The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms. The project started in 2003 to create a connection between the enzyme data collection of the BRENDA enzyme database and a structured network of source tissues and cell types. Currently, BTO contains more than 4600 different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. The content of the ontology is constantly curated with ∼1000 new terms each year. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues. Important areas of applications of the BTO terms are the detection of enzymes in tissues and the provision of a solid basis for text-mining approaches in this field. It is widely used by lab scientists, curators of genomic and biochemical databases and bioinformaticians. The BTO is freely available at http://www.obofoundry.org

EndoNet: an information resource about regulatory networks of cell-to-cell communication†

EndoNet is an information resource about intercellular regulatory communication. It provides information about hormones, hormone receptors, the sources (i.e. cells, tissues and organs) where the hormones are synthesized and secreted, and where the respective receptors are expressed. The database focuses on the regulatory relations between them. An elementary communication is displayed as a causal link from a cell that secretes a particular hormone to those cells which express the corresponding hormone receptor and respond to the hormone. Whenever expression, synthesis and/or secretion of another hormone are part of this response, it renders the corresponding cell an internal node of the resulting network. This intercellular communication network coordinates the function of different organs. Therefore, the database covers the hierarchy of cellular organization of tissues and organs as it has been modeled in the Cytomer ontology, which has now been directly embedded into EndoNet. The user can query the database; the results can be used to visualize the intercellular information flow. A newly implemented hormone classification enables to browse the database and may be used as alternative entry point. EndoNet is accessible at: http://endonet.bioinf.med.uni-goettingen.de

Development of dynamic database structures using OWL ontologies

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2007.Includes bibliographical references (leaves 22-23).Standard query language database systems cannot provide the level of flexibility and functionality needed to store all of the data that a modem biologist requires. OWL ontologies provide much more information about how fields relate to each other including adding annotations with each field, but do not allow for the storage of mass amounts of data. By integrating OWL ontologies with modem database systems, scientists will be able to build ontology-based databases that combine the ease of development of ontologies with the power of the modem database. In addition, other scientists can now search ontology-based databases and know that even though the databases are different, the types of data are the same because they are based on a consistent ontology. The use of ontologies in building modem databases will create a new environment where users can customize databases to account for new methods in biology, while at the same time maintaining the ability for others to effectively search the modified databases.by Kurt R. Stiehl.S.B