nested structures and ubiquitous entities present in the pathway data. In addition, the queries may be related to each other through "AND" and "OR" operators, and can be recursively organized into a tree, in which the result of one query might be a source and/or target for another, to form more complex queries. The algorithms were implemented within the querying component of a new version of the software tool P<smcaps>ATIKA</smcaps><it>web </it>(Pathway Analysis Tool for Integration and Knowledge Acquisition) and have proven useful for answering a number of biologically significant questions for large graph-based pathway databases.</p> <p>Conclusion</p> <p>The P<smcaps>ATIKA</smcaps> Project Web site is <url>http://www.patika.org</url>. P<smcaps>ATIKA</smcaps><it>web </it>version 2.1 is available at <url>http://web.patika.org</url>.</p

Prospective comparison of tissue trauma after laparoscopic hysterectomy types with retroperitoneal lateral transsection of uterine vessels using ligasure and abdominal hysterectomy

Objective The aim of this study was to evaluate the level of tissue trauma after laparoscopic and total laparoscopic hysterectomy with retroperitoneal lateral transsection of uterine vessels using ligasure as compared with abdominal hysterectomy

A Compound Graph Layout Algorithm for Biological Pathways

We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented within Patika, a pathway analysis tool for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and pathway abstractions. Experimental results show that execution times and quality of the produced drawings with respect to commonly accepted layout criteria and pathway drawing conventions are quite satisfactory

Laparoscopy versus laparotomy for the management of endometrial carcinoma in morbidly obese patients: a prospective study

Objective: To compare the results of total laparoscopic hysterectomy and total abdominal hysterectomy in morbidly obese women with early stage endometrial cancer

Laparoscopy versus laparotomy for the management of endometrial carcinoma in morbidly obese patients: a prospective study

Objective: To compare the results of total laparoscopic hysterectomy and total abdominal hysterectomy in morbidly obese women with early stage endometrial cancer

Collision tumor: serous cystadenocarcinoma and dermoid cyst in the same ovary

Collision tumor means the coexistence of two adjacent, but histologically distinct tumors without histologic admixture in the same tissue or organ. Collision tumors involving ovaries are extremely rare

Factors Associated With Pulmonary Hypertension And Long-Term Survival In Bronchiectasis Subjects

Background: The development of pulmonary hypertension (PH) and its effect on long-term survival in bronchiectasis subjects has not been explored. The present study aims to analyze the factors associated with PH and its effect on long-term survival in bronchiectasis subjects. Methods: We prospectively evaluated 23 bronchiectasis subjects without PH and 16 with PH, as well as 20 healthy volunteers. Results: Bronchiectasis subjects with PH were more hypoxemic and had a greater number of involved lobes in high resolution computed tomography (HRCT) than did the bronchiectasis subjects without PH (P < 0.001 and P < 0.001, respectively). At three years, the survival rate was 95.7% for bronchiectasis subjects without PH and 56.3% for bronchiectasis with PH, and at 5 years, these rates were 95.7% and 62.5%, respectively (P = 0.002). Multivariate Cox regression analysis revealed that only the Medical Research Council (MRC) dyspnea score was independently related to poor survival in all bronchiectasis subjects (hazard ratio: 6.98; 95% CI: 2.41-20.23; P < 0.00001). Conclusions: Subjects with PH are more hypoxemic and have a greater number of involvements in the lobes of the lungs. Bronchiectasis subjects with PH have worse survival than do bronchiectasis subjects without PH. MRC dyspnea score is an independent predictor of long-term survival. (C) 2016 Elsevier Ltd. All rights reserved.WoSScopu