Figure1shows a screenshot of the AmiGO ontology browser at the Gene Ontology depicting “”GO: 0012501 programmed cell death”" and its child terms [1]. In addition to the terms describing classes of PCD, the GO contains three other terms, also shown in Figure1, that describe types of PCD regulation: “”GO: 0043067 regulation of programmed cell death”", “”GO: 0043069 negative regulation of programmed cell death”", and “”GO: 0043068

positive regulation of programmed cell death”". Taken together, these terms describing both classes of PCD and regulation of PCD allow for annotations that capture various aspects of PCD as a biological process. Figure 1 “”GO: 0012501 programmed cell death”" and its child terms mTOR activation depicted in a

screenshot of the Gene Ontology AmiGO browser[1]. Tanespimycin cell line Most terms shown here below “”GO: 0012501 programmed cell death”" are types of programmed cell STI571 ic50 death, symbolized by the logo showing an “”I”" inside a square, which denotes the “”is_a”" relationship. However, three terms (various logos with “”R”") describe the “”regulates”" type of relationship. For more information on ontology structure, including term-term relationships, see [13]. Apoptosis and necrosis Several types of PCD related to defense have been distinguished in the literature, for example apoptosis and the hypersensitive response (HR). Autophagy, a highly conserved PCD pathway related to protein and organelle turnover, OSBPL9 also has been implicated in plant innate immunity (reviewed in [14]). Another commonly used but poorly defined term, “”necrosis”", is not included as a term in the GO because it is a phenotype, i.e. post-mortem observation of dead cells, not a process, and the GO does not include terms for describing phenotypes. Necrosis indicates that

cell death has occurred, but not necessarily the process by which it was achieved [15]. There may be some cases where necrosis proceeds as a programmed process, but this is still poorly understood (see Note added in proof). Necrosis exists in the GO only as a synonym of the terms “”GO: 0008219 cell death”", “”GO: 0001906 cell killing”", “”GO: 0019835 cytolysis”", and “”GO: 0012501 programmed cell death”", but its use in describing a process is discouraged without great caution whether or not one is using GO. Similarly, use of the phrase “”necrotic tissue”" is discouraged in describing the results of cell death. “”GO: 0006915 apoptosis”", on the other hand, exists in the GO as it constitutes a well-defined process. Apoptosis includes condensation of chromatin at the nuclear periphery, condensation and vacuolization of the cytoplasm and plasma membrane blebbing, followed by breakdown of the nucleus and fragmentation of the cell to form apoptotic bodies.