Two algorithms for maintaining order in a list
STOC '87 Proceedings of the nineteenth annual ACM symposium on Theory of computing
Efficient management of transitive relationships in large data and knowledge bases
SIGMOD '89 Proceedings of the 1989 ACM SIGMOD international conference on Management of data
Accelerating XPath location steps
Proceedings of the 2002 ACM SIGMOD international conference on Management of data
New Strategies for Computing the Transitive Closure of a Database Relation
VLDB '87 Proceedings of the 13th International Conference on Very Large Data Bases
Reachability and Distance Queries via 2-Hop Labels
SIAM Journal on Computing
Graph indexing: a frequent structure-based approach
SIGMOD '04 Proceedings of the 2004 ACM SIGMOD international conference on Management of data
Mining scale-free networks using geodesic clustering
Proceedings of the tenth ACM SIGKDD international conference on Knowledge discovery and data mining
Twig query processing over graph-structured XML data
Proceedings of the 7th International Workshop on the Web and Databases: colocated with ACM SIGMOD/PODS 2004
ICDE '05 Proceedings of the 21st International Conference on Data Engineering
An injection with tree awareness: adding staircase join to postgreSQL
VLDB '04 Proceedings of the Thirtieth international conference on Very large data bases - Volume 30
Fast and practical indexing and querying of very large graphs
Proceedings of the 2007 ACM SIGMOD international conference on Management of data
On Browsing Domain Ontologies for Information Base Content
IFSA '07 Proceedings of the 12th international Fuzzy Systems Association world congress on Foundations of Fuzzy Logic and Soft Computing
Conceptual querying through ontologies
Fuzzy Sets and Systems
On querying OBO ontologies using a DAG pattern query language
DILS'06 Proceedings of the Third international conference on Data Integration in the Life Sciences
Implementing a linguistic query language for historic texts
EDBT'06 Proceedings of the 2006 international conference on Current Trends in Database Technology
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In many areas of life science, such as biology and medicine, ontologies are nowadays commonly used to annotate objects of interest, such as biological samples, clinical pictures, or species in a standardized way. In these applications, an ontology is merely a structured vocabulary in the form of a tree or a directed acyclic graph of concepts. Typically, ontologies are stored together with the data they annotate in relational databases. Querying such annotations must obey the special semantics encoded in the structure of the ontology, i.e. relationships between terms, which is not possible using standard SQL alone. In this paper, we develop a new method for querying DAGs using a pre-computed index structure. Our new indexing method extends the pre-/ postorder ranking scheme, which has been studied intensively for trees, to DAGs. Using typical queries on ontologies, we compare our approach to two other commonly used methods, i.e., a recursive database function and the pre-computation of the transitive closure of a DAG. We show that pre-computed indexes are an order of magnitude faster than recursive methods. Clearly, our new scheme is slower than usage of the transitive closure, but requires only a fraction of the space and is therefore applicable even for very large ontologies with more than 200,000 concepts.