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

Dönitz J, Goemann B, Lizé M, Michael H, Sasse N, Wingender E, Potapov AP - Nucleic Acids Res. (2007)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, University of Göttingen/Medical School, D-37077 Göttingen.

ABSTRACT
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/.

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Schematic view of the information flow between the components of EndoNet and Cytomer.
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Figure 3: Schematic view of the information flow between the components of EndoNet and Cytomer.

Mentions: Cytomer is stored and modeled with the Web Ontology Language (OWL). This allows to access Cytomer via Application Programming Interfaces (API) such as the Jena-API and the Protégé-API. Both are generic toolkits designed to handle any ontology based on OWL. Because of the need for functionality that is specific to an anatomical ontology, we have developed the Cytomer connector, which uses the Protégé-API and provides simple access to Cytomer (Figure 3).Figure 3.


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

Dönitz J, Goemann B, Lizé M, Michael H, Sasse N, Wingender E, Potapov AP - Nucleic Acids Res. (2007)

Schematic view of the information flow between the components of EndoNet and Cytomer.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238947&req=5

Figure 3: Schematic view of the information flow between the components of EndoNet and Cytomer.
Mentions: Cytomer is stored and modeled with the Web Ontology Language (OWL). This allows to access Cytomer via Application Programming Interfaces (API) such as the Jena-API and the Protégé-API. Both are generic toolkits designed to handle any ontology based on OWL. Because of the need for functionality that is specific to an anatomical ontology, we have developed the Cytomer connector, which uses the Protégé-API and provides simple access to Cytomer (Figure 3).Figure 3.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, University of Göttingen/Medical School, D-37077 Göttingen.

ABSTRACT
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/.

Show MeSH