Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base-1

<p><b>Copyright information:</b></p><p>Taken from "Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base"</p><p>http://www.biomedcentral.com/1471-2105/8/177</p><p>BMC Bioinformatics 2007;8():177-177.</p><p>Published online 30 May 2007</p><p>PMCID:PMC1904246.</p><p></p>olecularStructure concept. Each MolecularStructure is created with an instance of MethodType, and may be analyzed by many computational methods (instances of Analysis). MethodType has two subclasses: IdentificationMethod, which is used to identify the oligomer, and CreationMethod, which is used to create the MolecularStructure. IdentificationMethod and CreationMethod can have many sub-concepts that describe the precise type of method. In this figure we show only a few examples of such concepts

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base-2

<p><b>Copyright information:</b></p><p>Taken from "Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base"</p><p>http://www.biomedcentral.com/1471-2105/8/177</p><p>BMC Bioinformatics 2007;8():177-177.</p><p>Published online 30 May 2007</p><p>PMCID:PMC1904246.</p><p></p> protomers oligomerize. There are three types of phenotypic change that are described by the ontology: changes in internalization, changes in signaling, and differences in the ligand binding of the oligomer as compared to any of the constituent protomers. The effect that ligand(s) binding to one or more of the protomers in an oligomer may have on binding of ligands to other protomers, or on the change in signaling, is described by the CrossTalk concept. The Internalization concept is used to describe changes that different ligands have on the trafficking of the Oligomer to the cell membrane. Any information that is available about the mechanism of activation of the Oligomer is stored in the MechanismOfActivation concept. The PhysiologicalRelevance concept stores information about the Oligomer

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base-0

<p><b>Copyright information:</b></p><p>Taken from "Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base"</p><p>http://www.biomedcentral.com/1471-2105/8/177</p><p>BMC Bioinformatics 2007;8():177-177.</p><p>Published online 30 May 2007</p><p>PMCID:PMC1904246.</p><p></p> for each concept are listed in the middle section of the box. Arrows represent relationships between concepts, and open-ended arrows indicate "is a" relationships. The relationship of one concept to another is indicated by the text on each arrow. Arrows with [0..*] (zero or more) or [1..*] (one or more) indicate the number of instances of the concept at the end of the arrow that is associated with the concept at the beginning of the arrow. The Oligomer concept is central to the GPCR oligomerization ontology and all other concepts in the ontology relate to it either directly (e.g., Oligomer ''is described by'' IdentificationStudy) or indirectly (e.g., Oligomer ''is composed of'' one or more [1..*] Protein that ''belongs to'' Family)