Biomedical subjects

Aaron Birkland

Publications and source records attributed to Aaron Birkland.

3 recordsLinked to original sources

PubMed2006

BIOZON: a system for unification, management and analysis of heterogeneous biological data.

BACKGROUND: Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. DESCRIPTION: Here we present a system (Biozon) that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways). It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. CONCLUSION: The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at http://biozon.org.

Animals↗

PubMed2006

BIOZON: a hub of heterogeneous biological data.

Biological entities are strongly related and mutually dependent on each other. Therefore, there is a growing need to corroborate and integrate data from different resources and aspects of biological systems in order to analyze them effectively. Biozon is a unified biological database that integrates heterogeneous data types such as proteins, structures, domain families, protein-protein interactions and cellular pathways, and establishes the relationships between them. All data are integrated on to a single graph schema centered around the non-redundant set of biological objects that are shared by each source. This integration results in a highly connected graph structure that provides a more complete picture of the known context of a given object that cannot be determined from any one source. Currently, Biozon integrates roughly 2 million protein sequences, 42 million DNA or RNA sequences, 32,000 protein structures, 150,000 interactions and more from sources such as GenBank, UniProt, Protein Data Bank (PDB) and BIND. Biozon augments source data with locally derived data such as 5 billion pairwise protein alignments and 8 million structural alignments. The user may form complex cross-type queries on the graph structure, add similarity relations to form fuzzy queries and rank the results based on analysis of the edge structure similar to Google PageRank, online at Biozon.org.

Computer Graphics↗

PubMed2005

Correcting BLAST e-values for low-complexity segments.

The statistical estimates of BLAST and PSI-BLAST are of extreme importance to determine the biological relevance of sequence matches. While being very effective in evaluating most matches, these estimates usually overestimate the significance of matches in the presence of low complexity segments. In this paper, we present a model, based on divergence measures and statistics of the alignment structure, that corrects BLAST e-values for low complexity sequences without filtering or excluding them and generates scores that are more effective in distinguishing true similarities from chance similarities. We evaluate our method and compare it to other known methods using the Gene Ontology (GO) knowledge resource as a benchmark. Various performance measures, including ROC analysis, indicate that the new model improves upon the state of the art. The program is available at biozon.org/ftp/ and www.cs.technion.ac.il/ approximately itaish/lowcomp/.

Amino Acid Sequence↗