Domain specialist

SynGO - Synapse Biology

Overview

The Synapse Gene Ontology and Annotation Initiative (SynGO) aims to:
  • Improve the Gene Ontology to accurately describe cellular components (CC) and biological processes (BP) important for synapse biology
  • Provide expert curated annotations of pre- and postsynaptic genes using the improved Gene Ontology classes

SynGO is funded by the Stanley Center for Psychiatric Research at the Broad Institute

TermGenie

TermGenie is a web-based tool for requesting new Gene Ontology classes. TermGenie also allows for an ontology developer to review all generated terms before they are committed to the ontology. The system makes extensive use of OWL axioms (logical definitions), but can be easily used without understanding these axioms.

Representing "phases" in GO biological process

The GOC has recently introduced a new term biological phase (GO:0044848), as a direct subclass of biological process. This class represents a distinct period or stage during which biological processes can occur. Biological phases do not share any is_a parent terms with other biological processes (i.e. they are is_a disjoint). They can be related to other biological processes with happens_during relationships e.g. DNA replication happens_during S-phase. They can also be regulated by other biological processes.

Reciprocal Meiotic Recombination

The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate is known as Reciprocal Meiotic Recombination. This process results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. The reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.

Detection and Response To Stimulus

Terms and Structure

The response of a cell or an organism to a stimulus is all the processes that occur as a result of the stimulus occurring within or outside the cell or organism. Detection of the stimulus, the process in which a stimulus is received by a cell and converted into a molecular signal, is thus a class of stimulus response. The general structure of this node is as follows:

  • response to stimulus
    • [i] detection of stimulus
      • [i] detection of [stimulus type] stimulus

Development

The set of standard terms below can be applied to each developing structure in each species covered in the ontology. However it is generally not practical to implement every term for every structure, since this would lead to a massive proliferation of terms. Where one term e.g. x development, is present, the rest of the terms for the development of x are considered to be implied, without having actually been implemented. Further terms are generally only implemented when they are required for annotation.

The Cell Cycle

The representation of the cell cycle in GO is split into two sections: the physical processes that occur and the temporal stages—prophase, anaphase and so on—used to describe sets of events. This method of representation is used to prevent true path problems when organisms differ from the "canonical" (usually S. cerevisiae) cell cycle.

Terms and Structure

The cell cycle node sits under cellular process ; GO:0007049 and is split into types of cell cycle (meiotic or mitotic) and stages (M phase, S phase, etc.), plus a regulation term.

  • cell cycle

    Ontology Related Information

    The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, the parts of a cell or its extracellular environment; molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; and biological process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.