Algorithms for effective querying of compound graph-based pathway databases
نویسندگان
چکیده
منابع مشابه
Querying Graph Databases
Graph data is an emerging model for representing a variety of database contexts ranging from object-oriented databases to hypertext data. Also many of the recursive queries that arise in relational databases are, in practice, graph traversals. In this paper we present a language for searching graph-like databases. The language permits us to express paths in a graph by means of extended regular ...
متن کاملQuerying Best Paths in Graph Databases
Querying graph databases has recently received much attention. We propose a new approach to this problem, which balances competing goals of expressive power, language clarity and computational complexity. A distinctive feature of our approach is the ability to express properties of minimal (e.g. shortest) and maximal (e.g. most valuable) paths satisfying given criteria. To express complex prope...
متن کاملCyclone: java-based querying and computing with Pathway/Genome databases
UNLABELLED Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibili...
متن کاملQuerying Inconsistent Databases: Algorithms and Implementation
In this paper, an algorithm for obtaining consistent answers to queries posed to inconsistent relational databases is presented. This is a query rewriting algorithm proven to be sound, terminating and complete for some classes of integrity constraints that extend those previously considered in [1]. Complexity issues are addressed. The implementation of the algorithm in XSB presented here takes ...
متن کاملSearch Algorithms for Conceptual Graph Databases
We consider a database composed of a set of conceptual graphs. Using conceptual graphs and graph homomorphism it is possible to build a basic query-answering mechanism based on semantic search. Graph homomorphism defines a partial order over conceptual graphs. Since graph homomorphism checking is an NP-Complete problem, the main requirement for database organizing and managing algorithms is to ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2009
ISSN: 1471-2105
DOI: 10.1186/1471-2105-10-376